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Preface.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
PMID: 19914409 [PubMed - as supplied by publisher] (Source: Journal of Proteomics)
Source: Journal of Proteomics - November 12, 2009 Category: Biochemistry Authors: Zolla L Tags: J Proteomics Source Type: journals

Red Cell Storage.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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, ...
Source: Journal of Proteomics - November 12, 2009 Category: Biochemistry Authors: Hess JR Tags: J Proteomics Source Type: journals

A computational platform for MALDI-TOF mass spectrometry data: Application to serum and plasma samples.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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)
Source: Journal of Proteomics - November 12, 2009 Category: Biochemistry Authors: Mantini D, Petrucci F, Pieragostino D, Del Boccio P, Sacchetta P, Candiano G, Ghiggeri GM, Lugaresi A, Federici G, Di Ilio C, Urbani A Tags: J Proteomics Source Type: journals

In Vivo Pharmaco-Proteomic Analysis of Hydroxyurea Induced Changes in the Sickle Red Blood Cell Membrane Proteome.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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 compon...
Source: Journal of Proteomics - November 12, 2009 Category: Biochemistry Authors: Ghatpande SS, Choudhary PK, Quinn CT, Goodman SR Tags: J Proteomics Source Type: journals

Analysis of abscisic acid responsive proteins in Brassica napus guard cells by multiplexed isobaric tagging.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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)
Source: Journal of Proteomics - November 10, 2009 Category: Biochemistry Authors: Zhu M, Simons B, Zhu N, Oppenheimer DG, Chen S Tags: J Proteomics Source Type: journals

Proteomic signature of muscle atrophy in rainbow trout.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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...
Source: Journal of Proteomics - November 7, 2009 Category: Biochemistry Authors: Salem M, Kenney PB, Rexroad CE, Yao J Tags: J Proteomics Source Type: journals

Combining low- and high-energy tandem mass spectra for optimized peptide quantification with isobaric tags.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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 pr...
Source: Journal of Proteomics - November 7, 2009 Category: Biochemistry Authors: Dayon L, Pasquarello C, Hoogland C, Sanchez JC, Scherl A Tags: J Proteomics Source Type: journals

A single fixation protocol for proteome-wide immunofluorescence localization studies.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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...
Source: Journal of Proteomics - November 4, 2009 Category: Biochemistry Authors: Stadler C, Skogs M, Brismar H, Uhlén M, Lundberg E Tags: J Proteomics Source Type: journals

Multidimensional Protein fractionation of Blood Proteins Coupled to Data-Independent nanoLC-MS/MS Analysis.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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 overla...
Source: Journal of Proteomics - November 4, 2009 Category: Biochemistry Authors: Levin Y, Jaros JA, Schwarz E, Bahn S Tags: J Proteomics Source Type: journals

Automated Imaging MS: Toward High Throughput Imaging Mass Spectrometry.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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 demonstr...
Source: Journal of Proteomics - November 4, 2009 Category: Biochemistry Authors: McDonnell LA, van Remoortere A, van Zeijl RJ, Dalebout H, Bladergroen MR, Deelder AM Tags: J Proteomics Source Type: journals

Investigation of the effect of nitrogen on severity of Fusarium head blight in barley.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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). Identi...
Source: Journal of Proteomics - November 3, 2009 Category: Biochemistry Authors: Yang F, Jensen JD, Spliid NH, Svensson B, Jacobsen S, Jørgensen LN, Jørgensen HJ, Collinge DB, Finnie C Tags: J Proteomics Source Type: journals

Differential gel electrophoresis (DIGE) to quantitatively monitor early symbiosis- and pathogenesis- induced changes of the Medicago truncatula root proteome.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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 defe...
Source: Journal of Proteomics - November 3, 2009 Category: Biochemistry Authors: Schenkluhn L, Hohnjec N, Niehaus K, Schmitz U, Colditz F Tags: J Proteomics Source Type: journals

Interaction between proteins and peptide libraries in proteome analysis: pH involvement for a larger capture of species.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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 u...
Source: Journal of Proteomics - October 29, 2009 Category: Biochemistry Authors: Fasoli E, Farinazzo A, Sun CJ, Kravchuk AV, Guerrier L, Fortis F, Boschetti E, Righetti PG Tags: J Proteomics Source Type: journals

