MedWorm.com provides a medical RSS filtering service. Over 6000 RSS medical sources are combined and output via different filters. This feed contains the latest items from the 'Journal of Proteomics' source. Sat, 20 Mar 2010 16:01:41 +0100 http://www.medworm.com/index.php?rid=3379607&cid=s_37286_60_f&fid=37286&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20230923%26dopt%3DAbstract Authors: Ge F, Xiao CL, Yin XF, Lu CH, Zeng HL, He QY Multiple myeloma (MM) is a malignant disorder of differentiated B cells. Clonal expansion of the tumor results in the excessive production of monoclonal immunoglobulin (Ig) which is a diagnostic feature of this disease. Previous investigations have demonstrated the alteration of the ERK, jun kinase, STAT, and AKT kinase signaling cascades in MM cells, suggesting that deregulated phosphorylation may contribute to MM pathogenesis. However, systematic analysis of the phosphoproteome in MM cells has not been reported. Here, we described a large-scale phosphorylation analysis of primary MM cells. Using a separation strategy involving immunomagnetic bead-positive selection of MM cells, preparative SDS-PAGE for prefractionation, in-gel dig... Journal of Proteomics journals http://www.medworm.com/rss/comments.php?id=3379607 Fri, 12 Mar 2010 00:00:00 +0100 3379607 http://www.medworm.com/index.php?rid=3379606&cid=s_37286_60_f&fid=37286&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20230925%26dopt%3DAbstract Authors: Shirran SL, Botting CH The accuracy of quantification obtained using the iTRAQ labelling methodology for measuring protein ratios more extreme than 1:1 was investigated. A comparison of nLC-ESI MSMS and nLC-MALDI MSMS analysis routes was performed. A fixed concentration of a standard six protein mix was spiked with two proteins at a range of concentrations. The two data analysis programmes, Mascot and ProteinPilot Paragon, were also compared. Whilst the lower ratios could be measured accurately, greater discrepancies were seen for the higher ratios, particularly by nLC-ESI MSMS. Filtering out the weaker reporter ion signals improved the accuracy of the ratios: this is likely due to several factors which are explored in more detail. Overall, analysis by nLC-MALDI MSMS followed ... Journal of Proteomics journals http://www.medworm.com/rss/comments.php?id=3379606 Fri, 12 Mar 2010 00:00:00 +0100 3379606 http://www.medworm.com/index.php?rid=3379604&cid=s_37286_60_f&fid=37286&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20230924%26dopt%3DAbstract Authors: Rodríguez-Piñeiro AM, Blanco-Prieto S, Sánchez-Otero N, Rodríguez-Berrocal FJ, la Cadena MP The current imperative need for new biomarkers of non-small cell lung cancer (NSCLC) prompted us to compare the proteome of serum and pleural effusion samples from cancer patients with those with benign lung diseases as pneumonia or tuberculosis. Samples were prefractionated through affinity chromatography prior to 2D-DIGE to detect proteins with altered expression in cancer patients. Overall, we identified more potential biomarkers in pleural effusion, which is closer to the affected organ, than in serum. Nevertheless, in both cases principal component analysis demonstrated that the pattern of significantly altered proteins discriminates between disease groups. The ... Journal of Proteomics journals http://www.medworm.com/rss/comments.php?id=3379604 Fri, 12 Mar 2010 00:00:00 +0100 3379604 http://www.medworm.com/index.php?rid=3379605&cid=s_37286_60_f&fid=37286&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20227539%26dopt%3DAbstract Authors: D'Imperio M, Corte AD, Facchiano A, Di Michele M, Ferrandina G, Donati MB, Rotilio D A growing body of literature defines MALDI-TOF MS as a technique for studying plasma and serum, thus enabling the detection of proteins, and the generation of reproducible protein profile mass spectra, potentially able to discriminate correctly different biological systems. In this work, the different steps of the pre-analytical phase that may affect the reproducibility of plasma proteome analysis have been carefully considered. The results showed that the method is highly accurate (9.1%) and precise (8.9%) and the calibration curve for the ACTH (18-39), in human plasma, gave a good correlation coefficient (r >0.99 and r2 >0.98). The limit of detection (LOD) and the limit of quantificati... Journal of Proteomics journals http://www.medworm.com/rss/comments.php?id=3379605 Thu, 11 Mar 2010 00:00:00 +0100 3379605 http://www.medworm.com/index.php?rid=3379608&cid=s_37286_60_f&fid=37286&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20226888%26dopt%3DAbstract Authors: D'Amato A, Bachi A, Fasoli E, Boschetti E, Peltre G, Sénéchal H, Sutra JP, Citterio A, Righetti PG The proteome of Hevea brasiliensis latex has been explored in depth via combinatorial peptide ligand libraries. A total of 300 unique gene products have been identified in this latex, whose proteome has been largely unknown up to the present. In search for unknown allergens, control latex and eluates from the ligand libraries have been fractionated by two-dimensional mapping, blotted and confronted with sera of 18 patients. In addition to the already known and named Hevea major allergens, we have unambiguously detected several others like, for instance: heat shock protein (81kDa), proteasome subunit (30kDa), protease inhibitor (8kDa), hevamine A (43kDa) and glyceraldehy... Journal of Proteomics journals http://www.medworm.com/rss/comments.php?id=3379608 Wed, 10 Mar 2010 00:00:00 +0100 3379608 http://www.medworm.com/index.php?rid=3354018&cid=s_37286_60_f&fid=37286&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20211283%26dopt%3DAbstract Authors: Tucholska M, Florentinus A, Williams D, Marshall JG Many peptides of biological or medicinal importance may be derived from proteolytic actions and are found at low concentrations in human blood fluids. Endogenous polypeptides from human serum were precipitated in acetonitrile and the precipitate was then selectively extracted with water modified by organic solvents and collected over C18 resin. Extraction of serum with C18 alone, and the acetonitrile supernatant or ultrafiltration collected over C18, served as controls. The samples were analyzed by SDS PAGE, or C18 high pressure liquid chromatography with electrospray ionization with a Paul ion trap and Qq-TOF. Spectra were correlated without specifying an enzyme using the X!TANDEM or the Paragon algorithms. Multiple endogeno... Journal of Proteomics journals http://www.medworm.com/rss/comments.php?id=3354018 Fri, 05 Mar 2010 00:00:00 +0100 3354018 http://www.medworm.com/index.php?rid=3354017&cid=s_37286_60_f&fid=37286&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20215060%26dopt%3DAbstract Authors: Gonçalves LD, Soares MR, Nogueira FC, Garcia C, Camisasca DR, Domont G, Feitosa AC, Pereira DD, Zingali RB, Brown GA Chronic periodontal disease is a chronic inflammatory process affecting tooth supporting tissues in the presence of pathogenic bacterial biofilm. There is some evidence for changes in the protein composition of whole saliva from chronic periodontitis patients, but there have been no studies using a proteomic approach. Hence, the aim of this study was to compare the protein profiles of unstimulated whole saliva from patients with periodontitis and healthy subjects by two complementary approaches (2D-gel electrophoresis and liquid chromatography). Protein spots of interest were analyzed by MALDI-TOF-TOF, and the data was complemented by an ESI-Q-TOF experimen... Journal of Proteomics journals http://www.medworm.com/rss/comments.php?id=3354017 Thu, 04 Mar 2010 00:00:00 +0100 3354017 http://www.medworm.com/index.php?rid=3346985&cid=s_37286_60_f&fid=37286&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20206311%26dopt%3DAbstract Authors: Molares Vila A, Rupérez Pérez de Arrilucea P, Caso Peláez E, Gago-Martínez A Sample pre-treatment is a critical step for an efficient and reliable analysis and it is highly dependent on the complexity of the matrix. This work shows an example of application of an immunoprecipitation approach using a new magnetic beads-based format, which allows a selective/specific extraction of potential biomarkers from metastatic prostate cancer. Results obtained on the development of this method, and its application for the extraction and pre-concentration of certain biomarkers present in metastatic cell lines of prostate cancer, are presented and discussed. It is concluded that the efficiency of the immunoprecipitation step is clearly compromised by the crosslinking... Journal of Proteomics journals http://www.medworm.com/rss/comments.php?id=3346985 Tue, 02 Mar 2010 00:00:00 +0100 3346985 http://www.medworm.com/index.php?rid=3327925&cid=s_37286_60_f&fid=37286&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20193786%26dopt%3DAbstract Authors: Végvári A, Fehniger TE, Gustavsson L, Nilsson A, Andrén PE, Kenne K, Nilsson J, Laurell T, Marko-Varga G PMID: 20193786 [PubMed - as supplied by publisher] (Source: Journal of Proteomics) Journal of Proteomics journals http://www.medworm.com/rss/comments.php?id=3327925 Fri, 26 Feb 2010 00:00:00 +0100 3327925 http://www.medworm.com/index.php?rid=3327929&cid=s_37286_60_f&fid=37286&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20188221%26dopt%3DAbstract Authors: Franck J, Meriaux C, Wisztorski M, Salzet M, Fournier I Lipids are a major component of cells and play a variety of roles in organisms. In general, they play a key role in the structural composition of membranes. Some lipids, such as sphingoglycolipids, however, are also mediators of different biological processes, including protein transport, regulation of cell growth, cellular morphogenesis, neuronal plasticity, and regulation of the immune response. With the advent of MALDI mass spectrometry imaging (MALDI MSI), lipids have begun to be intensively investigated by several groups.. Here we present a novel development in the detection and study of lipids using an automatic microspotter coupled to specific liquid ionic matrixes based on a 2,5-DHB matrix (i.e., 2,5-DHB/ANI, 2,5-... Journal of Proteomics journals http://www.medworm.com/rss/comments.php?id=3327929 Tue, 23 Feb 2010 00:00:00 +0100 3327929 http://www.medworm.com/index.php?rid=3327928&cid=s_37286_60_f&fid=37286&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20188222%26dopt%3DAbstract Authors: Niu D, Feng H, Chen WN The development of hepatocellular carcinoma (HCC) can be considered as an end-stage outcome of chronic hepatitis B virus (HBV) infection. Early prognostic markers are needed to allow effective treatments and prevent HCC from developing. Proteomics analysis has been used to identify markers from clinical samples from HCC patients. This approach can be further improved by identifying early biomarkers before the onset of HCC. One way would be to use the cell-based HBV replication system, which is reflective of the early stage of virus infection and thus secreted proteins identified at this stage may have relevance in HCC prognosis. In this review, we focus the discussion on the current status of proteomics analysis of cellular proteins and HCC biomarker ide... Journal of Proteomics journals http://www.medworm.com/rss/comments.php?id=3327928 Tue, 23 Feb 2010 00:00:00 +0100 3327928 http://www.medworm.com/index.php?rid=3327927&cid=s_37286_60_f&fid=37286&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20188223%26dopt%3DAbstract Authors: Marques-da-Silva D, Samhan-Arias AK, Tiago T, Gutierrez-Merino C The presence of cytosolic calcium microcompartments in neurons is well established. L-type voltage calcium channels play a leading role in the rise of cytosolic calcium in the neuronal soma and are sensitive to redox modulation. In a recent work [Samhan-Arias, A.K., García-Bereguiaín, M.A., Martín-Romero, F.J. and Gutiérrez-Merino, C. (2009) Mol. and Cell. Neurosci. 40, 14-26], we have shown that cytochrome b(5) reductase, whose deregulation leads to an overshot of superoxide anion production at the neuronal plasma membrane that triggers apoptosis in primary cultures of cerebellar granule neurons in culture, forms a large mesh of redox centres associated with lipid rafts in these neurons. In t... Journal of Proteomics journals http://www.medworm.com/rss/comments.php?id=3327927 Tue, 23 Feb 2010 00:00:00 +0100 3327927 http://www.medworm.com/index.php?rid=3327926&cid=s_37286_60_f&fid=37286&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20188224%26dopt%3DAbstract Authors: Songsrirote K, Li Z, Ashford D, Bateman A, Thomas-Oates J PGRN is a modular protein with 7(1/2) repeats of the granulin domain separated by short spacer sequences. Elevated expression of PGRN is associated with cancer growth, while mutations of PGRN cause frontotemporal lobar degeneration (FTLD), an early onset form of dementia. PGRN is a glycoprotein, containing five N-glycosylation consensus sequons, three of which fall within granulin domains. A method tailored to enable detailed analysis of the PGRN oligosaccharides and glycopeptides has been developed. The approach involves in-gel deglycosylation using peptide-N-glycosidase F (PNGase F) followed by permethylation of the released oligosaccharides. Permethylation was applied for rapid sample clean-up and to improve sensitiv... Journal of Proteomics journals http://www.medworm.com/rss/comments.php?id=3327926 Tue, 23 Feb 2010 00:00:00 +0100 3327926 http://www.medworm.com/index.php?rid=3302730&cid=s_37286_60_f&fid=37286&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20176152%26dopt%3DAbstract Authors: Waybright T, Avellino AM, Ellenbogen RG, Hollinger BJ, Veenstra TD, Morrison RS The continuing expansion of proteomic technology has been fueled by the potential for discovering novel biomarkers that may be used for the early detection of disease. It has been proposed that human cerebrospinal fluid (CSF), which surrounds and protects the brain and spinal cord from traumatic injury, may be a valuable target for the diagnosis of a variety of conditions such as Alzheimer's disease, traumatic brain injury, amyotrophic lateral sclerosis and Parkinson's disease. The immense complexity of biofluids, however, still requires that considerable development be made in the analytical techniques used so that comprehensive coverage of the proteins present in such samples is achieved. Using a... Journal of Proteomics journals http://www.medworm.com/rss/comments.php?id=3302730 Fri, 19 Feb 2010 00:00:00 +0100 3302730 http://www.medworm.com/index.php?rid=3302729&cid=s_37286_60_f&fid=37286&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20176153%26dopt%3DAbstract In this study we have investigated the stability of human plasma samples by spiking stable isotope-labeled peptides into the plasma and monitoring their degradation under different storage conditions. FPA-1, C4A and C3f were synthesized with isotopically labeled amino acids, and used as reference peptides. The mixture of internal calibrants was spiked into plasma at the starting point of investigation, mimicking the time of collection for future biobanking efforts, and their qualitative and quantitative changes were analyzed over time by using both MALDI-MS (LTQ Orbitrap XL) and nanoLC-ESI-MS (LTQ XL ETD). We have found that all three synthetic peptides were stable in plasma at -20 and -80 degrees C during the examined 2-month period. However, different proteolytic degradation profiles of ... Journal of Proteomics journals http://www.medworm.com/rss/comments.php?id=3302729 Fri, 19 Feb 2010 00:00:00 +0100 3302729 http://www.medworm.com/index.php?rid=3302728&cid=s_37286_60_f&fid=37286&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20176154%26dopt%3DAbstract Authors: Insenser MR, Hernáez ML, Nombela C, Molina M, Molero G, Gil C The study of Saccharomyces cerevisiae cell surface proteins was performed because of their important role in cell wall biogenesis and in the physiology of the yeast. Two different proteomic approaches were carried out. First, proteins loosely associated or S-S linked to structural wall components were released by treatment of whole intact cells with dithiothreitol, separated by 2D-PAGE and identified by mass spectrometry. Second, cell surface-exposed proteins (surfome) were digested with trypsin and DTT from whole intact cells, and analysed by LC-MS/MS. Ninety-nine different proteins were identified: 67 with DTT treatment and 52 with DTT and trypsin digestion. These proteins were classified in different cellula... Journal of Proteomics journals http://www.medworm.com/rss/comments.php?id=3302728 Fri, 19 Feb 2010 00:00:00 +0100 3302728 http://www.medworm.com/index.php?rid=3302732&cid=s_37286_60_f&fid=37286&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20170763%26dopt%3DAbstract Authors: Fujii K, Nakamura S, Takahashi K, Inagaki F Interferon regulatory factor 3 (IRF-3) is a critical transcription factor that regulates innate immune responses against viral infection. Upon infection, IRF-3 is activated through phosphorylation of Ser/Thr residues in its C-terminal domain by the kinases, IKK-i and/or TBK-1. This phosphorylation triggers IRF-3 to interact with the co-activators to form a complex that activates target genes in the nucleus. However, the phosphorylation sites that determine the active/inactive status of IRF-3, estimated using biochemical methods such as mutagenesis and kinase assays, remain controversial. In the present study, phosphorylated IRF-3 189-427 (IRF-3 189C) was prepared by co-expression with IKK-i and was specifically fractionated into 3 ma... Journal of Proteomics journals http://www.medworm.com/rss/comments.php?id=3302732 Tue, 16 Feb 2010 00:00:00 +0100 3302732 http://www.medworm.com/index.php?rid=3302731&cid=s_37286_60_f&fid=37286&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20170764%26dopt%3DAbstract Authors: Bowden P, Pendrak V, Zhu P, Marshall JG Sequence analysis of the blood peptides and their qualities will be key to understanding the mechanisms that contribute to error in LC-ESI-MS/MS. Analysis of peptides and their proteins at the level of sequences is a much more direct and informative than the comparison of disparate accession numbers. A portable database of all blood peptide and protein sequences with descriptor fields and Gene Ontology terms might be useful for designing immunological or MRM assays from human blood. The results of twelve studies of human blood peptides and/or proteins identified by LC-MS/MS and correlated against a disparate array of genetic libraries were parsed and matched to proteins from the human Ensembl, SwissProt and RefSeq databases by SQL. The r... Journal of Proteomics journals http://www.medworm.com/rss/comments.php?id=3302731 Tue, 16 Feb 2010 00:00:00 +0100 3302731 