Molecular and Cellular Proteomics : MCPThis is an RSS file. You can use it to subscribe to this data in your favourite RSS reader, such as GoogleReader, or to display this data on your own website or blog. Subscribe to this data using MyMedWorm.Subscribe to this data using GoogleReader.Subscribe to this data using Bloglines.Subscribe to this data using MyYahoo.

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343 records returned

Application of proteomic marker ensembles to subcellular organelle identification.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Compartmentalization of biological processes and the associated cellular components is crucial for cell function. Typically, the location of a component is revealed through a co-localization and/or co-purification with an organelle marker. Therefore, the identification of reliable markers is critical for a thorough understanding of cellular function and dysfunction. We fractionated macrophage-like RAW264.7 cells, both in the resting and in the endotoxin-activated state, into six fractions representing the major organelles/ compartments: nuclei, mitochondria, cytoplasm, endoplasmic reticulum and plasma membrane, as well...
Source: Molecular and Cellular Proteomics : MCP - November 2, 2009 Category: Molecular Biology Authors: Andreyev AY, Shen Z, Guan Z, Ryan A, Fahy E, Subramaniam S, Raetz CR, Briggs S, Dennis EA Tags: Mol Cell Proteomics Source Type: journals

Proteomic-based refinement of Deinococcus deserti genome annotation reveals an unwonted use of non-canonical translation initiation codons.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Deinococcaceae are a family of extremely radiation tolerant bacteria that are currently subjected to numerous studies aimed at understanding the molecular mechanisms for such radiotolerance. To achieve a comprehensive and accurate annotation of the Deinococcus deserti genome, we performed an N-terminal-oriented characterization of its proteome. For this, we used a labeling reagent, N-Tris(2,4,6-trimethoxyphenyl)phosphonium acetyl succinimide (TMPP), to selectively derivatize protein N-termini. The large scale identification of TMPP-modified N-terminal-most peptides by shotgun liquid chromatography-tandem mass spectrome...
Source: Molecular and Cellular Proteomics : MCP - October 29, 2009 Category: Molecular Biology Authors: Baudet M, Ortet P, Gaillard JC, Fernandez B, Guérin P, Enjalbal C, Subra G, de Groot A, Barakat M, Dedieu A, Armengaud J Tags: Mol Cell Proteomics Source Type: journals

A proteomic investigation of ligand-dependent HSP90 complexes reveals CHORDC1 as a novel ADP-dependent HSP90 interacting protein.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Structural studies of the chaperone HSP90 have revealed that nucleotide and drug ligands induce several distinct conformational states; however, little is known how these conformations affect interactions with co-chaperones and client proteins. Here we use TAP purification and LC-MS/MS to investigate the proteome-wide effects of ATP, ADP and geldanamycin on the constituents of the human HSP90 interactome. We identified 52 known and novel components of HSP90 complexes that are regulated by these ligands including several co-chaperones. Interestingly, our results also show that geldanamycin treatment causes HSP90 complex...
Source: Molecular and Cellular Proteomics : MCP - October 28, 2009 Category: Molecular Biology Authors: Gano JJ, Simon JA Tags: Mol Cell Proteomics Source Type: journals

High content screening for inhibitors of protein interactions and post-translational modifications in primary cells by proximity ligation.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
The cost of developing new drugs is a major obstacle for pharmaceutical companies and academia, with many drugs identified in the drug discovery process failing approval for clinical use due to lack of intended effect or because of severe side effects. Since the early 1990s, high-throughput screening of drug compounds has increased enormously in capacity but has not resulted in a higher success rate of the identified drugs. Thus, there is a need for methods that can identify biologically relevant compounds and more accurately predict in vivo effects early in the drug discovery process. To address this, we developed a p...
Source: Molecular and Cellular Proteomics : MCP - October 27, 2009 Category: Molecular Biology Authors: Leuchowius KJ, Jarvius M, Wickström M, Rickardson L, Landegren U, Larsson R, Söderberg O, Fryknäs M, Jarvius J Tags: Mol Cell Proteomics Source Type: journals

A CPTAC inter-laboratory study characterizing a yeast performance standard for benchmarking LC-MS Platform performance.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
In this study, we describe a standard operating protocol for large-scale production of the yeast performance standard, and offer aliquots to the community through the National Institute of Standards and Technology, where the yeast proteome is under development as a certified reference material to meet the long-term needs of the community. Using a series of metrics that characterize LC-MS performance, we provide a reference dataset demonstrating typical performance of commonly used ion trap instrument platforms in expert laboratories; the results provide a basis for laboratories to benchmark their own performance, to improv...
Source: Molecular and Cellular Proteomics : MCP - October 26, 2009 Category: Molecular Biology Authors: Paulovich AG, Billheimer D, Ham AJ, Vega-Montoto LJ, Rudnick PA, Tabb DL, Wang P, Blackman RK, Bunk DM, Cardasis HL, Clauser KR, Kinsinger CR, Schilling B, Tegeler TJ, Variyath AM, Wang M, Whiteaker JR, Zimmerman LJ, Fenyo D, Carr SA, Fisher SJ, Gibson BW Tags: Mol Cell Proteomics Source Type: journals