Proteomic approaches to study Staphylococcus aureus pathogenesis.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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...
Source: Journal of Proteomics - October 28, 2009 Category: Biochemistry Authors: François P, Scherl A, Hochstrasser D, Schrenzel J Tags: J Proteomics Source Type: journals

Blood proteomics.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
PMID: 19861186 [PubMed - as supplied by publisher] (Source: Journal of Proteomics)
Source: Journal of Proteomics - October 24, 2009 Category: Biochemistry Authors: Tissot JD Tags: J Proteomics Source Type: journals

Proteomics of the response of Arabidopsis thaliana to infection with Alternaria brassicicola.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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 decr...
Source: Journal of Proteomics - October 23, 2009 Category: Biochemistry Authors: Mukherjee AK, Carp MJ, Zuchman R, Ziv T, Horwitz BA, Gepstein S Tags: J Proteomics Source Type: journals

Proteomic analysis in NSAIDs-Treated primary cardiomyocytes.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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 m...
Source: Journal of Proteomics - October 19, 2009 Category: Biochemistry Authors: Baek SM, Ahn JS, Noh HS, Park J, Kang SS, Kim DR Tags: J Proteomics Source Type: journals

Changes of defense proteins in the extracellular proteome of grapevine (Vitis vinifera cv. Gamay) cell cultures in response to elicitors.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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: th...
Source: Journal of Proteomics - October 8, 2009 Category: Biochemistry Authors: Martinez-Esteso MJ, Sellés-Marchart S, Vera-Urbina JC, Pedreño MA, Bru-Martinez R Tags: J Proteomics Source Type: journals

A proteomic analysis of secretory proteins of a pre-vacuolar mutant of Candida albicans.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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...
Source: Journal of Proteomics - October 7, 2009 Category: Biochemistry Authors: Thomas DP, Lopez-Ribot JL, Lee SA Tags: J Proteomics Source Type: journals

Use of proteomics for validation of the isolation process of clotting factor IX from human plasma.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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 imm...
Source: Journal of Proteomics - October 7, 2009 Category: Biochemistry Authors: Clifton J, Huang F, Gaso-Sokac D, Brilliant K, Hixson D, Josic D Tags: J Proteomics Source Type: journals

Wheat quality related differential expressions of albumins and globulins revealed by two-dimensional difference gel electrophoresis (2-D DIGE).Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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 ...
Source: Journal of Proteomics - October 4, 2009 Category: Biochemistry Authors: Gao L, Wang A, Li X, Dong K, Wang K, Appels R, Ma W, Yan Y Tags: J Proteomics Source Type: journals

Blood proteomics and transfusion safety.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
PMID: 19800434 [PubMed - as supplied by publisher] (Source: Journal of Proteomics)
Source: Journal of Proteomics - September 29, 2009 Category: Biochemistry Authors: Hess JR, Grazzini G Tags: J Proteomics Source Type: journals

Higher sequence coverage and improved confidence in the identification of cysteine-rich proteins from the wool cuticle using combined chemical and enzymatic digestion.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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 tr...
Source: Journal of Proteomics - September 27, 2009 Category: Biochemistry Authors: Koehn H, Clerens S, Deb-Choudhury S, Morton JD, Dyer JM, Plowman JE Tags: J Proteomics Source Type: journals

OMICS-rooted studies of milk proteins, oligosaccharides and lipids.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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 bioa...
Source: Journal of Proteomics - September 26, 2009 Category: Biochemistry Authors: Casado B, Affolter M, Kussmann M Tags: J Proteomics Source Type: journals

Differential proteomics of the plasma of individuals with sepsis caused by Acinetobacter baumannii.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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 detect...
Source: Journal of Proteomics - September 23, 2009 Category: Biochemistry Authors: Soares AJ, Santos MF, Trugilho MR, Ferreira AG, Perales J, Domont GB Tags: J Proteomics Source Type: journals