http://www.medworm.com/index.php?rid=3291259&cid=s_37286_60_f&fid=37286&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20167298%26dopt%3DAbstract Authors: Nasso S, Silvestri F, Tisiot F, Di Camillo B, Pietracaprina A, Toffolo GM As an emerging field, MS-based proteomics still requires software tools for efficiently storing and accessing experimental data. In this work, we focus on the management of LC-MS data, which are typically made available in standard XML-based portable formats. The structures that are currently employed to manage these data can be highly inefficient, especially when dealing with high-throughput profile data. LC-MS datasets are usually accessed through 2D range queries. Optimizing this type of operation could dramatically reduce the complexity of data analysis. We propose a novel data structure for LC-MS datasets, called mzRTree, which embodies a scalable index based on the R-tree data structure. mzRTree ca... Journal of Proteomics journals http://www.medworm.com/rss/comments.php?id=3291259 Mon, 15 Feb 2010 00:00:00 +0100 3291259 http://www.medworm.com/index.php?rid=3291258&cid=s_37286_60_f&fid=37286&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20167299%26dopt%3DAbstract Authors: Hernáez ML, Ximénez-Embún P, Martínez-Gomariz M, Gutiérrez D, Nombela C, Gil C We have set up a fast and easy methodology to identify cell surface proteins in live yeasts. A non-gel proteomic approach was based on a short period of trypsin treatment followed by peptide separation and identification using nano-LC followed by off-line MS/MS. Candida albicans was used as a model organism and proteins involved in cell wall organization, cell rescue, defense, virulence, transport, protein fate and metabolism were identified. This strategy is a powerful tool to study host-pathogen interactions and to look for potential vaccine candidates and drug targets. PMID: 20167299 [PubMed - as supplied by publisher] (Source: Journal of Proteomics) Journal of Proteomics journals http://www.medworm.com/rss/comments.php?id=3291258 Mon, 15 Feb 2010 00:00:00 +0100 3291258 http://www.medworm.com/index.php?rid=3276559&cid=s_37286_60_f&fid=37286&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20153845%26dopt%3DAbstract Authors: Lemmens I, Lievens S, Tavernier J Many processes in a cell depend on protein-protein interactions (PPIs) and perturbations of these interactions can lead to diseases. Comprehensive knowledge of PPI networks will not only give us information on how the cell is organized, but will also provide new drug targets. Current binary PPI networks are mainly generated by high-throughput yeast two-hybrid. Due to the small overlap of these maps, it has long been assumed that these maps are of low quality containing many false positives. However, by using an orthogonal two-hybrid method, MAPPIT (mammalian protein-protein interaction trap), these maps were shown to be of high quality suggesting that the limited overlap is likely due to low sensitivity and not to low specificity. PMID: 20... Journal of Proteomics journals http://www.medworm.com/rss/comments.php?id=3276559 Thu, 11 Feb 2010 00:00:00 +0100 3276559 http://www.medworm.com/index.php?rid=3276558&cid=s_37286_60_f&fid=37286&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20153846%26dopt%3DAbstract This study has used mass spectrometry-based proteomics to investigate the fate of the aging rat muscle proteome. Using nonionic detergent phase extraction, this report shows that the aged gastrocnemius muscle exhibits a generally perturbed protein expression pattern in both the detergent-extracted fraction and the aqueous protein complement from senescent muscle tissue. In the detergent-extracted fraction, the expression of ATP synthase, isocitrate dehydrogenase, enolase, tropomyosin and beta-actin was increased. Different isoforms of creatine kinase and prohibitin showed differential changes. In the aqueous fraction, malate dehydrogenase, sulfotransferase, triosephosphate isomerase, aldolase, cofilin-2 and lactate dehydrogenase showed increased levels. Interestingly, differential effects ... Journal of Proteomics journals http://www.medworm.com/rss/comments.php?id=3276558 Thu, 11 Feb 2010 00:00:00 +0100 3276558 http://www.medworm.com/index.php?rid=3276557&cid=s_37286_60_f&fid=37286&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20153847%26dopt%3DAbstract This study led to the extension and refinement of our current model for the global response of Pseudomonas putida KT2440 to phenol by getting insights into the adaptive response mechanisms involving the membrane proteome. A two-dimensional gel electrophoresis based protocol was optimized to allow the quantitative comparison of membrane proteins, by combining inner and outer membrane fractionation with membrane protein solubilization using the detergent dodecylmaltoside. Following phenol exposure, a coordinate increased content of protein subunits of known or putative solvent efflux pump systems (e.g. TtgA, TtgC, Ttg2A, Ttg2C, PP_1516-7) and a decreased content of porins OprB, OprF, OprG and OprQ was registered, consistent with an adaptive response to reduce phenol intracellular concentrati... Journal of Proteomics journals http://www.medworm.com/rss/comments.php?id=3276557 Thu, 11 Feb 2010 00:00:00 +0100 3276557 http://www.medworm.com/index.php?rid=3276556&cid=s_37286_60_f&fid=37286&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20153848%26dopt%3DAbstract We present a novel approach to perform C-terminal sequence analysis by discriminating the C-terminal peptide in a mass spectral analysis of a CNBr digest. During CNBr cleavage, all Met-Xxx peptide bonds are cleaved and the generated internal peptides all end with a homoserine lactone (hsl)-derivative. The partial opening of the hsl-derivatives, by using a slightly basic buffer solution, results in the formation of m/z doublets (Deltam=18Da) for all internal peptides and allows to identify the C-terminal peptide which appears as a singlet in the mass spectra. Using two model proteins we demonstrate that this approach can be applied to study proteins purified in gel or in solution. The chemical opening of the hsl-derivative does not require any sample clean-up and therefore, the sensitivity ... Journal of Proteomics journals http://www.medworm.com/rss/comments.php?id=3276556 Thu, 11 Feb 2010 00:00:00 +0100 3276556 http://www.medworm.com/index.php?rid=3254864&cid=s_37286_60_f&fid=37286&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20139037%26dopt%3DAbstract Authors: Schaaij-Visser TB, Brakenhoff RH, Leemans CR, Heck AJ, Slijper M Squamous cell carcinoma of the head and neck (HNSCC) is the sixth most common cancer world-wide. Despite improvements in diagnosis and treatment, the five-year-survival rate of advanced HNSCC has only moderately increased, which is largely due to the high proportion of patients that present with advanced disease stage and the frequent development of relapse and second primary tumors. Protein biomarkers allowing early detection of primary HNSCC or relapse may aid to improve clinical outcome. Screening for precursor changes in the mucosal linings preceding the development of invasive tumors and for accurate prediction of risk of malignant transformation, may be propitious opportunities, which are as yet difficult. ... Journal of Proteomics journals http://www.medworm.com/rss/comments.php?id=3254864 Thu, 04 Feb 2010 00:00:00 +0100 3254864 http://www.medworm.com/index.php?rid=3244540&cid=s_37286_60_f&fid=37286&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20123049%26dopt%3DAbstract Authors: Brandão AR, Barbosa HS, Arruda MA Considering the importance of bidimensional electrophoresis and image analysis in comparative proteomics, the parameters that influence the analysis of protein expression of transgenic and non-transgenic soybean seeds were evaluated. The loaded mass of the proteins (150-500microg), the pH separation range (3-10 or 4-7), and manual/automatic image editing were evaluated. Additionally, after optimizing the conditions, histograms and matchings were obtained in order to accurately analyze the variations (90%) in protein expression. From this, 10 proteins displayed significant differences in expression, and eight of them were characterized and identified by mass spectrometry. PMID: 20123049 [PubMed - as supplied by publisher] (Source: Jour... Journal of Proteomics journals http://www.medworm.com/rss/comments.php?id=3244540 Sat, 30 Jan 2010 00:00:00 +0100 3244540 http://www.medworm.com/index.php?rid=3236572&cid=s_37286_60_f&fid=37286&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20114090%26dopt%3DAbstract Authors: Hägglund P, Bunkenborg J, Yang F, Harder LM, Finnie C, Svensson B Thioredoxins are ubiquitous disulfide reductases involved in a wide range of cellular processes including DNA synthesis, oxidative stress response and apoptosis. In cereal seeds thioredoxins are proposed to facilitate the germination process by reducing disulfide bonds in storage proteins and other targets in the starchy endosperm. Here we have applied a thiol-specific labeling approach to identify specific disulfide targets of barley thioredoxin in proteins released from barley aleurone layers incubated in buffer containing gibberellic acid. PMID: 20114090 [PubMed - as supplied by publisher] (Source: Journal of Proteomics) Journal of Proteomics journals http://www.medworm.com/rss/comments.php?id=3236572 Fri, 29 Jan 2010 00:00:00 +0100 3236572 http://www.medworm.com/index.php?rid=3236570&cid=s_37286_60_f&fid=37286&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20117255%26dopt%3DAbstract Authors: Hovsepyan M, Sargsyan E, Bergsten P Elevated blood levels of glucose and lipids in individuals with type 2 diabetes mellitus have been observed to cause impairment of insulin secretion from pancreatic beta-cells. Chronic exposure to either of the circulating fatty acid oleate or palmitate has different effects on the beta-cell. Whereas palmitate causes functional impairment of the beta-cell and apoptosis, oleate has only minor negative effects on beta-cell function and mass. The aim of the present study was to delineate mechanisms by which the fatty acids affect the beta-cell differently. In particular, the aim was to identify beta-cell proteins exclusively regulated by palmitate. INS-1E cells were cultured for 24hours in medium supplemented with palmitate or oleate. After cul... Journal of Proteomics journals http://www.medworm.com/rss/comments.php?id=3236570 Thu, 28 Jan 2010 00:00:00 +0100 3236570 http://www.medworm.com/index.php?rid=3236569&cid=s_37286_60_f&fid=37286&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20117256%26dopt%3DAbstract We report proteomic profiles of PCTVs isolated from the enteric ER in the small intestine of the fructose-fed hamster, an established model of diet-induced insulin resistance. Using 2D gel electrophoresis and tandem mass spectrometry, PCTVs were characterized and proteomic profiles of PCTV-associated proteins from insulin-resistant and control enterocytes were developed, with the intention of identifying proteins involved in insulin signaling attenuation and lipoprotein overproduction. A number of PCTV-associated proteins were found to be differentially expressed including microsomal triglyceride transfer protein (MTP), apoB-48, Sar1 and VAMP7. We postulate that altered expression of Sar1 and MTP may contribute to increased chylomicron assembly in the fructose-fed hamster. These findings h... Journal of Proteomics journals http://www.medworm.com/rss/comments.php?id=3236569 Thu, 28 Jan 2010 00:00:00 +0100 3236569 http://www.medworm.com/index.php?rid=3236571&cid=s_37286_60_f&fid=37286&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20116462%26dopt%3DAbstract Authors: Bonnette PC, Robinson BS, Silva JC, Stokes MP, Brosius AD, Baumann A, Buckbinder L The PYK2 tyrosine kinase is a negative regulator of bone formation, but aside from the requirement for PYK2 kinase activity there has been little progress toward understanding of the molecular mechanism involved in this function. To gain insight into the signaling pathways modulated by PYK2 we sought to identify PYK2 substrates. Challenges inherent to a quantitative phosphoproteomic analysis for non-receptor tyrosine kinases were overcome by employing an inducible PYK2 overexpression system in NIH3T3 cells in combination with a selective PYK2 inhibitor. The identification of a number of known PYK2 substrates and interacting partners validated the methodology. Results of the inducible cell system... Journal of Proteomics journals http://www.medworm.com/rss/comments.php?id=3236571 Wed, 27 Jan 2010 00:00:00 +0100 3236571 http://www.medworm.com/index.php?rid=3217919&cid=s_37286_60_f&fid=37286&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20102753%26dopt%3DAbstract Authors: Végvári A, Rezeli M, Welinder C, Malm J, Lilja H, Marko-Varga G, Laurell T Measurements of the prostate-specific antigen (PSA) levels in blood are widely used as diagnostic, predictive and prognostic marker of prostate disease. The selective detection of molecular forms of PSA can contribute clinically to meaningful enhancements of the conventional PSA-test. As it is plausible that an in-depth search for structural variants of PSA gene products may increase our ability to discriminate distinct patho-biological basis and stages of prostate diseases, we have developed a multi-step protocol comprising gel-based methods followed by mass spectrometric identification. Our current aim was to provide a comprehensive identification of PSA variants occurring in seminal fluid. ... Journal of Proteomics journals http://www.medworm.com/rss/comments.php?id=3217919 Sat, 23 Jan 2010 00:00:00 +0100 3217919 http://www.medworm.com/index.php?rid=3212510&cid=s_37286_60_f&fid=37286&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20097317%26dopt%3DAbstract Authors: Martinez-Bartolome S, Blanco F, Albar JP ProteoRed, a Spanish Initiative in the field of proteomics, is reaching international standards. Here we present ProteoRed as an example of collaborative initiative in the field of proteomics. Being established as a high level proteomics service provider, it also has consolidated as one of the first institutions really involved in implementing proteomics standards developed by the HUPO consortium. As a collaborative network it has proved a valuable platform to coordinate multi-centric experiments aiming at evaluating the robustness of laboratory workflows as well as the implementation of standards. In addition, this initiative has been very active in promoting the interaction between clinicians and basic researchers by means of courses,... Journal of Proteomics journals http://www.medworm.com/rss/comments.php?id=3212510 Thu, 21 Jan 2010 00:00:00 +0100 3212510 http://www.medworm.com/index.php?rid=3212512&cid=s_37286_60_f&fid=37286&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20096812%26dopt%3DAbstract Authors: Helbig AO, Heck AJ, Slijper M The analysis of proteins in biological membranes forms a major challenge in proteomics. Despite continuous improvements and the development of more sensitive analytical methods, the analysis of membrane proteins has always been hampered by their hydrophobic properties and relatively low abundance. In this review, we describe recent successful strategies that have lead to in-depth analyses of the membrane proteome. To facilitate membrane proteome analysis, it is essential that biochemical enrichment procedures are combined with special analytical workflows that are all optimized to cope with hydrophobic polypeptides. These include techniques for protein solubilization, and also well-matched developments in protein separation and protein digestion p... Journal of Proteomics journals http://www.medworm.com/rss/comments.php?id=3212512 Wed, 20 Jan 2010 00:00:00 +0100 3212512 http://www.medworm.com/index.php?rid=3200920&cid=s_37286_60_f&fid=37286&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20093204%26dopt%3DAbstract Authors: Ottervald J, Franzén B, Nilsson K, Andersson LI, Khademi M, Eriksson B, Kjellström S, Marko-Varga G, Végvári A, Harris RA, Laurell T, Miliotis T, Matusevicius D, Salter H, Ferm M, Olsson T Multiple Sclerosis (MS) is a neuroinflammatory and neurodegenerative disease that results in damage to myelin sheaths and axons in the central nervous system and which preferentially affects young adults. We performed a proteomics-based biomarker discovery study in which cerebrospinal fluid (CSF) from MS and control individuals was analyzed (n=112). Ten candidate biomarkers were selected for evaluation by quantitative immunoassay using an independent cohort of MS and control subjects (n=209). In relapsing-remitting MS (RRMS) patients there were significant increases in th... Journal of Proteomics journals http://www.medworm.com/rss/comments.php?id=3200920 Tue, 19 Jan 2010 00:00:00 +0100 3200920 http://www.medworm.com/index.php?rid=3194481&cid=s_37286_60_f&fid=37286&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20083244%26dopt%3DAbstract Authors: Fischer JD, Liao L, Carvalho PC, Barbosa VC, Domont GB, Carvalho MD, Yates JR Perillyl alcohol (POH) is a naturally occurring terpene and a promising chemotherapeutic agent for glioblastoma multiform; yet, little is known about its molecular effects. Here we present results of a semi-quantitative proteomic analysis of A172 cells exposed to POH for different time-periods (1', 10', 30', 60', 4h, and 24h). The analysis identified more than 4,000 proteins; which were clustered using PatternLab for proteomics and then linked to Ras signaling, tissue homeostasis, induction of apoptosis, metallopeptidase activity, and ubiquitin-protein ligase activity. Our results make available one of the most complete protein repositories for the A172. Moreover, we detected the phosphorylation of G... Journal of Proteomics journals http://www.medworm.com/rss/comments.php?id=3194481 Fri, 15 Jan 2010 00:00:00 +0100 3194481 http://www.medworm.com/index.php?rid=3186157&cid=s_37286_60_f&fid=37286&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20080220%26dopt%3DAbstract Authors: D'Alessandro A, Righetti PG, Fasoli E, Zolla L Combinatorial peptide ligand libraries have recently allowed considerable advances in the mapping of chicken egg yolk and white proteomics. Data from literature have been regrouped and elaborated for network and pathway analyses in order to convey a unified view of these proteomes. Redundant proteins were excluded, while isoforms of the same proteins were maintained to reach a total of 260 distinct gene products for egg yolk and 148 for egg white having a match in the database. From these analyses, a role for proteins involved in cell development, proliferation and migration, cell-to-cell interaction and hematological