A centrifugal ultrafiltration strategy for isolating the low-molecular weight (Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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 e...
Source: Journal of Proteomics - September 23, 2009 Category: Biochemistry Authors: Greening DW, Simpson RJ Tags: J Proteomics Source Type: journals

Comparative proteomics and transcriptomics analyses of livers from two different Bos taurus breeds: "Chianina and Holstein Friesian"Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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 on...
Source: Journal of Proteomics - September 23, 2009 Category: Biochemistry Authors: Timperio AM, D'Alessandro A, Pariset L, D'Amici GM, Valentini A, Zolla L Tags: J Proteomics Source Type: journals

Proteomic analysis of sugar beet apomictic monosomic addition line M14.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
This study has generated potential protein markers important for apomictic development. PMID: 19782777 [PubMed - as supplied by publisher] (Source: Journal of Proteomics)
Source: Journal of Proteomics - September 23, 2009 Category: Biochemistry Authors: Li H, Cao H, Wang Y, Pang Q, Ma C, Chen S Tags: J Proteomics Source Type: journals

Cancer-specific maldi-tof profiles of blood serum and plasma: Biological meaning and perspectives.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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 possibl...
Source: Journal of Proteomics - September 23, 2009 Category: Biochemistry Authors: Karpova MA, Moshkovskii SA, Toropygin IY, Archakov AI Tags: J Proteomics Source Type: journals

Blood Proteomics and the dynamic range: Some light at the end of the tunnel?Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
PMID: 19782159 [PubMed - as supplied by publisher] (Source: Journal of Proteomics)
Source: Journal of Proteomics - September 22, 2009 Category: Biochemistry Authors: Righetti PG, Boschetti E Tags: J Proteomics Source Type: journals

Proteomics and Human Proteome From bench to bedside.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
PMID: 19781669 [PubMed - as supplied by publisher] (Source: Journal of Proteomics)
Source: Journal of Proteomics - September 21, 2009 Category: Biochemistry Authors: Corrales FJ Tags: J Proteomics Source Type: journals

Validation of serum protein profiles by a dual antibody array approach.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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...
Source: Journal of Proteomics - September 21, 2009 Category: Biochemistry Authors: Rimini R, Schwenk JM, Sundberg M, Sjöberg R, Klevebring D, Gry M, Uhlén M, Nilsson P Tags: J Proteomics Source Type: journals

A proteomics approach to study in vivo protein N(alpha)-modifications.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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 ...
Source: Journal of Proteomics - September 21, 2009 Category: Biochemistry Authors: Zhang X, Ye J, Højrup P Tags: J Proteomics Source Type: journals

Quantitative erythrocyte membrane proteome analysis with Blue-Native/SDS PAGE.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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...
Source: Journal of Proteomics - September 20, 2009 Category: Biochemistry Authors: van Gestel RA, van Solinge WW, van der Toorn HW, Rijksen G, Heck AJ, van Wijk R, Slijper M Tags: J Proteomics Source Type: journals

Candidate verification of iron-regulated Neisseria meningitidis proteins using isotopic versions of tandem mass tags (TMT) and single reaction monitoring.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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 ve...
Source: Journal of Proteomics - September 20, 2009 Category: Biochemistry Authors: Byers HL, Campbell J, van Ulsen P, Tommassen J, Ward MA, Schulz-Knappe P, Prinz T, Kuhn K Tags: J Proteomics Source Type: journals

Proteome analysis of Citrus sinensis L. (Osbeck) flesh at ripening time.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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-expresse...
Source: Journal of Proteomics - September 19, 2009 Category: Biochemistry Authors: Muccilli V, Licciardello C, Fontanini D, Russo MP, Cunsolo V, Saletti R, Recupero GR, Foti S Tags: J Proteomics Source Type: journals

Low temperature restoring effect on F508del-CFTR misprocessing: A proteomic approach.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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 ...
Source: Journal of Proteomics - September 19, 2009 Category: Biochemistry Authors: Gomes-Alves P, Neves S, Coelho AV, Penque D Tags: J Proteomics Source Type: journals

Pre-analytical operating procedures for serum low molecular weight protein profiling.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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)
Source: Journal of Proteomics - September 16, 2009 Category: Biochemistry Authors: Di Girolamo F, Alessandroni J, Somma P, Guadagni F Tags: J Proteomics Source Type: journals