system development emerged. Although it might turn out that, notwithstanding the extensive mapping, the currently ... Journal of Proteomics journals http://www.medworm.com/rss/comments.php?id=3186157 Thu, 14 Jan 2010 00:00:00 +0100 3186157 http://www.medworm.com/index.php?rid=3186158&cid=s_37286_60_f&fid=37286&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20079470%26dopt%3DAbstract Authors: Auer J, Camoin L, Guillonneau F, Rigourd V, Chelbi ST, Leduc M, Laparre J, Mignot TM, Vaiman D In order to identify new protein markers modified in placental diseases, high-throughput analysis of proteins in the plasma of pregnant women was carried out for normal and pathological pregnancies (Preeclampsia and/or Intra Uterine Growth Restriction) using iTRAQ technology. We could identify 166 proteins that were modified (p<0.05) and the technique used allowed the detection of previously undetected factors, such as various members of the SERPINA clade. The modifications of two proteins (C reactive protein and antichymotrypsin, SERPINA3) were validated on individual samples. Complement and coagulation cascades proteins were significantly enriched among modified protein clusters... Journal of Proteomics journals http://www.medworm.com/rss/comments.php?id=3186158 Tue, 12 Jan 2010 00:00:00 +0100 3186158 http://www.medworm.com/index.php?rid=3171295&cid=s_37286_60_f&fid=37286&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20067847%26dopt%3DAbstract Authors: Kjellsen TD, Shiryaeva L, Schröder WP, Strimbeck GR Differential expression of proteins in needles of the extreme freezing tolerant conifer Picea obovata during September, October and November was analyzed using DIGE technology and multivariate analysis. More than 1200 spots were detected, and the abundance of 252 of these spots were significantly altered during the course of acclimation. The 252 spots were clustered into five distinct expression profiles. Among the protein spots showing differential expression, 43 were identified by MALDI-TOF/TOF and twelve of them matched proteins associated with various biotic and abiotic stress responses in other plants. Dehydrins, Hsp70s, AAA(+) ATPases, lipocalin, cyclophilins, glycine rich protein (GNP) and several reactive oxygen ... Journal of Proteomics journals http://www.medworm.com/rss/comments.php?id=3171295 Sat, 09 Jan 2010 00:00:00 +0100 3171295 http://www.medworm.com/index.php?rid=3164183&cid=s_37286_60_f&fid=37286&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20060077%26dopt%3DAbstract Authors: Agarwal R, Matros A, Melzer M, Mock HP, Sainis JK Cell free extracts of Synechocystis 6803 were fractionated by successive ultracentrifugation at 40,000xg, 90,000xg and 150,000xg to obtain the three thylakoid fractions designated as 40k, 90k and 150k fractions respectively. These fractions showed differences in absorption and emission spectra. Nano-LC-ESI-Q-TOF MS analysis identified 123 proteins belonging to membrane as well as cytosolic fraction. Out of these proteins, there were 22 proteins with transmembrane helices and 12 proteins with signal peptide. There were 77 proteins common across all the three fractions. Most of these proteins were subunits of photosynthetic complexes, CF(0)-CF(1) ATP Synthase or ribosomal proteins. Among the rest of the proteins, 8 were exclusive... Journal of Proteomics journals http://www.medworm.com/rss/comments.php?id=3164183 Tue, 05 Jan 2010 00:00:00 +0100 3164183 http://www.medworm.com/index.php?rid=3157838&cid=s_37286_60_f&fid=37286&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20056176%26dopt%3DAbstract Authors: Cuervo P, Domont GB, De Jesus JB Leishmania spp., Trypanosoma cruzi, and Trypanosoma brucei are protozoan parasites that cause a spectrum of fatal human diseases around the world. Recent completion of the genomic sequencing of these parasites has enormous relevance to the study of their biology and the pathogenesis of the diseases they cause because it opens the door to high-throughput proteomic technologies. This review encompasses studies using diverse proteomic approaches with these organisms to describe and catalogue global protein profiles, reveal changes in protein expression during development, elucidate the subcellular localisation of gene products, and evaluate host-parasite interactions. PMID: 20056176 [PubMed - as supplied by publisher] (Source: Journal of Prote... Journal of Proteomics journals http://www.medworm.com/rss/comments.php?id=3157838 Mon, 04 Jan 2010 00:00:00 +0100 3157838 http://www.medworm.com/index.php?rid=3146683&cid=s_37286_60_f&fid=37286&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20045494%26dopt%3DAbstract This study was designed to 1) profile native proteins secreted by undifferentiated hESC and 2) determine their biological effects on primary neonatal cardiomyocytes. We utilized multi-analyte, immunochemical assays to characterize media conditioned by undifferentiated hESC versus unconditioned media. Expression profiling was performed on cardiomyocytes subjected to these different media conditions and altered transcripts were mapped to critical pathways. Thirty-two of 109 proteins were significantly elevated in conditioned media ranging in concentration from thrombospondin (57.2+/-5.0ng/ml) to nerve growth factor (7.4+/-1.2pg/ml) and comprising chemokines, cytokines, growth factors, and proteins involved in cell adhesion and extracellular matrix remodeling. Conditioned media induced karyok... Journal of Proteomics journals http://www.medworm.com/rss/comments.php?id=3146683 Wed, 30 Dec 2009 00:00:00 +0100 3146683 http://www.medworm.com/index.php?rid=3146682&cid=s_37286_60_f&fid=37286&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20045495%26dopt%3DAbstract Authors: Anagnostopoulos AK, Kolialexi A, Mavrou A, Vougas K, Papantoniou N, Antsaklis A, Kanavakis E, Fountoulakis M, Tsangaris GT Klinefelter syndrome is a sex chromosomal abnormality (47, XXY karyotype), occurring approximately in 1 in 1000 male live births. In the present study proteomic analysis was performed in twelve 2(nd) trimester amniotic fluid samples, eight coming from pregnancies with normal males and four with Klinefelter syndrome foetuses, as shown by routine prenatal cytogenetic analysis. Samples were analysed by 2-DE, coupled with MALDI-TOF-MS analysis . Three proteins (Ceruloplasmin, Alpha-1-antitrypsin and Zinc-alpha-2-glycoprotein) were found to be up-regulated in samples obtained from pregnancies with Klinefelter syndrome foetuses, whereas four proteins (Apolipopro... Journal of Proteomics journals http://www.medworm.com/rss/comments.php?id=3146682 Wed, 30 Dec 2009 00:00:00 +0100 3146682 http://www.medworm.com/index.php?rid=3146681&cid=s_37286_60_f&fid=37286&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20045496%26dopt%3DAbstract Authors: George J, Prasad S, Mahmood Z, Shukla Y Glyphosate is a widely used board spectrum herbicide, reported to induce various toxic effects in non-target species, but its carcinogenic potential is still unknown. Here we showed the carcinogenic effects of glyphosate using 2-stage mouse skin carcinogenesis model and proteomic analysis. Carcinogenicity study revealed that glyphosate has tumor promoting activity. Proteomic analysis using 2-Dimensional gel electrophoresis and mass spectrometry showed 22 spots were differentially expressed (>2 fold) on glyphosate, 7, 12-dimethylbenz[a]anthracene (DMBA) and 12-O-tetradecanoyl-phorbol-13-acetate (TPA) application over untreated control. Among them, 9 proteins (translation elongation factor eEF-1 alpha chain, carbonic anhydrase III, anne... Journal of Proteomics journals http://www.medworm.com/rss/comments.php?id=3146681 Wed, 30 Dec 2009 00:00:00 +0100 3146681 http://www.medworm.com/index.php?rid=3119382&cid=s_37286_60_f&fid=37286&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20026292%26dopt%3DAbstract Meeting Report & Perspective Quantitative Proteomics: A Central Technology for Systems Biology. J Proteomics. 2009 Dec 17; Authors: Ahrens CH, Brunner E, Basler K PMID: 20026292 [PubMed - as supplied by publisher] (Source: Journal of Proteomics) Journal of Proteomics journals http://www.medworm.com/rss/comments.php?id=3119382 Thu, 17 Dec 2009 00:00:00 +0100 3119382 http://www.medworm.com/index.php?rid=3119384&cid=s_37286_60_f&fid=37286&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20026262%26dopt%3DAbstract We report the 2DE-based proteomic characterization of the venom of the medically important African puff adder, Bitis arietans, after prefractionation by incubation with a solid-phase combinatorial hexapeptide ligand library (CPLL) at three different pH values. This approach yielded partially overlapping yet clearly distinct sets of proteins. The B. arietans venom proteome, merged from the four sets of proteins comprises at least 43 distinct proteins from 9 toxin families. In line with a previous reverse-phase HPLC-based venomic characterization on the same species, SVMPs, serine proteinases, C-type lectin-like proteins, and to a minor extent PLA(2), disintegrin bitistatin, and cystatin, comprise the major toxins in the venom of B. arietans. However, the 2D-CPLL approach employed here ident... Journal of Proteomics journals http://www.medworm.com/rss/comments.php?id=3119384 Wed, 16 Dec 2009 00:00:00 +0100 3119384 http://www.medworm.com/index.php?rid=3119383&cid=s_37286_60_f&fid=37286&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20026263%26dopt%3DAbstract We present data from CCMS experiments on two biological lysates from E.coli and from human-derived Hek293 cells. The GDP Capture Compound robustly captures a wide range of different GTPases from both systems and will be a valuable tool for the proteomic profiling of this important protein family. PMID: 20026263 [PubMed - as supplied by publisher] (Source: Journal of Proteomics) Journal of Proteomics journals http://www.medworm.com/rss/comments.php?id=3119383 Wed, 16 Dec 2009 00:00:00 +0100 3119383 http://www.medworm.com/index.php?rid=3119386&cid=s_37286_60_f&fid=37286&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20026003%26dopt%3DAbstract Authors: Dos Santos MF, de Pádua VL, de Matos Nogueira E, Hemerly AS, Domont GB Gluconacetobacter diazotrophicus is a micro-aerobic bacterium able to fix atmospheric nitrogen in endophytic mode. A proteomic approach was used to analyze proteins differentially expressed in the presence and absence of sugarcane plantlets. Two-dimensional gel electrophoresis (2-DE) showed 42 spots with altered levels of expression. Analysis of these spots by matrix-assisted laser desorption ionization time-of-flight in tandem (MALDI-TOF-TOF) identified 38 proteins. Differentially expressed proteins were associated with carbohydrate and energy metabolism, folding, sorting and degradation processes, and transcription and translation. Among proteins expressed in co-cultivated bacteria, four belong to me... Journal of Proteomics journals http://www.medworm.com/rss/comments.php?id=3119386 Tue, 15 Dec 2009 00:00:00 +0100 3119386 http://www.medworm.com/index.php?rid=3119385&cid=s_37286_60_f&fid=37286&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20026004%26dopt%3DAbstract In this study, we aim to identify the HBx-induced protein profile in HepG2 cells by LC-MS/MS proteomics analysis. Our results indicated that proteins were differentially expressed in HepG2 cells transfected by HBx of various genotypes. Proteins associated with cytoskeleton were found to be either up-regulated (MACF1, HMGB1, Annexin A2) or down-regulated (Lamin A/C). These may in turn result in the decrease of focal adhesion and increase of cell migration in response to HBx. Levels of other cellular proteins with reported impact on the function of extracellular matrix (ECM) proteins and cell migration, including Ca(2+)-binding proteins (S100A11, S100A6, and S100A4) and proteasome protein (PSMA3), were affected by HBx. The differential protein profile identified in this study was also suppor... Journal of Proteomics journals http://www.medworm.com/rss/comments.php?id=3119385 Tue, 15 Dec 2009 00:00:00 +0100 3119385 http://www.medworm.com/index.php?rid=3105309&cid=s_37286_60_f&fid=37286&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20004755%26dopt%3DAbstract Authors: Candiano G, Santucci L, Petretto A, Bruschi M, Dimuccio V, Urbani A, Bagnasco S, Ghiggeri GM The discovery of urinary biomarkers is a main topics in clinical medicine. The development of proteomics has rapidly changed the knowledge on urine protein composition and probably will modify it again. Two-Dimensional electrophoresis (2D-PAGE) coupled with mass spectrometry has represented for years the technique of choice for the analysis of urine proteins and it is time to draw some conclusions. This review will focus major methodological aspects related to urine sample collection, storage and analysis by 2D-PAGE and attempt to define an advanced normal urine protein map. Overall, 1118 spots were reproducibly found in normal urine samples but only 275 were characterized as isoforms ... Journal of Proteomics journals http://www.medworm.com/rss/comments.php?id=3105309 Tue, 08 Dec 2009 00:00:00 +0100 3105309 http://www.medworm.com/index.php?rid=3105310&cid=s_37286_60_f&fid=37286&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20004262%26dopt%3DAbstract Authors: Wu HJ, Seib KL, Srikhanta YN, Edwards J, Kidd SP, Maguire TL, Hamilton A, Pan KT, Hsiao HH, Yao CW, Grimmond SM, Apicella MA, McEwan AG, Wang AH, Jennings MP Neisseria gonorrhoeae has evolved a complex and novel network of oxidative stress responses, including defense mechanisms that are dependent on manganese (Mn). We performed systematic analyses at the transcriptomic and proteomic (1D SDS-PAGE and Isotope-Coded Affinity Tag [ICAT]) levels to investigate the global expression changes that take place in a high Mn environment, which results in a Mn-dependent oxidative stress resistance phenotype. These studies revealed that there were proteins regulated at the post-transcriptional level under conditions of increased Mn concentration, including proteins involved in virulence (e... Journal of Proteomics journals http://www.medworm.com/rss/comments.php?id=3105310 Mon, 07 Dec 2009 00:00:00 +0100 3105310 http://www.medworm.com/index.php?rid=3080103&cid=s_37286_60_f&fid=37286&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19995621%26dopt%3DAbstract In this study, cell nuclei from aneuploid breast cancer samples were sorted with respect to DNA content into pure diploid and aneuploid fractions using flow cytometry. The nuclear proteins were then separated by one-dimensional gel electrophoresis (1D-PAGE) and differences in protein expression patterns, between diploid and aneuploid nuclei from the same tumours, were compared. Using a combination of peptide finger printing and peptide identification by MALDI-TOF mass spectrometry, we identified proteins and confirmed that the proteins were of nuclear origins. The results in this study add further information to the knowledge about the breast cancer disease complexity and heterogeneity at molecular level. For some of the tumours studied different nuclei protein patterns were obtained, in t... Journal of Proteomics journals http://www.medworm.com/rss/comments.php?id=3080103 Sat, 05 Dec 2009 00:00:00 +0100 3080103 http://www.medworm.com/index.php?rid=3080102&cid=s_37286_60_f&fid=37286&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19995622%26dopt%3DAbstract Authors: Gibson D, Banha J, Penque D, Costa L, Conrads TP, Cahill D, O'Brien J, Rooney M Current clinical, laboratory or radiological parameters can not accurately diagnose or predict disease outcomes in a range of autoimmune disorders. Biomarkers which can diagnose at an earlier time point, predict outcome or help guide therapeutic strategies in autoimmune diseases could improve clinical management of this broad group of debilitating disorders. Additionally, there is a growing need for a deeper understanding of multi-factorial autoimmune disorders. Proteomics platforms offering a multiplex approach are more likely to reflect the complexity of autoimmune disease processes. Findings from proteomic based studies of three distinct autoimmune diseases are presented and strategies compared.... Journal of Proteomics journals http://www.medworm.com/rss/comments.php?id=3080102 Sat, 05 Dec 2009 00:00:00 +0100 3080102 http://www.medworm.com/index.php?rid=3031275&cid=s_37286_60_f&fid=37286&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19938305%26dopt%3DAbstract Authors: Righetti PG A short survey of electrophoresis and a celebration of its bicentennial, with some remarkable mementos and a list of books that shaped the field. Where one also learns of a secret production plant with a huge-scale electrophoretic apparatus for skimming of latex from Hevea brasiliensis and keeping the wheels of the Ally Army running during World War II. And of cyber (mammoth) 2D gels of 1.5 x 1 m in size accommodating >12,000 spots. PMID: 19938305 [PubMed - in process] (Source: Journal of Proteomics) Journal of Proteomics journals http://www.medworm.com/rss/comments.php?id=3031275 Fri, 27 Nov 2009 11:16:05 +0100 3031275 http://www.medworm.com/index.php?rid=3031276&cid=s_37286_60_f&fid=37286&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19931659%26dopt%3DAbstract Authors: Lion N, Crettaz D, Rubin O, Tissot JD The availability of stored Red Blood Cells (RBCs) for transfusion remains an important aspects of the treatment of polytrauma, acute anaemia or major bleedings. RBCs are prepared by blood banks from whole blood donations and stored in the cold in additive solutions for typically six weeks. These far from physiological storage conditions result in the so-called red cell storage lesion that is of importance both to blood bankers and to clinical practicionners. Here we review the current state of knowledge about the red cell storage lesion from a proteomic perspective. In particular, we describe the current models accounting for RBC aging and response to lethal stresses, review the published proteomic studies carried out to uncover the molecu... Journal of Proteomics journals http://www.medworm.com/rss/comments.php?id=3031276 Wed, 18 Nov 2009 00:00:00 +0100 3031276 http://www.medworm.com/index.php?rid=3031277&cid=s_37286_60_f&fid=37286&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19931431%26dopt%3DAbstract Authors: Marcus K, Schmidt C, Urlaub H The field of proteomics is rapidly evolving and has emerged as a routine application in many laboratories. It covers not only the identification of proteins but also the quantification and analysis of post-translational protein modifications. During the last few years a series of summer schools teaching comprehensive knowledge in proteomic research and applied techniques has been held. Various research areas were dealt with by international experts in lectures and workshops. The summer schools were addressed to master's and graduate students as well as young post-docs currently moving into the field of proteomics. Here, we give a report on the third European Summer School "Quantification and Post-translational Modifications of Proteins" held at th... Journal of Proteomics journals http://www.medworm.com/rss/comments.php?id=3031277 Tue, 17 Nov 2009 00:00:00 +0100 3031277 http://www.medworm.com/index.php?rid=3000499&cid=s_37286_60_f&fid=37286&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19914409%26dopt%3DAbstract Authors: Zolla L PMID: 19914409 [PubMed - as supplied by publisher] (Source: Journal of Proteomics) Journal of Proteomics journals http://www.medworm.com/rss/comments.php?id=3000499 Thu, 12 Nov 2009 00:00:00 +0100 3000499 http://www.medworm.com/index.php?rid=3000498&cid=s_37286_60_f&fid=37286&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19914410%26dopt%3DAbstract Authors: Hess JR Blood component storage allows the donor and recipient to be separated in time and space. This separation converts transfusion from a desperate clinical act into a planned, orderly healthcare logistic activity with concomitant increases in both blood product availability and safety. However, storage has the potential to reduce the efficacy of transfused blood components by reducing their flow, functional capacity, and survival. Storage time also allows the accumulation of leaked potassium from red cells and the growth of contaminating bacteria. Many different aspects of the red cell storage lesion have been described, including changes in metabolism, shape, and rheology changes, loss of membrane carbohydrates, lipids and proteins, and alterations in secretion, oxygen d... Journal of Proteomics journals http://www.medworm.com/rss/comments.php?id=3000498 Thu, 12 Nov 2009 00:00:00 +0100 3000498 http://www.medworm.com/index.php?rid=3000497&cid=s_37286_60_f&fid=37286&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19914411%26dopt%3DAbstract CONCLUSIONS: The analysis approach implemented in MASCAP may simplify biomarker detection, by assisting the recognition of proteomic expression signatures of the disease. A MATLAB implementation of the software and the data used for its validation are available at http://www.unich.it/proteomica/bioinf. PMID: 19914411 [PubMed - as supplied by publisher] (Source: Journal of Proteomics) Journal of Proteomics journals http://www.medworm.com/rss/comments.php?id=3000497 Thu, 12 Nov 2009 00:00:00 +0100 3000497 http://www.medworm.com/index.php?rid=3000496&cid=s_37286_60_f&fid=37286&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19914412%26dopt%3DAbstract Authors: Ghatpande SS, Choudhary PK, Quinn CT, Goodman SR Hydroxyurea (HU) is an effective drug for the treatment of sickle cell disease (SCD). The main clinical benefit of HU is thought to derive from its capacity to increase fetal hemoglobin (HbF) production. However, other effects leading to clinical benefit, such as improved blood rheology, have been suggested. In order to understand HU-induced changes at the proteomic level, we profiled sickle RBC membranes from of HU-treated and untreated patients. Our previous in vitro profiling studies on sickle RBC membranes identified a significant increase in predominantly anti-oxidant enzymes, protein repair and degradation components and a few RBC cytoskeletal proteins. In the present study, using 2D-DIGE (Two-Dimensional Difference In-Gel... Journal of Proteomics journals http://www.medworm.com/rss/comments.php?id=3000496 Thu, 12 Nov 2009 00:00:00 +0100 3000496 http://www.medworm.com/index.php?rid=3000500&cid=s_37286_60_f&fid=37286&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19913118%26dopt%3DAbstract This study not only established a comprehensive inventory of ABA responsive proteins, but also identified new proteins for further investigation of their functions in guard cell ABA signaling. PMID: 19913118 [PubMed - as supplied by publisher] (Source: Journal of Proteomics) Journal of Proteomics journals http://www.medworm.com/rss/comments.php?id=3000500 Tue, 10 Nov 2009 00:00:00 +0100 3000500 http://www.medworm.com/index.php?rid=2983921&cid=s_37286_60_f&fid=37286&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19903543%26dopt%3DAbstract Authors: Salem M, Kenney PB, Rexroad CE, Yao J Muscle deterioration arises as a physiological response to elevated energetic demands of fish during sexual maturation and spawning. Previously, we used this model to characterize the transcriptomic mechanisms associated with fish muscle degradation and identified potential biological markers of muscle growth and quality. However, transcriptional measurements do not necessarily reflect changes in active mature proteins. Here we report the characterization of proteomic profile in degenerating muscle of rainbow trout in relation to the female reproductive cycle using a LC/MS-based label-free protein quantification method. A total of 146 significantly changed proteins in atrophying muscles (FDR <5%) was identified. Proteins were clustered ... Journal of Proteomics journals http://www.medworm.com/rss/comments.php?id=2983921 Sat, 07 Nov 2009 00:00:00 +0100 2983921 http://www.medworm.com/index.php?rid=2983920&cid=s_37286_60_f&fid=37286&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19903544%26dopt%3DAbstract Authors: Dayon L, Pasquarello C, Hoogland C, Sanchez JC, Scherl A Isobaric tagging, via TMT or iTRAQ, is widely used in quantitative proteomics. To date, tandem mass spectrometric analysis of isobarically-labeled peptides with hybrid ion trap-orbitrap (LTQ-OT) instruments has been mainly carried out with higher-energy C-trap dissociation (HCD) or pulsed q dissociation (PQD). HCD provides good fragmentation of the reporter-ions, but peptide sequence-ion recovery is generally poor compared to collision-induced dissociation (CID). Herein, we describe an approach where CID and HCD spectra are combined. The approach ensures efficiently both identification and relative quantification of proteins. Tandem mass tags (TMTs) were used to label digests of human plasma and LC-MS/MS was performed wi... Journal of Proteomics journals http://www.medworm.com/rss/comments.php?id=2983920 Sat, 07 Nov 2009 00:00:00 +0100 2983920 http://www.medworm.com/index.php?rid=2977782&cid=s_37286_60_f&fid=37286&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19896565%26dopt%3DAbstract Authors: Stadler C, Skogs M, Brismar H, Uhlén M, Lundberg E Immunofluorescence microscopy is a valuable tool for analyzing protein expression and localization at a subcellular level thus providing information regarding protein function, interaction partners and its role in cellular processes. When performing sample fixation, parameters such as difference in accessibility of proteins present in various cellular compartments as well as the chemical composition of the protein to be studied, needs to be taken into account. However, in systematic and proteome-wide efforts, a need exists for standard fixation protocol(s) that works well for the majority of all proteins independent of subcellular localization. Here, we report on a study with the goal to find a standardized protocol based... Journal of Proteomics journals http://www.medworm.com/rss/comments.php?id=2977782 Wed, 04 Nov 2009 00:00:00 +0100 2977782 http://www.medworm.com/index.php?rid=2977781&cid=s_37286_60_f&fid=37286&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19896566%26dopt%3DAbstract We present the coupling of label-free SAX chromatography and IMAC to a data-independent nanoLC-MS/MS (nanoLC-MS(E)) platform for analysis of blood plasma and serum proteins. The methods were evaluated using protein standards added at different concentrations to two groups of samples. The results demonstrate that both techniques enable accurate protein quantitation using low sample volumes and a minimal number of fractions. Combining both methods, 883 unique proteins were identified, of which 423 proteins showed high reproducibility. The two approaches resulted in identification of unique molecular signatures with an overlap of approximately 30%, thus providing complimentary information on sub-proteomes. These methods are potentially useful for systems biology, biomarker discovery, and inve... Journal of Proteomics journals http://www.medworm.com/rss/comments.php?id=2977781 Wed, 04 Nov 2009 00:00:00 +0100 2977781 http://www.medworm.com/index.php?rid=2977780&cid=s_37286_60_f&fid=37286&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19896567%26dopt%3DAbstract Authors: McDonnell LA, van Remoortere A, van Zeijl RJ, Dalebout H, Bladergroen MR, Deelder AM The term molecular histology has been used to convey the potential of imaging mass spectrometry to describe tissue by its constituent peptides and proteins, and to link this with established histological features. The low throughput of imaging mass spectrometry has been one of the factors inhibiting a full investigation of the clinical potential of molecular histology. Here we report the development of an automated set-up, consisting of a controlled environment sample storage chamber, a sample loading robot, and a MALDI-TOF/TOF mass spectrometer, all controlled by single user interface. The automated set up is demonstrated to have the positional stability and experimental reproducibility neces... Journal of Proteomics journals http://www.medworm.com/rss/comments.php?id=2977780 Wed, 04 Nov 2009 00:00:00 +0100 2977780 http://www.medworm.com/index.php?rid=2977784&cid=s_37286_60_f&fid=37286&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19895910%26dopt%3DAbstract Authors: Yang F, Jensen JD, Spliid NH, Svensson B, Jacobsen S, Jørgensen LN, Jørgensen HJ, Collinge DB, Finnie C The effect of nitrogen on Fusarium Head Blight (FHB) in a susceptible barley cultivar was investigated using gel-based proteomics. Barley grown with either 15 or 100kgha(-1)N fertilizer was inoculated with Fusarium graminearum (Fg). The storage protein fraction did not change significantly in response either to N level or Fg, whereas eighty protein spots in the water-soluble albumin fraction increased and 108 spots decreased more than two-fold in intensity in response to Fg. Spots with greater intensity in infected plants contained fungal proteins (9 spots) and proteolytic fragments of plant proteins (65 spots). Identified fungal proteins included two superoxide di... Journal of Proteomics journals http://www.medworm.com/rss/comments.php?id=2977784 Tue, 03 Nov 2009 00:00:00 +0100 2977784 http://www.medworm.com/index.php?rid=2977783&cid=s_37286_60_f&fid=37286&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19895911%26dopt%3DAbstract Authors: Schenkluhn L, Hohnjec N, Niehaus K, Schmitz U, Colditz F Symbiosis- and pathogenesis- related early protein induction patterns in the model legume Medicago truncatula were analysed with two-dimensional differential gel electrophoresis. Two symbiotic soil microorganisms (Glomus intraradices, Sinorhizobium meliloti) were used in single infections and in combination with a secondary pathogenic infection by the oomycete Aphanomyces euteiches. Proteomic analyses performed 6 and 24 hours after inoculations led to identification of 87 differentially induced proteins which likely represent the M. truncatula root 'interactome'. A set of proteins involved in a primary antioxidant defense reaction was detected during all associations investigated. Symbiosis-related protein induction incl... Journal of Proteomics journals http://www.medworm.com/rss/comments.php?id=2977783 Tue, 03 Nov 2009 00:00:00 +0100 2977783 http://www.medworm.com/index.php?rid=2959790&cid=s_37286_60_f&fid=37286&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19879985%26dopt%3DAbstract Authors: Fasoli E, Farinazzo A, Sun CJ, Kravchuk AV, Guerrier L, Fortis F, Boschetti E, Righetti PG When capturing proteins via combinatorial peptide ligand libraries, a method well known for drastically reducing the concentration of high-abundance proteins and substantially magnifying the signal of low-abundance species, thus leading to the discovery of a large number of proteins previously undetected in proteomes, we had constantly noticed that there would be a loss of species initially present in the untreated sample, to the tune of 5%, up to 15% in some cases. Such losses are a nuisance and hamper to some extent the unique performance of the method. In order to verify if such losses could be reduced and also to understand some mechanisms of the capture process, we introduce here an... Journal of Proteomics journals http://www.medworm.com/rss/comments.php?id=2959790 Thu, 29 Oct 2009 00:00:00 +0100 2959790 http://www.medworm.com/index.php?rid=2959791&cid=s_37286_60_f&fid=37286&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19879388%26dopt%3DAbstract Authors: François P, Scherl A, Hochstrasser D, Schrenzel J Staphylococcus aureus is an important human and veterinary pathogen that causes a wide variety of infections ranging from benign skin infections to life threatening diseases. Recently, important changes in the epidemiology have been reported demonstrating that S. aureus, and particularly its methicillin-resistant variant, is now recognized as a ubiquitous pathogen responsible for both, hospital- and community-acquired infections. In these settings, the bacterium is responsible for various acute or chronic diseases and shows particular ability to adapt its metabolism to major environmental changes. Despite the fact that S. aureus infections are common worldwide, the factors triggering the different steps of infection (colon... Journal of Proteomics journals http://www.medworm.com/rss/comments.php?id=2959791 Wed, 28 Oct 2009 00:00:00 +0100 2959791 http://www.medworm.com/index.php?rid=2943951&cid=s_37286_60_f&fid=37286&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19861186%26dopt%3DAbstract Authors: Tissot JD PMID: 19861186 [PubMed - as supplied by publisher] (Source: Journal of Proteomics) Journal of Proteomics journals http://www.medworm.com/rss/comments.php?id=2943951 Sat, 24 Oct 2009 00:00:00 +0100 2943951 http://www.medworm.com/index.php?rid=2935194&cid=s_37286_60_f&fid=37286&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19857612%26dopt%3DAbstract Authors: Mukherjee AK, Carp MJ, Zuchman R, Ziv T, Horwitz BA, Gepstein S We have studied the proteome of the model plant Arabidopsis thaliana infected with a necrotrophic fungal pathogen, Alternaria brassicicola. The Arabidopsis-Alternaria brassicicola host-pathogen pair is being developed as a model genetic system for incompatible plant-fungal interactions, in which the spread of disease is limited by plant defense responses. After confirming that a defense response was induced at the transcriptional level, we identified proteins whose abundance on 2-DE gels increased or decreased in infected leaves. At least 11 protein spots showed reproducible differences in abundance, increasing or decreasing during the progress of the infection. The pathogenesis-related protein PR4, a glycosyl hyd... Journal of Proteomics journals http://www.medworm.com/rss/comments.php?id=2935194 Fri, 23 Oct 2009 00:00:00 +0100 2935194 http://www.medworm.com/index.php?rid=2923920&cid=s_37286_60_f&fid=37286&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19850159%26dopt%3DAbstract In this study, we tried to identify proteins responding to the cellular toxicity in NSAIDs-treated primarily cultured cardiomyocytes using 2-D proteomic analysis. We used seven different NSAIDs (celecoxib, rofecoxib, valdecoxib, diclofenac, naproxen, ibuprofen, meloxicam) possessing each different degree of cardiovascular risk. Overall protein spots were similar in all NSAIDs-treated cells although numbers of decreased proteins were about 2-fold higher in celecoxib or rofecoxib-treated cells than in cells incubated with other NSAIDs. Many stress-related proteins, cardiac muscle movement proteins and proteins involving in membrane organization have been isolated. Among them, Septin-8, a filament scaffolding protein, showed its specific expression pattern depending on the extent of drug toxi... Journal of Proteomics journals http://www.medworm.com/rss/comments.php?id=2923920 Mon, 19 Oct 2009 00:00:00 +0100 2923920 http://www.medworm.com/index.php?rid=2895164&cid=s_37286_60_f&fid=37286&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19822229%26dopt%3DAbstract Authors: Martinez-Esteso MJ, Sellés-Marchart S, Vera-Urbina JC, Pedreño MA, Bru-Martinez R In plant cells, elicitors induce defense responses that resemble those triggered by pathogen attack, such as the synthesis of phytoalexins and pathogen-related proteins which accumulate in the extracellular space. In the search for the particular proteins involved in defense responses, we investigated the changes in the extracellular proteome of a grapevine (Vitis vinifera cv. Gamay) cell suspension in response to elicitation with methylated cyclodextrins (MBCD) and methyl jasmonate (MeJA). Twenty-five of the 39 spots differentially expressed in 2-D gels were identified and found to be encoded by 10 different genes: three secretory peroxidases, chitinase-III, beta-1,3-glucanase, thaumat... Journal of Proteomics journals http://www.medworm.com/rss/comments.php?id=2895164 Thu, 08 Oct 2009 23:00:00 +0100 2895164 http://www.medworm.com/index.php?rid=2887207&cid=s_37286_60_f&fid=37286&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19819358%26dopt%3DAbstract Authors: Thomas DP, Lopez-Ribot JL, Lee SA S. cerevisiae mutants lacking VPS4 missort several vacuolar proteins to the extracellular space, including carboxypeptidase (CPY), vacuolar protease A (PrA), and vacuolar protease B (PrB). In addition, certain soluble secretory proteins, such as invertase and acid phosphatase, are missorted from the pre-vacuolar compartment (PVC) to the general secretory pathway prior to exocytosis. Although little is known about sorting of proteins via the PVC in C. albicans, we have previously demonstrated that the C. albicans vps4 null mutant missorts PrA and CPY extracellularly, but fails to secrete the aspartyl proteases Sap2p and Sap4-6p. To further define the role of C. albicans VPS4 in the trafficking of pre-vacuolar proteins, we have used 2 dimensiona... Journal of Proteomics journals http://www.medworm.com/rss/comments.php?id=2887207 Wed, 07 Oct 2009 23:00:00 +0100 2887207 http://www.medworm.com/index.php?rid=2887206&cid=s_37286_60_f&fid=37286&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19819359%26dopt%3DAbstract Authors: Clifton J, Huang F, Gaso-Sokac D, Brilliant K, Hixson D, Josic D The use of proteomic techniques in the monitoring of different production steps of plasma-derived clotting factor IX (pd F IX) was