Current knowledge about the functional roles of phosphorylative changes of membrane proteins in normal and diseased red cells.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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 cons...
Source: Journal of Proteomics - September 12, 2009 Category: Biochemistry Authors: Pantaleo A, De Franceschi L, Ferru E, Vono R, Turrini F Tags: J Proteomics Source Type: journals

Mass and charge selective protein fractionation for the differential analysis of T-cell and CD34(+) stem cell proteins from cord blood.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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)
Source: Journal of Proteomics - September 12, 2009 Category: Biochemistry Authors: Ly L, Wasinger VC Tags: J Proteomics Source Type: journals

Proteomic analysis of lymphoid and haematopoietic neoplasms: There's more than biomarker discovery.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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...
Source: Journal of Proteomics - September 11, 2009 Category: Biochemistry Authors: Zamò A, Cecconi D Tags: J Proteomics Source Type: journals

The stability of the circulating human proteome to variations in sample collection and handling procedures measured with an aptamer-based proteomics array.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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 ...
Source: Journal of Proteomics - September 11, 2009 Category: Biochemistry Authors: Ostroff R, Foreman T, Keeney TR, Statford S, Walker JJ, Zichi D Tags: J Proteomics Source Type: journals

A software program for more reliable precursor ion assignation from LC-MS analysis using LTQ ultra zoom scan.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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 p...
Source: Journal of Proteomics - September 2, 2009 Category: Biochemistry Authors: Shinkawa T, Nagano K, Inomata N, Haramura M Tags: J Proteomics Source Type: journals

Optimization of protein solubilization for the analysis of the CD14 human monocyte membrane proteome using LC-MS/MS.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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...
Source: Journal of Proteomics - August 22, 2009 Category: Biochemistry Authors: Ye X, Johann DJ, Hakami RM, Xiao Z, Meng Z, Ulrich RG, Issaq HJ, Veenstra TD, Blonder J Tags: J Proteomics Source Type: journals

Glycopeptide profiling of beta-2-glycoprotein I by mass spectrometry reveals attenuated sialylation in patients with antiphospholipid syndrome.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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-Ar...
Source: Journal of Proteomics - August 21, 2009 Category: Biochemistry Authors: Kondo A, Miyamoto T, Yonekawa O, Giessing AM, Osterlund EC, Jensen ON Tags: J Proteomics Source Type: journals

Tandem mass spectrometry of human tryptic blood peptides calculated by a statistical algorithm and captured by a relational database with exploration by a general statistics analysis system.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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 ...
Source: Journal of Proteomics - August 20, 2009 Category: Biochemistry Authors: Bowden P, Beavis R, Marshall J Tags: J Proteomics Source Type: journals

Proteomic characterization of the released/secreted proteins of Leishmania (Viannia) braziliensis promastigotes.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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)
Source: Journal of Proteomics - August 20, 2009 Category: Biochemistry Authors: Cuervo P, De Jesus JB, Saboia-Vahia L, Mendonça-Lima L, Domont GB, Cupolillo E Tags: J Proteomics Source Type: journals

In situ chemical cross-linking on living cells reveals CD9P-1 cis-oligomer at cell surface.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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 analyse...
Source: Journal of Proteomics - August 20, 2009 Category: Biochemistry Authors: André M, Chambrion C, Charrin S, Soave S, Chaker J, Boucheix C, Rubinstein E, Le Naour F Tags: J Proteomics Source Type: journals

Proteomics meets blood banking: Identification of protein targets for the improvement of platelet quality.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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 plat...
Source: Journal of Proteomics - August 11, 2009 Category: Biochemistry Authors: Schubert P, Devine DV Tags: J Proteomics Source Type: journals

Alterations in cellular proteome and secretome upon differentiation from monocyte to macrophage by treatment with phorbol myristate acetate: Insights into biological processes.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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 id...
Source: Journal of Proteomics - August 11, 2009 Category: Biochemistry Authors: Sintiprungrat K, Singhto N, Sinchaikul S, Chen ST, Thongboonkerd V Tags: J Proteomics Source Type: journals