demonstrated. The first step, solid-phase extraction with a weak anion-exchange resin, fractionates the bulk of human serum albumin (HSA), immunoglobulin G, and other non-binding proteins from F IX. The proteins that strongly bind to the anion-exchange resin are eluted by higher salt concentrations. In the second step, anion-exchange chromatography, residual HSA, some proteases and other contaminating proteins are separated. In the last chromatographic step, affinity chromatography with immobilized heparin, the majority of the residual impurities are removed. However, some contaminati... Journal of Proteomics journals http://www.medworm.com/rss/comments.php?id=2887206 Wed, 07 Oct 2009 23:00:00 +0100 2887206 http://www.medworm.com/index.php?rid=2881473&cid=s_37286_60_f&fid=37286&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19815103%26dopt%3DAbstract In this study, the non-prolamin expression profiles during grain development of two common or bread wheat cultivars (Triticum aestivum L.), Jing 411 and Sunstate, with different quality properties were analyzed using two-dimensional difference gel electrophoresis (2-D DIGE). Five grain developmental stages during the post-anthesis period were sampled corresponding to the cumulative averages of daily temperatures ( degrees Cd: 156 degrees Cd, 250 degrees Cd, 354 degrees Cd, 447 degrees Cd and 749.5 degrees Cd). More than 400 differential protein spots detected at one or more of the developmental stages of the two cultivars were monitored, among which 230 proteins were identified by MS. Of the identified proteins, more than 85% were enzymes possessing different physiological functions. A tot... Journal of Proteomics journals http://www.medworm.com/rss/comments.php?id=2881473 Sun, 04 Oct 2009 23:00:00 +0100 2881473 http://www.medworm.com/index.php?rid=2863083&cid=s_37286_60_f&fid=37286&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19800434%26dopt%3DAbstract Authors: Hess JR, Grazzini G PMID: 19800434 [PubMed - as supplied by publisher] (Source: Journal of Proteomics) Journal of Proteomics journals http://www.medworm.com/rss/comments.php?id=2863083 Tue, 29 Sep 2009 23:00:00 +0100 2863083 http://www.medworm.com/index.php?rid=2858107&cid=s_37286_60_f&fid=37286&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19796715%26dopt%3DAbstract Authors: Koehn H, Clerens S, Deb-Choudhury S, Morton JD, Dyer JM, Plowman JE Keratin-associated proteins (KAPs) are important constituents of the wool cuticle, comprised of the endo-, exocuticle and a-layers, which contribute significantly to the fibre's molecular and mechanical characteristics. Relatively little is known about the distribution of specific KAPs across these layers, and correct protein identification of individual KAPs is difficult due to extensive homology and identity among individual KAPs. We here present evidence that, by specifically exploiting the high-cysteine content of KAPs in the wool cuticle, using 2-nitro-5-thiocyanobenzoic acid (NTCB) cleavage in combination with tryptic digestion, a larger number of KAPs can be identified than with standard trypsin-only di... Journal of Proteomics journals http://www.medworm.com/rss/comments.php?id=2858107 Sun, 27 Sep 2009 23:00:00 +0100 2858107 http://www.medworm.com/index.php?rid=2855898&cid=s_37286_60_f&fid=37286&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19793547%26dopt%3DAbstract Authors: Casado B, Affolter M, Kussmann M Milk has co-evolved with mammals and mankind to nourish their offspring and is a biological fluid of unique complexity and richness. It contains all necessary nutrients for the growth and development of the newborn. Structure and function of biomolecules in milk such as the macronutrients (glyco-) proteins, lipids, and oligosaccharides are central topics in nutritional research. Omics disciplines such as proteomics, glycomics, glycoproteomics, and lipidomics enable comprehensive analysis of these biomolecule components in food science and industry. Mass spectrometry has largely expanded our knowledge on these milk bioactives as it enables identification, quantification and characterization of milk proteins, carbohydrates, and lipids. In this ar... Journal of Proteomics journals http://www.medworm.com/rss/comments.php?id=2855898 Sat, 26 Sep 2009 23:00:00 +0100 2855898 http://www.medworm.com/index.php?rid=2846944&cid=s_37286_60_f&fid=37286&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19782774%26dopt%3DAbstract This study examines alterations in the plasma proteome in ten adults affected by sepsis caused by Acinetobacter baumannii as compared to paired healthy controls. 2-DE profiles of plasma from patients and paired healthy donors, depleted of the six most abundant proteins, were analysed by the DIGE technique. Protein spot detection and quantification were performed with the Differential In-gel Analysis and Biological Variation Analysis modules of the DeCyder(TM) software. Differentially expressed proteins were identified by mass spectrometry (MALDI-TOF/TOF) after colloidal Coomassie blue staining. Almost 900 spots were detected on a unique 2D gel by the DIGE technique. A total of 269 protein spots of differential abundance were shown to be statistically significant (2.5-fold) with p values of... Journal of Proteomics journals http://www.medworm.com/rss/comments.php?id=2846944 Wed, 23 Sep 2009 23:00:00 +0100 2846944 http://www.medworm.com/index.php?rid=2846943&cid=s_37286_60_f&fid=37286&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19782775%26dopt%3DAbstract In this study, a separation and enrichment strategy based on centrifugal ultrafiltration was developed for the LMF (i.e., </=25K) of plasma routinely prepared from normal, healthy volunteers. Four commercially-available filter membranes of similar nominal molecular weight cut-off (NMWC), but differing membrane chemistries and filter orientations (Microcon(R), Millipore; Centrisart(R), Sartorius; Amicon Ultra(R), Millipore; Vivaspin(R), Sartorius), were evaluated. Of these filtration devices, only the Sartorius Vivaspin(R) tangential membrane, NMWC 20K was effective in the non-retention of M(r)>50K, and recovery and enrichment of low-M(r) components from human plasma. This filter membrane device was further optimized with respect to plasma buffer composition, centrifugal force, durati... Journal of Proteomics journals http://www.medworm.com/rss/comments.php?id=2846943 Wed, 23 Sep 2009 23:00:00 +0100 2846943 http://www.medworm.com/index.php?rid=2846942&cid=s_37286_60_f&fid=37286&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19782776%26dopt%3DAbstract Authors: Timperio AM, D'Alessandro A, Pariset L, D'Amici GM, Valentini A, Zolla L The Holstein Friesian and Chianina cattle breeds are representative of extreme selection for milk and meat traits, respectively, with significant changes in metabolism resulting from human selection over the past centuries. In the present study, we wanted to assess whether selection for different purposes has had a measurable effect on liver metabolism through a comparison of the protein and gene expression profiles of the two breeds. We applied 2-DE in order to identify proteins which were differentially expressed in the livers of the two breeds and relate them to different liver functions. We expected to find that only a small number of proteins would be differentially expressed, due to the relatively s... Journal of Proteomics journals http://www.medworm.com/rss/comments.php?id=2846942 Wed, 23 Sep 2009 23:00:00 +0100 2846942 http://www.medworm.com/index.php?rid=2846941&cid=s_37286_60_f&fid=37286&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19782777%26dopt%3DAbstract This study has generated potential protein markers important for apomictic development. PMID: 19782777 [PubMed - as supplied by publisher] (Source: Journal of Proteomics) Journal of Proteomics journals http://www.medworm.com/rss/comments.php?id=2846941 Wed, 23 Sep 2009 23:00:00 +0100 2846941 http://www.medworm.com/index.php?rid=2846940&cid=s_37286_60_f&fid=37286&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19782778%26dopt%3DAbstract Authors: Karpova MA, Moshkovskii SA, Toropygin IY, Archakov AI MALDI-TOF mass-spectrometry has become a popular tool of cancer research during the last decade. High throughput and relative simplicity of this technology have made it attractive for biomarker discovery and validation across various platforms in blood serum/plasma. Many technical approaches have been developed for plasma/serum profiling including protein-chip based SELDI-TOF mass-spectrometry, purification of serum on magnetic beads, analysis of carrier-associated fraction and mass-spectrometric immunoassays. Extensive data about the identity of differential features detected on mass-spectra up to now makes it possible to draw conclusions about potency and perspectives of MALDI-TOF mass-spectrometry in this field. A great ... Journal of Proteomics journals http://www.medworm.com/rss/comments.php?id=2846940 Wed, 23 Sep 2009 23:00:00 +0100 2846940 http://www.medworm.com/index.php?rid=2846945&cid=s_37286_60_f&fid=37286&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19782159%26dopt%3DAbstract Authors: Righetti PG, Boschetti E PMID: 19782159 [PubMed - as supplied by publisher] (Source: Journal of Proteomics) Journal of Proteomics journals http://www.medworm.com/rss/comments.php?id=2846945 Tue, 22 Sep 2009 23:00:00 +0100 2846945 http://www.medworm.com/index.php?rid=2846948&cid=s_37286_60_f&fid=37286&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19781669%26dopt%3DAbstract Authors: Corrales FJ PMID: 19781669 [PubMed - as supplied by publisher] (Source: Journal of Proteomics) Journal of Proteomics journals http://www.medworm.com/rss/comments.php?id=2846948 Mon, 21 Sep 2009 23:00:00 +0100 2846948 http://www.medworm.com/index.php?rid=2846947&cid=s_37286_60_f&fid=37286&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19781670%26dopt%3DAbstract In this study, we describe a path towards the production of an antibody microarray to allow protein profiling of biotinylated human serum samples with reproducible sensitivity in the picomolar range. With the availability of growing numbers of affinity reagents, protein profiles are to be validated in efficient manners and we describe a cross-platform strategy based on data concordance with a suspension bead array to interrogate the identical set of antibodies with the same cohort of serum samples. Comparative analysis enabled to screen for high-performing antibodies, which were displaying consistent results across the two platforms and targeting known serum components. Moreover, data processing methods such as sample referencing and normalization were evaluated for their effects on inter-... Journal of Proteomics journals http://www.medworm.com/rss/comments.php?id=2846947 Mon, 21 Sep 2009 23:00:00 +0100 2846947 http://www.medworm.com/index.php?rid=2846946&cid=s_37286_60_f&fid=37286&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19781671%26dopt%3DAbstract Authors: Zhang X, Ye J, Højrup P In this article we present a simple method to enrich peptides containing in vivo N(alpha)-modified protein N-termini. We demonstrate that CNBr-activated Sepharose, a commercial amine reactive matrix, can selectively couple peptides via the alpha-NH(2) group under mild conditions. Following digestion by trypsin, a simple incubation step with the CNBr-activated Sepharose by which the free alpha-NH(2) containing peptides are coupled with matrix through a covalent bond, allows the separation of N(alpha)-modified peptides from massive free alpha-NH(2) containing peptides. The removal of contaminant peptides with artificial N(alpha)-modifications, like cyclization of N-terminal S-carbamoylmethylcysteine and glutamine, are also discussed. Application of t... Journal of Proteomics journals http://www.medworm.com/rss/comments.php?id=2846946 Mon, 21 Sep 2009 23:00:00 +0100 2846946 http://www.medworm.com/index.php?rid=2834884&cid=s_37286_60_f&fid=37286&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19778645%26dopt%3DAbstract Authors: van Gestel RA, van Solinge WW, van der Toorn HW, Rijksen G, Heck AJ, van Wijk R, Slijper M The erythrocyte membrane plays a pivotal role in erythrocyte functioning. Many membrane protein aberrations are known that result in hemolytic anemia, however, the origin of numerous disorders is not known to date. To extend the current set of diagnostic tools, we used a novel proteome-wide approach to quantitatively analyze membrane proteins of healthy donor and patient erythrocytes. Blue-native PAGE has proven to be a powerful tool for separation of membrane proteins and their complexes, but has hitherto not been applied to erythrocyte membranes to find biomarkers. Using this technique, we detected almost 150 protein spots, from which more than 500 proteins could be identified by LC-MS... Journal of Proteomics journals http://www.medworm.com/rss/comments.php?id=2834884 Sun, 20 Sep 2009 23:00:00 +0100 2834884 http://www.medworm.com/index.php?rid=2834883&cid=s_37286_60_f&fid=37286&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19778646%26dopt%3DAbstract Authors: Byers HL, Campbell J, van Ulsen P, Tommassen J, Ward MA, Schulz-Knappe P, Prinz T, Kuhn K Tandem Mass Tags (TMT) are suited to both global and targeted quantitation approaches of proteins and peptides. Different versions of these tags allow for the generation of both isobaric and isotopic sets of reagents sharing the same common structure. This feature allows for a straightforward transfer of data obtained during discovery studies into targeted investigations. In prior discovery studies, an isobaric set of these reagents was used to identify Neisseria meningitidis proteins expressed under iron-limitation. Here, we apply isotopic versions of those reagents in combination with single reaction monitoring to verify selected candidates found to be differentially regulated in these ... Journal of Proteomics journals http://www.medworm.com/rss/comments.php?id=2834883 Sun, 20 Sep 2009 23:00:00 +0100 2834883 http://www.medworm.com/index.php?rid=2829004&cid=s_37286_60_f&fid=37286&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19775598%26dopt%3DAbstract Authors: Muccilli V, Licciardello C, Fontanini D, Russo MP, Cunsolo V, Saletti R, Recupero GR, Foti S A combination of 2-DE and LC-MSMS approaches was used to identify the differentially expressed proteome of a pigmented sweet orange (Citrus sinensis, cv. Moro) in comparison with a common cultivar (Cadenera) at ripening time. The comparison of the protein patterns of Moro and Cadenera showed 64 differential expressed protein spots. Fifty-five differentially expressed proteins were identified. Proteins were classified according to their putative function and known biosynthetic pathways. Most of the protein related to sugar metabolism were over-expressed in Moro, while those related to stress responses were over-expressed in Cadenera. The abundance of proteins belonging to Unknown/Unname... Journal of Proteomics journals http://www.medworm.com/rss/comments.php?id=2829004 Sat, 19 Sep 2009 23:00:00 +0100 2829004 http://www.medworm.com/index.php?rid=2829003&cid=s_37286_60_f&fid=37286&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19775599%26dopt%3DAbstract Authors: Gomes-Alves P, Neves S, Coelho AV, Penque D To gain insight into the proteins potentially involved in the low temperature-induced F508del-CFTR rescue process, we have explored by two-dimensional electrophoresis (2DE) the proteome of BHK cell lines expressing wt or F508del-CFTR, grown at 37 masculineC or 26 masculineC/24h or 26 masculineC/48h followed by 3h of metabolic labelling with [(35)S]-methionine. A set of 139 protein spots (yielding 125 mass spectrometry identifications) were identified as differentially expressed (p ANOVA <0.05) among the six phenotypic groups analysed. The data analysis suggests that the unfolded protein response (UPR) induction and some cell-metabolism repression are the major cold-shock responses that may generate a favourable cellular environmen... Journal of Proteomics journals http://www.medworm.com/rss/comments.php?id=2829003 Sat, 19 Sep 2009 23:00:00 +0100 2829003 http://www.medworm.com/index.php?rid=2821415&cid=s_37286_60_f&fid=37286&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19766745%26dopt%3DAbstract In conclusion, the use of standardized preanalytical and storage procedures together with an automated peptide purification might minimize potential bias on serum LMW profiling results, thus allowing a better homogeneity and reproducibility in futures proteomics studies. PMID: 19766745 [PubMed - as supplied by publisher] (Source: Journal of Proteomics) Journal of Proteomics journals http://www.medworm.com/rss/comments.php?id=2821415 Wed, 16 Sep 2009 23:00:00 +0100 2821415 http://www.medworm.com/index.php?rid=2810092&cid=s_37286_60_f&fid=37286&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19758581%26dopt%3DAbstract Authors: Pantaleo A, De Franceschi L, Ferru E, Vono R, Turrini F With the advent of proteomic techniques the number of known post translational modifications (PTMs) affecting red cell membrane proteins is rapidly growing but the understanding of their role under physiological and pathological conditions is incompletely established. The wide range of hereditary diseases affecting different red cell membrane functions and the membrane modifications induced by malaria parasite intracellular growth represent an unique opportunity to study PTMs in response of variable cellular stresses. In the present review, some of the major areas of interest in red cell membrane research has been considered modifications of erythrocyte deformability and maintenance of the surface area, membrane transport... Journal of Proteomics journals http://www.medworm.com/rss/comments.php?id=2810092 Sat, 12 Sep 2009 23:00:00 +0100 2810092 http://www.medworm.com/index.php?rid=2810091&cid=s_37286_60_f&fid=37286&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19758582%26dopt%3DAbstract In this study, partitioning by charge and mass using the Microflow MF10 has been applied to CD34(+) haematopoietic stem /progenitor cells and CD4(+)/CD8(+) T-cells to separate proteins restricted by cell number. Less than 10microg total protein per fraction was used for comparative analysis using SDS-PAGE and identification of silver stained bands by LC-MS/MS revealed differentially expressed proteins between the 3 cell populations, which may be involved in cell differentiation. PMID: 19758582 [PubMed - as supplied by publisher] (Source: Journal of Proteomics) Journal of Proteomics journals http://www.medworm.com/rss/comments.php?id=2810091 Sat, 12 Sep 2009 23:00:00 +0100 2810091 http://www.medworm.com/index.php?rid=2804721&cid=s_37286_60_f&fid=37286&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19755177%26dopt%3DAbstract Authors: Zamò A, Cecconi D Lymphoid and haematopoietic neoplasms comprise a broad spectrum of different tumours, classified by the World Health Organization (WHO) on the basis of a combination of morphology, immunophenotypic, genetic and clinical features. Up to date for many of these neoplasms no single feature is regarded as a diagnostic gold standard. The application of proteomics to the study of neoplastic haematological diseases could help in the search for new diagnostic and prognostic markers, as well as in the development of new therapeutic strategies. In this review, we focus on the actual role of proteomics technologies in the study of neoplastic haematology. In particular, we analyze the results obtained in the field of body fluid, cell lines, and tissues proteomics, an... Journal of Proteomics journals http://www.medworm.com/rss/comments.php?id=2804721 Fri, 11 Sep 2009 23:00:00 +0100 2804721 http://www.medworm.com/index.php?rid=2804720&cid=s_37286_60_f&fid=37286&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19755178%26dopt%3DAbstract Authors: Ostroff R, Foreman T, Keeney TR, Statford S, Walker JJ, Zichi D Blood-based protein biomarkers hold great promise to advance medicine with applications that detect and diagnose diseases and aid in their treatment. We are developing such applications with our proteomics technology that combines high-content with low limits of detection. Biomarker discovery relies heavily on archived blood sample collections. Blood is dynamic and changes with different sampling procedures potentially confounding biomarker studies. In order to better understand the effects of sampling procedures on the circulating proteome, we studied three sample collection variables commonly encountered in archived sample sets. These variables included (1) three different sample tube types, PPT plasma, SST seru... Journal of Proteomics journals http://www.medworm.com/rss/comments.php?id=2804720 Fri, 11 Sep 2009 23:00:00 +0100 2804720 http://www.medworm.com/index.php?rid=2775086&cid=s_37286_60_f&fid=37286&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19733703%26dopt%3DAbstract Authors: Shinkawa T, Nagano K, Inomata N, Haramura M We developed a software program (titled Precursor Ion Calibration software for LTQ or, in short, PICsL) that increases the reliability of precursor ion assignations from LC-MS analysis using ultra zoom scanning of LTQ linear ion trap MS and automatically corrects the assignations. Although existing software calculates the theoretical isotopic distribution according to m/z with a computational algorithm, our method simply searches for ions close to the theoretical mass value using both MS/MS raw data and Mascot search result files, followed by a second database search that identifies the proteins using the regenerated peak list files. Our software program mimics the manual inspection of the spectral data of precursor ions and is expec... Journal of Proteomics journals http://www.medworm.com/rss/comments.php?id=2775086 Wed, 02 Sep 2009 23:00:00 +0100 2775086 http://www.medworm.com/index.php?rid=2741951&cid=s_37286_60_f&fid=37286&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19709643%26dopt%3DAbstract The objective of this investigation was to explore and optimize solubilization of membrane proteins for shotgun membrane proteomics of the CD14 human monocytes by examining different systems that rely on: i) an organic solvent (methanol) ii) an acid-labile detergent 3-[3-(1,1-bisalkyloxyethyl)pyridin-1-yl]propane-1-sulfonate) (PPS), iii) a combination of both agents (methanol+PPS). Solubilization efficiency of different buffers was first compared using bacteriorhodopsin as a model membrane protein. Selected approaches were then applied on a membrane subproteome isolated from a highly enriched human monocyte population that was approximately 98% positive for CD14 expression by FACS analysis. A methanol-based buffer yielded 194 proteins of which 93 (48%) were mapped as integral membrane prot... Journal of Proteomics journals http://www.medworm.com/rss/comments.php?id=2741951 Sat, 22 Aug 2009 23:00:00 +0100 2741951 http://www.medworm.com/index.php?rid=2741952&cid=s_37286_60_f&fid=37286&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19706343%26dopt%3DAbstract Authors: Kondo A, Miyamoto T, Yonekawa O, Giessing AM, Osterlund EC, Jensen ON beta2-glycoprotein I (beta2GPI) is a five-domain protein associated with the antiphospholipid syndrome (APS), however, its normal biological function is yet to be defined. beta2GPI is N-glycosylated at several asparagine residues and the glycan moiety conjugated to residue 143 has been proposed to interact with the Gly40-Arg43 motif of beta2GPI. The Gly40-Arg43 motif has also been proposed to serve as the epitope for the anti-beta2GPI autoantibody associated with APS. We hypothesized that the structure or composition of the glycan at Asn-143 might be associated with the APS symptom by shielding or exposing the Gly40-Arg43 motif towards the anti-beta2GPI autoantibody. To test this hypothesis we used mass spec... Journal of Proteomics journals http://www.medworm.com/rss/comments.php?id=2741952 Fri, 21 Aug 2009 23:00:00 +0100 2741952 http://www.medworm.com/index.php?rid=2734915&cid=s_37286_60_f&fid=37286&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19703602%26dopt%3DAbstract Authors: Bowden P, Beavis R, Marshall J A goodness of fit test may be used to assign tandem mass spectra of peptides to amino acid sequences and to directly calculate the expected probability of mis-identification. The product of the peptide expectation values directly yields the probability that the parent protein has been mis identified. A relational database could capture the mass spectral data, the best fit results, and permit subsequent calculations by a general statistical analysis system. Thus the many files of the HuPO blood protein data correlated by X!TANDEM against the proteins of ENSEMBL were collected into a relational database. A redundant set of 247,077 proteins and peptides were correlated by X!TANDEM, and that was collapsed to a set of 34,956 peptides from 13,379 disti... Journal of Proteomics journals http://www.medworm.com/rss/comments.php?id=2734915 Thu, 20 Aug 2009 23:00:00 +0100 2734915 http://www.medworm.com/index.php?rid=2734914&cid=s_37286_60_f&fid=37286&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19703603%26dopt%3DAbstract This study reports a suitable approach to identify secreted proteins in the culture supernatant of L. braziliensis and provides new perspectives for the study of molecules potentially involved in the early stages of infection. PMID: 19703603 [PubMed - as supplied by publisher] (Source: Journal of Proteomics) Journal of Proteomics journals http://www.medworm.com/rss/comments.php?id=2734914 Thu, 20 Aug 2009 23:00:00 +0100 2734914 http://www.medworm.com/index.php?rid=2734913&cid=s_37286_60_f&fid=37286&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19703604%26dopt%3DAbstract Authors: André M, Chambrion C, Charrin S, Soave S, Chaker J, Boucheix C, Rubinstein E, Le Naour F Tetraspanins are integral membrane proteins involved in a variety of physiological and pathological processes. They associate with each other in multimolecular complexes containing numerous membrane proteins. As a first step towards the study of the supramolecular organization of tetraspanin complexes, we have implemented a proteomic approach based on in situ protein cross-linking on living cells followed by affinity purification of tetraspanin complexes. This allowed observing the presence of high molecular weight protein complexes that were characterized as containing CD9P-1/CD315 using LC-MS/MS. Western blot analyses and the use of different tags demonstrated the presence of CD9P-1... Journal of Proteomics journals http://www.medworm.com/rss/comments.php?id=2734913 Thu, 20 Aug 2009 23:00:00 +0100 2734913 http://www.medworm.com/index.php?rid=2712730&cid=s_37286_60_f&fid=37286&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19683081%26dopt%3DAbstract Authors: Schubert P, Devine DV Proteomics has brought new perspectives to the fields of hematology and transfusion medicine in the last decade. The steady improvement of proteomic technology is propelling novel discoveries of molecular mechanisms by studying protein expression, post-translational modifications and protein interactions. This review article focuses on the application of proteomics to the identification of molecular mechanisms leading to the deterioration of blood platelets during storage - a critical aspect in the provision of platelet transfusion products. Several proteomic approaches have been employed to analyse changes in the platelet protein profile during storage and the obtained data now need to be translated into platelet biochemistry in order to connect the resu... Journal of Proteomics journals http://www.medworm.com/rss/comments.php?id=2712730 Tue, 11 Aug 2009 23:00:00 +0100 2712730 http://www.medworm.com/index.php?rid=2712729&cid=s_37286_60_f&fid=37286&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19683082%26dopt%3DAbstract This study was to investigate alterations in cellular and secreted proteins after this differentiation phase. Macrophage was differentiated from U937 human monocytic cell line by treatment with 100ng/ml phorbol myristate acetate (PMA) for 48h. Cellular and secreted proteins extracted from PMA-treated cells (macrophages) were compared with those of untreated cells (monocytes) using 2-DE (n=5 gels/condition; stained with Deep Purple fluorescence dye). Quantitative intensity analysis revealed 81 and 67 protein spots whose levels were significantly altered in cellular proteome and secretome. These proteins were subsequently identified by Q-TOF MS and/or MS/MS analyses. The altered levels of cellular elongation factor-2 (EF-2) and secreted alpha-tubulin were confirmed by Western blot analysis. ... Journal of Proteomics journals http://www.medworm.com/rss/comments.php?id=2712729 Tue, 11 Aug 2009 23:00:00 +0100 2712729 http://www.medworm.com/index.php?rid=2712728&cid=s_37286_60_f&fid=37286&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19683083%26dopt%3DAbstract Authors: Castagna A, Campostrini N, Zaninotto F, Girelli D Hepcidin, a liver peptide hormone, is the central regulator of iron homeostasis. Hepcidin synthesis is modulated by iron stores, so that iron repletion increases its levels to prevent pathological overload, while iron deficiency strongly inhibits hepcidin to allow an increase in iron absorption from duodenal cells. The emerging pivotal role of hepcidin in iron homeostasis, along with its important links with basic pathways like inflammation, make the availability of an accurate hepcidin assay as a potentially powerful investigative tool to improve our understanding as well as our diagnostic/prognostic capabilities in many human diseases. There has been a great interest worldwide in developing a reliable and widely applicable as... Journal of Proteomics journals http://www.medworm.com/rss/comments.php?id=2712728 Tue, 11 Aug 2009 23:00:00 +0100 2712728 http://www.medworm.com/index.php?rid=2696606&cid=s_37286_60_f&fid=37286&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19666151%26dopt%3DAbstract In this study we present a systematic evaluation of sample storage and sampling conditions for clinical proteomics investigations. We have developed and validated a linear MALDI-TOF-MS protein profiling method to explore the low protein molecular weight region (5-20kDa) of serum samples. Data normalization and processing was performed using optimise peak detection routine (LIMPIC) able to describe each group under investigation. Data were acquired either from healthy volunteers and from multiple sclerosis patients in order to highlight ex vivo protein profile alteration related to different physio-pathological conditions. Our data showed critical conditions for serum protein profiles depending on storage times and temperatures : 23 degrees C, 4 degrees C, -20 degrees C and -80 degrees C. W... Journal of Proteomics journals http://www.medworm.com/rss/comments.php?id=2696606 Thu, 06 Aug 2009 23:00:00 +0100 2696606 http://www.medworm.com/index.php?rid=2696607&cid=s_37286_60_f&fid=37286&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19665598%26dopt%3DAbstract Snake venomics and antivenomics of Bothrops atrox venoms from Colombia and the Amazon regions of Brazil, Perú and Ecuador suggest the occurrence of geographic variation of venom phenotype by a trend towards paedomorphism. J Proteomics. 2009 Aug 6; Authors: Núñez V, Cid P, Sanz L, la Torre PD, Angulo Y, Lomonte B, Gutiérrez JM, Calvete JJ The venom proteomes of Bothrops atrox from Colombia, Brazil, Ecuador, and Perú were characterized using venomic and antivenomic strategies. Our results evidence the existence of two geographically differentiated venom phenotypes. The venom from Colombia comprises at least 26 different proteins belonging to 9 different groups of toxins. PI-metalloproteinases and K49-PLA(2) molecules represent the most abundant toxins. On... Journal of Proteomics journals http://www.medworm.com/rss/comments.php?id=2696607 Wed, 05 Aug 2009 23:00:00 +0100 2696607 http://www.medworm.com/index.php?rid=2696609&cid=s_37286_60_f&fid=37286&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19664733%26dopt%3DAbstract Authors: Greening DW, Glenister KM, Sparrow RL, Simpson RJ Human blood transfusion is the process of transferring blood or blood-based products from an individual into the circulatory system of another. From the theory of circulation of blood to the early practice of blood transfusion, transfusion medicine has been an important concept for many centuries. The practicality of transfusion, however, only became a possibility during and shortly after the Second World War. Today, blood and its derivatives play a critical role in worldwide health care systems, with blood components having direct clinical indications. Over the past several years worldwide organizations including the World Health Organization (WHO) have made a number of substantial improvements to the regulation of the worlds ... Journal of Proteomics journals http://www.medworm.com/rss/comments.php?id=2696609 Mon, 03 Aug 2009 23:00:00 +0100 2696609 http://www.medworm.com/index.php?rid=2696608&cid=s_37286_60_f&fid=37286&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19664734%26dopt%3DAbstract Authors: Chaves DF, de Souza EM, Monteiro RA, Pedrosa FD Herbaspirillum seropedicae is an endophytic bacterium that associates with rice, sugarcane and other economically important crops. Secreted proteins play a key role in the plant-bacterial interaction. Using 2D electrophoresis and peptide mass fingerprint mass spectrometry, 63 protein spots representing 41 different secreted proteins were identified during growth of H. seropedicae under nitrogen-sufficient conditions. In silico analysis showed that 25.4% of the proteins had signal peptides and 15.9% were predicted to be non-classically secreted. Among the most abundant were flagellar components and ABC-type transport system proteins. Nine secreted proteins had also been identified in the cellular proteome, suggesting they also pla... Journal of Proteomics journals http://www.medworm.com/rss/comments.php?id=2696608 Mon, 03 Aug 2009 23:00:00 +0100 2696608 http://www.medworm.com/index.php?rid=2682262&cid=s_37286_60_f&fid=37286&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19660581%26dopt%3DAbstract Authors: Bosman GJ, Lasonder E, Groenen-Döpp YA, Willekens FL, Werre JM, Novotný VM During aging in vivo and in vitro, erythrocytes display removal signals. Phagocytosis is triggered by binding of autologous IgG to a senescent cell antigen originating on band 3. Erythrocytes generate vesicles as an integral part of the aging process in vivo and in vitro, i.e. during storage. These vesicles display senescent cell antigens as well as phosphatidylserine, that is recognized by scavenger receptors. Recent comparative proteomic analyses of erythrocytes and their vesicles support the hypothesis that aging is accompanied by increased binding of modified hemoglobins to band 3, disruption of the band 3-mediated anchorage of the cytoskeleton to the lipid bilayer, vesicle formation, and ... Journal of Proteomics journals http://www.medworm.com/rss/comments.php?id=2682262 Sun, 02 Aug 2009 23:00:00 +0100 2682262 http://www.medworm.com/index.php?rid=2674954&cid=s_37286_60_f&fid=37286&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19651253%26dopt%3DAbstract We report identifications of 217 proteins (5773 peptides) with a false discovery rate of 1% or 254 proteins with 95% confidence, respectively. Relative quantification data were obtained for 234 (95% confidence) serum proteins, including species present in the concentration range of tissue leakage factors. The samples described here relate to pancreatic cancer; however the protocol can be applied to serum from other control or disease types. PMID: 19651253 [PubMed - as supplied by publisher] (Source: Journal of Proteomics) Journal of Proteomics journals http://www.medworm.com/rss/comments.php?id=2674954 Thu, 30 Jul 2009 23:00:00 +0100 2674954 http://www.medworm.com/index.php?rid=2674953&cid=s_37286_60_f&fid=37286&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19651254%26dopt%3DAbstract Authors: Novak EM, Lee EK, Innis SM, Keller BO Polyunsaturated fatty acids regulate metabolic pathways, which in early development could have important consequences to adaptation to extra-uterine life and programming of metabolic pathways. Female rats were fed one of two diets identical in all nutrients, except the fat in one diet was high in unsaturated fatty acids (UFA) and the other low UFA, through gestation and lactation. Tow-dimensional sodium dodecylsulfate polyacrylamide gel electrophoresis of protein extracts from 3-day old pup liver resolved over 800 proteins. Employing MALDI-TOF MS and peptide mapping we identified 11 proteins that differed more than three-fold between the groups, 10 up regulated and one down regulated in the high UFA group. The up-regulated proteins include... Journal of Proteomics journals http://www.medworm.com/rss/comments.php?id=2674953 Thu, 30 Jul 2009 23:00:00 +0100 2674953 http://www.medworm.com/index.php?rid=2645687&cid=s_37286_60_f&fid=37286&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19632367%26dopt%3DAbstract Authors: Licker V, Kövari E, Hochstrasser DF, Burkhard PR During the last decades, considerable advances in the understanding of specific mechanisms underlying neurodegeneration in Parkinson's disease have been achieved, yet neither definite etiology nor unifying sequence of molecular events have been formally established. Current unmet needs in Parkinson's disease research include exploring new hypotheses regarding disease susceptibility, occurrence and progression, identifying reliable diagnostic, prognostic and therapeutic biomarkers, and translating basic research into appropriate disease-modifying strategies. The most popular view proposes that Parkinson's disease results from the complex interplay between genetic and environmental factors and mechanisms believed to be at wor... Journal of Proteomics journals http://www.medworm.com/rss/comments.php?id=2645687 Wed, 22 Jul 2009 23:00:00 +0100 2645687 http://www.medworm.com/index.php?rid=2645688&cid=s_37286_60_f&fid=37286&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19631771%26dopt%3DAbstract Authors: Gianazza E, Mainini V, Castoldi G, Chinello C, Zerbini G, Bianchi C, Galbusera C, Stella A, Mauri G, Zoppis I, Magni F, Kienle MG Type 1 diabetes (insulin-dependent diabetes mellitus, IDDM) is an autoimmune disease affecting about 0.12 % of the world's population. Diabetic nephropathy (DN) is a major long-term complication of both types of diabetes and retains an high human, social and economic cost. Thus, the identification of markers for the early detection of DN represents a relevant target of diabetic research. The present work is a pilot study focused on proteomic analysis of serum of controls (n=9), IDDM patients (n=10) and DN patients (n=4) by the ClinProt profiling technology based on mass spectrometry. This approach allowed to identify a pattern of peptides able to di... Journal of Proteomics journals http://www.medworm.com/rss/comments.php?id=2645688 Tue, 21 Jul 2009 23:00:00 +0100 2645688 http://www.medworm.com/index.php?rid=2640001&cid=s_37286_60_f&fid=37286&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19628057%26dopt%3DAbstract In this study, we identified proteins with potential thiol switches involved in jasmonate signaling, which is essential for plant defense. Methyl jasmonate (MeJA) treatment led to enhanced production of hydrogen peroxide in Arabidopsis leaves and roots, indicating in vivo oxidative stress. With monobromobimane (mBBr) labeling to capture oxidized sulfhydryl groups and 2D gel separation, a total of 35 protein spots that displayed significant redox and/or total protein expression changes were isolated. Using LC-MS/MS, the proteins in 33 spots were identified in both control and MeJA treated samples. By comparative analysis of mBBr and SyproRuby gel images, we were able to determine many proteins that were redox responsive and proteins that displayed abundance changes in response to MeJA. Inte... Journal of Proteomics journals http://www.medworm.com/rss/comments.php?id=2640001 Sun, 19 Jul 2009 23:00:00 +0100 2640001 http://www.medworm.com/index.php?rid=2635010&cid=s_37286_60_f&fid=37286&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19622400%26dopt%3DAbstract Authors: Pasini EM, Lutz HU, Mann M, Thomas AW Membrane proteomics offers unprecedented possibilities to compare protein expression in health and disease leading potentially to the identification of markers, of targets for therapeutics and to a better understanding of disease mechanisms. From transfusion medicine to infectious diseases, from cardiovascular affections to diabetes, comparative proteomics has made a contribution to the identification of proteins unique to RBCs of patients with specific illnesses shedding light on possible RBC markers for systemic diseases. In this review we will provide a short overview of some of the main achievements obtained by comparative proteomics in the field of RBC-related local and systemic diseases and suggest some additional areas of RBCs resea... Journal of Proteomics journals http://www.medworm.com/rss/comments.php?id=2635010 Fri, 17 Jul 2009 23:00:00 +0100 2635010 http://www.medworm.com/index.php?rid=2627094&cid=s_37286_60_f&fid=37286&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19619680%26dopt%3DAbstract Authors: Lindermayr C, Durner J During the last two decades nitric oxide (NO) has emerged as a new chemical messenger in plant biology, which is involved in many different physiological processes, such as plant defense, transpiration and gas exchange, seed germination, and root development. Protein S-nitrosylation, the post-translational modification of thiol residues, has been suggested to be the most important mechanism for transduction of the bioactivity of NO. The characterization of protein S-nitrosylation as well as the physiological relevance of this type of modification is essential information, which is necessary to understand the function of NO in plants. In this review we focus on the formation of nitrosothiols and describe the chemistry of NO and thiol groups. Furthermore, ... Journal of Proteomics journals http://www.medworm.com/rss/comments.php?id=2627094 Thu, 16 Jul 2009 23:00:00 +0100 2627094 http://www.medworm.com/index.php?rid=2627093&cid=s_37286_60_f&fid=37286&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19619681%26dopt%3DAbstract Authors: Hortin GL, Sviridov D One of the greatest challenges in analyzing the plasma proteome is the wide range of concentration of different proteins. The current study examines the range of protein concentration for 18 proteins measured over a year in a clinical laboratory to provide data on pathological extremes in protein concentrations. The complete measured range, from upper limits for albumin to lowest values for thyroid-stimulating hormone (TSH), represented more than 10 logs of molar abundance. A number of plasma proteins measured in the clinical laboratory varied over a concentration range spanning more than 4 logs, and limits of detection of clinical assays were inadequate to assess full concentration ranges of several proteins. Considering reported values from studies usin... Journal of Proteomics journals http://www.medworm.com/rss/comments.php?id=2627093 Thu, 16 Jul 2009 23:00:00 +0100 2627093 http://www.medworm.com/index.php?rid=2627092&cid=s_37286_60_f&fid=37286&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19619682%26dopt%3DAbstract Authors: Sghaier-Hammami B, Drira N, Jorrín-Novo JV Two-dimensional gel electrophoresis coupled to mass spectrometry has been used to compare the proteome of date palm (Phoenix dactilyfera L. cv. Deglet Nour) zygotic and somatic embryos. Proteins were trichloroacetic acid-acetone-phenol extracted, quantified, and resolved by 2-DE in the 5 to 8 pH range. Total protein content and number of resolved spots were higher in zygotic (110+/-14.5mg/g DW; 349 spots) than in somatic (70.96+/-4.8mg/g DW; 210 spots) embryos. The 2-DE map of both systems showed qualitative (263) and quantitative (72) differences. Statistical analysis of spot intensity was performed by PCA, obtaining two accurate groupings of the samples and determining the most discriminating spots. Samples were also clustered ... Journal of Proteomics journals http://www.medworm.com/rss/comments.php?id=2627092 Thu, 16 Jul 2009 23:00:00 +0100 2627092 http://www.medworm.com/index.php?rid=2585269&cid=s_37286_60_f&fid=37286&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19580889%26dopt%3DAbstract Authors: Luerman GC, Uriarte SM, Rane MJ, McLeish KR Polymorphonuclear leukocytes or neutrophils are a primary effector cell of the innate immune system and contribute to the development of adaptive immunity. Neutrophils participate in both the initiation and resolution of inflammatory responses through a series of highly coordinated molecular and phenotypic changes. To accomplish these changes, neutrophils express numerous receptors and use multiple overlapping and redundant signal transduction pathways. Dysregulation of the activation or resolution pathways plays a role in a number of human diseases. A comprehensive understanding of the regulation of neutrophil responses can be provided by high throughput proteomic technologies and sophisticated computational analysis. The first step... Journal of Proteomics journals http://www.medworm.com/rss/comments.php?id=2585269 Thu, 02 Jul 2009 23:00:00 +0100 2585269 http://www.medworm.com/index.php?rid=2585268&cid=s_37286_60_f&fid=37286&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19580890%26dopt%3DAbstract Authors: Restuccia U, Boschetti E, Fasoli E, Fortis F, Guerrier L, Bachi A, Kravchuk AV, Righetti PG The pre-treatment of biological extracts with the aim of detecting very low-abundance proteins generates complexity requiring a proper fractionation. Therefore the success of identifying all newly detectable species depends on the selected fractionation methods. In this context and starting from a human serum, where the dynamic concentration range was reduced by means of a preliminary treatment with a combinatorial hexapeptide ligand library, we fractionated the sample using a novel method based on the differences in isoelectric points of proteins by means of Solid-State Buffers (SSB) associated with cation exchangers. The number of fractions was limited to four and was compared to a cl... Journal of Proteomics journals http://www.medworm.com/rss/comments.php?id=2585268 Thu, 02 Jul 2009 23:00:00 +0100 2585268 http://www.medworm.com/index.php?rid=2572149&cid=s_37286_60_f&fid=37286&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19573631%26dopt%3DAbstract Authors: Nair SV, Simonian M, Nell JA, Raftos DA The Sydney rock oyster, Saccostrea glomerata, is susceptible to infection by the protozoan parasite, Marteilia sydneyi, the causative agent of QX disease. M. sydneyi infection peaks during summer when QX disease can cause up to 95% mortality. The current study takes a proteomic approach using 2-dimensional electrophoresis and mass spectrometry to identify markers of QX disease resistance among Sydney rock oysters. Proteome maps were developed for QX disease -resistant and -susceptible oysters. Six proteins in those maps were clearly associated with resistance and so were characterized by mass spectrometry. Two of the proteins (p9 & p11) were homologous to superoxide dismutase-like molecules from the Pacific oyster, Crassostrea gigas,... Journal of Proteomics journals http://www.medworm.com/rss/comments.php?id=2572149 Sun, 28 Jun 2009 23:00:00 +0100 2572149 http://www.medworm.com/index.php?rid=2562596&cid=s_37286_60_f&fid=37286&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19567275%26dopt%3DAbstract Authors: Liumbruno G, D'Alessandro A, Grazzini G, Zolla L Blood-related proteomics is an emerging field, recently gaining momentum. Indeed, a wealth of data is now available and a plethora of groups have contributed to add pieces to the jigsaw puzzle of protein complexity within plasma and blood cells. In this review article we purported to sail across the mare magnum of the actual knowledge in this research endeavour. The main strides in proteomic investigations on red blood cells, platelets, plasma and white blood cells are hereby presented in a chronological order. Moreover, a glance is given at prospective studies which promise to shift the focus of attention from the end product to its provider, the donor, in a sort of Kantian "Copernican revolution". A well-rounded portrait of th... Journal of Proteomics journals http://www.medworm.com/rss/comments.php?id=2562596 Fri, 26 Jun 2009 23:00:00 +0100 2562596 http://www.medworm.com/index.php?rid=2562595&cid=s_37286_60_f&fid=37286&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19567276%26dopt%3DAbstract This study presents an efficient method for future qualitative assessments of proteins from functional isolated mitochondria from small samples of healthy and diseased skeletal muscle. PMID: 19567276 [PubMed - as supplied by publisher] (Source: Journal of Proteomics) Journal of Proteomics journals http://www.medworm.com/rss/comments.php?id=2562595 Fri, 26 Jun 2009 23:00:00 +0100 2562595 http://www.medworm.com/index.php?rid=2556659&cid=s_37286_60_f&fid=37286&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19559108%26dopt%3DAbstract Authors: D'Alessandro A, Liumbruno G, Grazzini G, Pupella S, Lombardini L, Zolla L The first umbilical cord blood (UCB) transplant to a sibling with Fanconi's anemia in 1988 represented a breakthrough in the field of transplantation. Thereon, several transplants have been performed with UCB-derived hematopoietic stem cells (HSCs) and a plethora of studies have investigated the plasticity of UCB-derived stem and progenitor-cells. However, these studies have not been hitherto translated into clinical trials and, although UCB is routinely used as an alternative source of HSCs, no substantial advances have been made in the field of clinical regenerative medicine. The real deal is the lack of knowledge about the molecular processes governing the events of differentiation which transform imm... Journal of Proteomics journals http://www.medworm.com/rss/comments.php?id=2556659 Mon, 22 Jun 2009 23:00:00 +0100 2556659 http://www.medworm.com/index.php?rid=2546213&cid=s_37286_60_f&fid=37286&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19540946%26dopt%3DAbstract Authors: Neupert S, Russell WK, Predel R, Russell DH, Strey OF, Teel PD, Nachman RJ Ticks (Ixodoidea) likely transmit the greatest variety of human and animal pathogens of any arthropod vector. Despite their medical significance little data is available about the messenger molecules in the central nervous system that coordinate all physiological processes in these animals, including behaviour. In our study, we performed the first comprehensive neuropeptidomic analysis of a tick species by using MALDI-TOF mass spectrometry. Specifically we analyzed the neuropeptides in the synganglion of Ixodes scapularis. The forthcoming sequence of the genome of this species will represent the first genomic analysis of a member of the large subphylum Chelicerata. For our approach we used information f... Journal of Proteomics journals http://www.medworm.com/rss/comments.php?id=2546213 Wed, 17 Jun 2009 23:00:00 +0100 2546213 http://www.medworm.com/index.php?rid=2546211&cid=s_37286_60_f&fid=37286&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19540947%26dopt%3DAbstract Authors: Santamaría E, Mora MI, Carro-Roldán E, Molina M, Fernández-Irigoyen J, Marconi P, Manservigi R, Greco A, Epstein AL, Prieto J, Hernández-Alcoceba R, Corrales FJ Recent studies based on animal models have shown the advantages and potential of oncolytic viral therapy using HSV-1 -based replication-competent vectors in the treatment of liver tumors, but little is known about the cellular targets that are modulated during viral infection. In the present work, we have studied the effects of intratumoral injections of HSV-1 Cgal(+) strain in a murine model of human hepatoma xenografts. Viral replication was assessed for more than 1 month, leading to a significant reduction of tumor growth rate mediated, in part, by a cyclin B dependent cell proliferation arrest. ... Journal of Proteomics journals http://www.medworm.com/rss/comments.php?id=2546211 Wed, 17 Jun 2009 23:00:00 +0100 2546211 http://www.medworm.com/index.php?rid=2546210&cid=s_37286_60_f&fid=37286&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19540948%26dopt%3DAbstract Authors: Candiano G, Petretto A, Bruschi M, Santucci L, Dimuccio V, Prunotto M, Gusmano R, Urbani A, Ghiggeri GM In humans, an increased synthesis of reactive oxygen species (ROS) may be a relevant cause of amplification of physiologic processes resulting in inflammatory organ damage or neoplasia. Efficient anti-oxidative systems targeting oxidative stress are thus essential to prevent tissue damage. In plasma, proteins proved to be the first line of defence against ROS and albumin, the highest concentration plasma protein, has a key role in this antioxidant function. Recent studies have clearly documented that albumin oxido-redox potential changes upon oxidation by different oxidants thus becoming a deputy biomarker of this process. ROS react primarily with the free (34)Cysteine ((34)... Journal of Proteomics journals http://www.medworm.com/rss/comments.php?id=2546210 Wed, 17 Jun 2009 23:00:00 +0100 2546210 http://www.medworm.com/index.php?rid=2546209&cid=s_37286_60_f&fid=37286&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19540949%26dopt%3DAbstract Authors: Pasini EM, Lutz HU, Mann M, Thomas AW Membrane proteomics is concerned with accurately and sensitively identifying molecules involved in cell compartmentalisation, including those controlling the interface between the cell and the outside world. The high lipid content of the environment in which these proteins are found often causes a particular set of problems that must be overcome when isolating the required material before effective HPLC-MS approaches can be performed. The membrane is an unusually dynamic cellular structure since it interacts with an ever changing environment. A full understanding of this critical cell component will ultimately require, in addition to proteomics, lipidomics, glycomics, interactomics and study of post-translational modifications. Devoid of n... Journal of Proteomics journals http://www.medworm.com/rss/comments.php?id=2546209 Wed, 17 Jun 2009 23:00:00 +0100 2546209 http://www.medworm.com/index.php?rid=2546214&cid=s_37286_60_f&fid=37286&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19539066%26dopt%3DAbstract Authors: Desmetz C, Cortijo C, Mangé A, Solassol J There is an important need to find relevant biomarkers that show high sensitivity and specificity for early diagnosis and prognosis of cancer. An immune response to cancer is elicited in humans, as demonstrated in part by the identification of autoantibodies against a number of tumor-associated antigens in sera from patients with different types of cancer. Identification of tumor-associated antigens and their cognate autoantibodies is a promising strategy for the discovery of relevant biomarkers. During the past few years, proteomic approaches, including SEREX, SERPA and, more recently, protein microarrays, have been the dominant strategies used to identify tumor-associated antigens and their cognate autoantibodies. In this review... Journal of Proteomics journals http://www.medworm.com/rss/comments.php?id=2546214 Sun, 14 Jun 2009 23:00:00 +0100 2546214 http://www.medworm.com/index.php?rid=2546222&cid=s_37286_60_f&fid=37286&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19527804%26dopt%3DAbstract Authors: Casanovas A, Carrascal M, Abián J, López-Tejero MD, Llobera M Lipoprotein lipase (LPL) plays a pivotal role in lipid metabolism and is implicated in several pathophysiological conditions. A large number of LPL studies have been performed in rat, although the amount of information derived from direct study of the protein in this species is limited. Here we attempted to examine possible modifications of LPL using proteomic tools. By combining high-resolution two-dimensional gel electrophoresis and Western blot with biological mass spectrometry we demonstrate the coexistence of multiple LPL pI isoforms in rat heart. We studied the origin of this pI heterogeneity by: (1) comparison with the 2D pattern of LPL from post-heparin rat plasma (as a source of mature LPL); (2) p... Journal of Proteomics journals http://www.medworm.com/rss/comments.php?id=2546222 Thu, 11 Jun 2009 23:00:00 +0100 2546222 http://www.medworm.com/index.php?rid=2546221&cid=s_37286_60_f&fid=37286&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19527805%26dopt%3DAbstract Authors: Thongboonkerd V Extracorporeal blood purification and peritoneal dialysis are widely used in renal replacement therapy for patients with end-stage renal disease (ESRD) and acute kidney injury (AKI). Additionally, extracorporeal blood purification can be used also for treatment of non-renal disorders to remove endogenous or exogenous toxins from the blood circulation. Efforts have been made to characterize these toxins removed by diffusion (dialysis), convection (ultrafiltration), and/or adsorption (toxins are adsorbed onto the dialysis membrane and are thus removed) using different types of dialysis membrane. This review summarizes important findings obtained from recent proteomic studies applied to extracorporeal blood purification and peritoneal dialysis in settings of ESRD,... Journal of Proteomics journals http://www.medworm.com/rss/comments.php?id=2546221 Thu, 11 Jun 2009 23:00:00 +0100 2546221 http://www.medworm.com/index.php?rid=2546223&cid=s_37286_60_f&fid=37286&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19523545%26dopt%3DAbstract Authors: Stessl M, Marchetti-Deschmann M, Winkler J, Lachmann B, Allmaier G, Noe CR The question of specificity and the elucidation of the exact molecular mechanism of action of post-transcriptional gene silencing agents are two major challenges for their establishment as therapeutics. A proteomic off-target effect study (2-DE with MS) in combination with DIGE comparing the phosphorothioate antisense oligonucleotide oblimersen (Genasense, G3139) to a Bcl-2-targeting siRNA-sequence on human melanoma cells showed that additional off-target effects contribute to the apoptotic effect of oblimersen. When both oligonucleotides were transfected with lipofectamine 2000, only oblimersen increased apoptosis as determined by annexin staining and caspase activity measurement. In contrast to the hi... Journal of Proteomics journals http://www.medworm.com/rss/comments.php?id=2546223 Tue, 09 Jun 2009 23:00:00 +0100 2546223 http://www.medworm.com/index.php?rid=2546227&cid=s_37286_60_f&fid=37286&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19477308%26dopt%3DAbstract Authors: Schittmayer M, Birner-Gruenberger R Lipids are the major energy source of humans. Their digestion, transport, formation, intracellular storage and mobilization are tightly controlled processes to ensure overall energy balance. Here we review discovery and investigation of lipases, which are key players in hydrolysis of lipids, by proteomic means. In particular, we cover the use of activity based probes for functional analysis of these enzymes. The regulation of lipolytic activity is crucial to ensure energy balance and to avoid lipotoxic effects as exerted by products of lipolysis such as free fatty acids. Therefore, transcriptional and post-translational regulation are involved in the equilibrium between lipid storage and mobilization. Moreover, substrate accessibility, which... Journal of Proteomics journals http://www.medworm.com/rss/comments.php?id=2546227 Tue, 26 May 2009 23:00:00 +0100 2546227 http://www.medworm.com/index.php?rid=2546224&cid=s_37286_60_f&fid=37286&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19481188%26dopt%3DAbstract Authors: Mercier C, Truntzer C, Pecqueur D, Gimeno JP, Belz G, Roy P This work is a statistical analysis of reproducibility of a MALDI-TOF mass spectrometry experiment. Its aim is to evaluate measurement variability and compare peak intensities from two types of MALDI-TOF platforms. We compared and commented on the abilities of Principal Component Analysis and mixed-model analysis of variance to evaluate the biological variability and the technical variability of peak intensities in different patients. The properties and hypotheses of both methods are summarized and applied to spectra from plasma of patients with Hodgkin lymphoma. Principal Component Analysis checks rapidly the balance between the two variabilities; however, a mixed-model analysis of variance is necessary to quantify t... Journal of Proteomics journals http://www.medworm.com/rss/comments.php?id=2546224 Tue, 26 May 2009 23:00:00 +0100 2546224 http://www.medworm.com/index.php?rid=2546225&cid=s_37286_60_f&fid=37286&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19477309%26dopt%3DAbstract Authors: Osman KM, Ali MM, Radwan MI, Kim HK, Han J Comparative proteomics analysis of the cytosolic proteins of Salmonella Gallinarum (SG) and Salmonella Enteritidis (SE) isolated from poultry was performed. The constantly detected spots of serovar SG with concomitant absence in SE serovar as well as those markedly over expressed in serovar SE were selected for MALDI-TOF-MS identification. The NCBI-matched proteins that show overregulation were then further confirmed on the mRNA level by quantitative real time PCR. Identified proteins were representing diverse functional activities including energy production, metabolism, and nucleic acid synthesis. Interestingly, some recognized proteins have some relevance to bacterial virulence e.g. Salmonella pathogenicity island 1 effector protei... Journal of Proteomics journals http://www.medworm.com/rss/comments.php?id=2546225 Sun, 24 May 2009 23:00:00 +0100 2546225 http://www.medworm.com/index.php?rid=2546229&cid=s_37286_60_f&fid=37286&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19470414%26dopt%3DAbstract Authors: Bettmer J, Montes Bayón M, Ruiz Encinar J, Fernández Sánchez ML, Fernández de la Campa MD, Sanz Medel A Quantitative proteomics and absolute determination of proteins are topics of fast growing interest, since only the quantity of proteins or changes in their abundance reflect the status and extent of changes of a given biological system. Quantification of the desired proteins has been carried out by molecule specific MS techniques, but relative quantifications are commonplace so far even resorting to stable isotope labelling techniques such as ICAT and SILAC. In the last decade the idea of using element-selective mass spectrometric detection (e.g. ICP-MS instruments) to achieve absolute quantification has been realised and ICP-MS stands now as a new tool i... Journal of Proteomics journals http://www.medworm.com/rss/comments.php?id=2546229 Sat, 23 May 2009 23:00:00 +0100 2546229 http://www.medworm.com/index.php?rid=2546228&cid=s_37286_60_f&fid=37286&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19470415%26dopt%3DAbstract Authors: Quintana M, Palicki O, Lucchi G, Ducoroy P, Chambon C, Salles C, Morzel M In order to document inter-individual variability in salivary protein patterns, unstimulated whole saliva was obtained from 12 subjects at 10 am and 3 pm of the same day. Saliva proteins were separated using two-dimensional gel electrophoresis, and semi-quantified using image analysis. One-way ANOVA was used to test the effects "time of sampling" and "subject". Data were further explored by multivariate analyses (PCA, hierarchical clustering). Spots of interest were identified by mass spectrometry (MALDI-TOF MS/MS and nanoLC ESI-IT MS/MS). A dataset of 509 spots matched in all gels was obtained. There was no diurnal statistical effect on salivary patterns while inter-individual variability was high with ... Journal of Proteomics journals http://www.medworm.com/rss/comments.php?id=2546228 Fri, 22 May 2009 23:00:00 +0100 2546228 http://www.medworm.com/index.php?rid=2546230&cid=s_37286_60_f&fid=37286&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19446051%26dopt%3DAbstract Authors: Schaaij-Visser TB, Brakenhoff RH, Jansen JW, O'Flaherty MC, Smeets SJ, Heck AJ, Slijper M The 5-year-survival rate of head and neck squamous cell carcinoma (HNSCC) has been only moderately improved over the last few decades. HNSCC develops in precursor fields of genetically altered mucosal cells, typically characterized by p53 pathway disruption, that mostly do not give any clinical symptoms. Patients present therefore often with invasive carcinomas in an advanced stage. After tumor resection, part of these fields frequently stays behind unnoticed, causing secondary tumors. Identification of these precursor fields would allow screening and early detection of both primary and secondary tumors. Our aim was to identify differential proteins related to p53 dysfunction. These prote... Journal of Proteomics journals http://www.medworm.com/rss/comments.php?id=2546230 Tue, 12 May 2009 23:00:00 +0100 2546230 http://www.medworm.com/index.php?rid=2546231&cid=s_37286_60_f&fid=37286&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19410666%26dopt%3DAbstract In conclusion, holothurian triterpene glycosides are thought to express their immuno-stimulatory effects by enhancing the natural cellular defense barrier that is necessary to fight pathogens and for which lymphocytes and splenocytes have to be recruited constantly due to limited lifetimes of B-cells and T-cells in the body. PMID: 19410666 [PubMed - as supplied by publisher] (Source: Journal of Proteomics) Journal of Proteomics journals http://www.medworm.com/rss/comments.php?id=2546231 Sat, 02 May 2009 23:00:00 +0100 2546231 http://www.medworm.com/index.php?rid=2546243&cid=s_37286_60_f&fid=37286&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19367682%26dopt%3DAbstract Authors: Robichaud S, Lalu M, Udenberg T, Schulz R, Sawicki R Marked contractile failure of the heart is important in both sepsis and endotoxemia, and an understanding of its molecular basis is lacking. We investigated changes in rat myocardial proteins in endotoxemia. Rats were injected with lipopolysaccharide (LPS) and sacrificed 3, 6, 12 and 24 h later. Control rats were injected with a vehicle and sacrificed 6 h later.In the LPS-6 h and LPS-12 h groups, plasma nitrites (NO(x)(-)), were elevated while mean arterial blood pressure (MAP) was depressed as compared to the controls. In the LPS-24 h group, plasma (NO(x)(-)) was returning to the base level whereas MAP was still decreased in comparison to the control group. Six proteins showed changes between groups. All six proteins were d... Journal of Proteomics journals http://www.medworm.com/rss/comments.php?id=2546243 Fri, 01 May 2009 23:00:00 +0100 2546243 http://www.medworm.com/index.php?rid=2546242&cid=s_37286_60_f&fid=37286&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19367684%26dopt%3DAbstract Authors: Gibson DS, Blelock S, Curry J, Finnegan S, Healy A, Scaife C, McAllister C, Pennington S, Dunn M, Rooney M Synovial fluid is a potential source of novel biomarkers for many arthritic disorders involving joint inflammation, including juvenile idiopathic arthritis. We first compared the distinctive protein 'fingerprints' of local inflammation in synovial fluid with systemic profiles within matched plasma samples. The synovial fluid proteome at the time of joint inflammation was then evaluated across clinical subgroups to identify early disease associated proteins. We measured the synovial fluid and plasma proteomes using the two-dimensional fluorescence difference gel electrophoresis approach. Image analysis software was used to highlight the expression levels of joint and subgr... Journal of Proteomics journals http://www.medworm.com/rss/comments.php?id=2546242 Fri, 01 May 2009 23:00:00 +0100 2546242 http://www.medworm.com/index.php?rid=2546241&cid=s_37286_60_f&fid=37286&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19367685%26dopt%3DAbstract Authors: McDonagh B, Ogueta S, Lasarte G, Padilla CA, Bárcena JA Post-translational redox modification of thiol groups can form the molecular basis of antioxidative protection and redox control. We have implemented a shotgun redox proteomic technique to identify the precise cysteines reversibly oxidised in key proteins. The method was applied to Saccharomyces cerevisiae subjected to peroxide treatment. Enrichment by covalent redox affinity chromatography allowed the isolation of a "redox subpeptidome" that was analysed by LC-MS/MS. Unique peptides containing specific reversibly oxidised cysteines were used to identify over 70 proteins in control and treated samples of which 27 were consistently present in all replicates. In most cases, the redox modification negatively affects the... Journal of Proteomics journals http://www.medworm.com/rss/comments.php?id=2546241 Fri, 01 May 2009 23:00:00 +0100 2546241 http://www.medworm.com/index.php?rid=2546240&cid=s_37286_60_f&fid=37286&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19367687%26dopt%3DAbstract Authors: Petrakis S, Malinowska A, Dadlez M, Sklaviadis T PrP(C), the cellular isoform of prion protein, is widely expressed in most tissues. Despite its involvement in several bioprocesses it still has no apparent physiological role. During propagation of Transmissible Spongiform Encephalopathies, PrP(C) is converted to the pathological isoform, PrP(Sc), in a process believed to be mediated by unknown host factors. PrP(Sc) has altered biochemical properties and forms amyloid aggregates that display infectious characteristics. PrP(Sc) is also the major component in biochemically enriched infectious samples. Other molecules co-purify with it, but the protein content of these aggregates remains unknown. The goal of this project was to identify other host molecules with high affinity for ... Journal of Proteomics journals http://www.medworm.com/rss/comments.php?id=2546240 Fri, 01 May 2009 23:00:00 +0100 2546240 http://www.medworm.com/index.php?rid=2546232&cid=s_37286_60_f&fid=37286&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19393779%26dopt%3DAbstract In this study, comparative and quantitative proteome analyses were performed to identify early changes in lysosomal protein expression/localization from U-937 cells undergoing apoptosis. In 2 independent experiments, among a total of more than 538 proteins putatively identified and quantitated by iTRAQ isobaric labeling and LC-ESI-MS/MS, 18 proteins were found to be upregulated and 9 downregulated in lysosomes purified from early apoptotic compared to control cells. Protein expression was validated by Western blotting on enriched lysosome fractions, and protein localization confirmed by fluorescence confocal microscopy of representative protein candidates, whose functions are associated with lysosomal membrane fluidity and dynamics. These include sterol-4-alpha-carboxylate 3-dehydrogenase ... Journal of Proteomics journals http://www.medworm.com/rss/comments.php?id=2546232 Wed, 22 Apr 2009 23:00:00 +0100 2546232 http://www.medworm.com/index.php?rid=2546234&cid=s_37286_60_f&fid=37286&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19375529%26dopt%3DAbstract Authors: Mertens BJ This paper present a summary and overview of an international competition on the construction of classifiers for mass spectrometry proteomic diagnosis. Design, data and preliminary results from the study are discussed. PMID: 19375529 [PubMed - as supplied by publisher] (Source: Journal of Proteomics) Journal of Proteomics journals http://www.medworm.com/rss/comments.php?id=2546234 Wed, 15 Apr 2009 23:00:00 +0100 2546234 http://www.medworm.com/index.php?rid=2546233&cid=s_37286_60_f&fid=37286&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19375530%26dopt%3DAbstract Authors: Masseroli M, Bachi A, Boschetti E, Righetti PG In analysing the red blood cell cytoplasmic proteome, in search for low abundance proteins, 15 amino acid (AA; Arg, Asn, Asp, Gln, Gly, His, Ile, Lys, Phe, Pro, Ser, Thr, Trp, Tyr, and Val) probes, used individually, captured a total of 787 unique gene products. Of those, 76 were found to be the common catch of all AA probes, 497 were captured by more than one (but not all) probe, and 214 were captured by only one probe. By using the InterPro database, for 151 of the 214 IPIs associated with proteins captured by a single amino acid, we have found 265 annotations of motifs (231 protein domains, 3 binding sites, 3 active sites, 13 conserved sites, and 15 repeats). Among these 151 proteins annotated, there are 75 domains, 2 active si... Journal of Proteomics journals http://www.medworm.com/rss/comments.php?id=2546233 Wed, 15 Apr 2009 23:00:00 +0100 2546233 http://www.medworm.com/index.php?rid=2546239&cid=s_37286_60_f&fid=37286&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19367730%26dopt%3DAbstract Authors: Jorrín-Novo JV, Maldonado AM, Echevarría-Zomeño S, Valledor L, Castillejo MA, Curto M, Valero J, Sghaier B, Donoso G, Redondo I This review is the continuation of three previously published articles [Jorrin JV, Maldonado AM, Castillejo MA. Plant proteome analysis: a 2006 update. Proteomics 2007; 7: 2947-2962; Rossignol M, Peltier JB, Mock HP, Matros A, Maldonado AM, Jorrin JV. Plant proteome analysis: a 2004-2006 update. Proteomics 2006; 6: 5529-5548; Canovas FM, Dumas-Gaudot E, Recorbet G, Jorrin J, Mock HP, Rossignol M. Plant proteome analysis. Proteomics 2004; 4: 285-298] and aims to update the contribution of Proteomics to plant research between 2007 and September 2008 by reviewing most of the papers, which number approximately 250, that appeared in the Plan... Journal of Proteomics journals http://www.medworm.com/rss/comments.php?id=2546239 Sun, 12 Apr 2009 23:00:00 +0100 2546239 http://www.medworm.com/index.php?rid=2546238&cid=s_37286_60_f&fid=37286&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19367732%26dopt%3DAbstract Authors: Balbuena TS, Silveira V, Junqueira M, Dias LL, Santa-Catarina C, Shevchenko A, Floh EI Araucaria angustifolia is the only native conifer of economic importance in the Brazilian Atlantic Rainforest. Due to a clear-cutting form of exploitation this species has received the status of vulnerable. The aim of this work was to investigate and characterize changes in protein expression profile during seed development of this endangered species. For this, the proteome of developing seeds was characterized by 2-DE and LC-MS/MS. Ninety six proteins were confidently identified and classified according to their biological function and expression profile. Overaccumulated proteins in early seed development indicated a higher control on oxidative stress metabolism during this phase. In contra... Journal of Proteomics journals http://www.medworm.com/rss/comments.php?id=2546238 Sun, 12 Apr 2009 23:00:00 +0100 2546238