An automated and multiplexed method for high throughput peptide immunoaffinity enrichment and multiple reaction monitoring mass spectrometry-based quantification of protein biomarkers.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
There is an urgent need for quantitative assays in verifying and validating the large numbers of protein biomarker candidates produced in modern "-omics" experiments. SISCAPA (Stable Isotope Standards with Capture by Anti-Peptide Antibodies) has shown tremendous potential to meet this need by combining peptide immunoaffinity enrichment with quantitative mass spectrometry. In this paper, we describe three significant advances to the SISCAPA technique. First, we develop a method for an automated magnetic bead-based platform capable of high throughput processing. Second, we implement the automated method in a multiplexed ...
Source: Molecular and Cellular Proteomics : MCP - October 19, 2009 Category: Molecular Biology Authors: Whiteaker JR, Zhao L, Anderson L, Paulovich AG Tags: Mol Cell Proteomics Source Type: journals

Proteomic analysis reveals overlapping functions of clustered protocadherins.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
The three tandem-arrayed protocadherin (Pcdh) gene clusters, namely Pcdh-a, Pcdh-ss and Pcdh-, play important roles in the development of the vertebrate central nervous system. To gain insight into the molecular action of Pcdhs, we performed a systematic proteomic analysis of Pcdh--associated protein complexes. We identified a list of 154 non-redundant proteins in the Pcdh- complexes. This list includes nearly 30 members of clustered Pcdh -a, -ss and - families as core components of the complexes and additional over 120 putative Pcdh associated proteins. We validated a selected subset of Pcdh--associated proteins using...
Source: Molecular and Cellular Proteomics : MCP - October 19, 2009 Category: Molecular Biology Authors: Han MH, Lin C, Meng S, Wang X Tags: Mol Cell Proteomics Source Type: journals

Performance metrics for liquid chromatography-tandem mass spectrometry systems in proteomic analyses and evaluation by the CPTAC network.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Wang P, Whiteaker JR, Zimmerman LJ, Carr SA, Fisher SJ, Gibson BW, Paulovich AG, Regnier FE, Rodriguez H A major unmet need in liquid chromatography-tandem mass spectrometry (LC-MS/MS)-based proteomic analyses is a set of tools for quantitative assessment of system performance and evaluation of technical variability. Here we describe 46 system performance metrics for monitoring chromatographic performance, electrospray source stability, MS1 and MS2 signals, dynamic sampling of ions for MS/MS and peptide identification. Applied to datasets from replicate LC-MS/MS analyses, these metrics display consistent, reasonable r...
Source: Molecular and Cellular Proteomics : MCP - October 15, 2009 Category: Molecular Biology Authors: Rudnick PA, Clauser KR, Kilpatrick LE, Tchekhovskoi DV, Neta P, Blonder N, Billheimer DD, Blackman RK, Bunk DM, Cardasis HL, Ham AJ, Jaffe JD, Kinsinger CR, Mesri M, Neubert TA, Schilling B, Tabb DL, Tegeler TJ, Vega-Montoto L, Mulayath Variyath A, Wang M Tags: Mol Cell Proteomics Source Type: journals

Proteomic analysis of A33-immunoaffinity-purified exosomes released from the human colon tumor cell line LIM1215 reveals a tissue-specific protein signature.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Exosomes are 40-100 nm diameter nanovesicles of endocytic origin that are released from diverse cell types. To better understand the biological role of exosomes and to avoid confounding data arising from proteinaceous contaminants, it is important to work with highly-purified material. Here, we describe an immunoaffinity-capture method using the colon epithelial cell specific A33 antibody to purify colorectal cancer cell (LIM1215) -derived exosomes. LC-MS/MS revealed 394 unique exosomal proteins of which 112 proteins (28%) contained signal peptides and a significant enrichment of proteins containing coiled-coil, RAS an...
Source: Molecular and Cellular Proteomics : MCP - October 15, 2009 Category: Molecular Biology Authors: Mathivanan S, Lim JW, Tauro BJ, Ji H, Moritz RL, Simpson RJ Tags: Mol Cell Proteomics Source Type: journals

A dual pressure linear ion trap - Orbitrap instrument with very high sequencing speed.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Since its introduction a few years ago, the linear ion trap-Orbitrap (LTQ Orbitrap) instrument has become a powerful tool in proteomics research. For high resolution MS measurements ions are accumulated in the linear ion trap and passed on to the Orbitrap analyzer. Simultaneously with acquisition of this signal, the major peaks are isolated in turn, fragmented and recorded at high sensitivity in the linear ion trap, combining the strengths of both mass analyzer technologies. Here we describe a next generation LTQ Orbitrap system termed Velos, with significantly increased sensitivity and scan speed. This is achieved by ...
Source: Molecular and Cellular Proteomics : MCP - October 13, 2009 Category: Molecular Biology Authors: Olsen JV, Schwartz JC, Griep-Raming J, Nielsen ML, Damoc E, Denisov E, Lange O, Remes P, Taylor D, Splendore M, Wouters ER, Senko M, Makarov A, Mann M, Horning S Tags: Mol Cell Proteomics Source Type: journals

Proteomic analysis of the nucleolus in adenovirus-infected cells.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Adenoviruses replicate primarily in the host cell nucleus and it is well established that adenovirus infection affects the structure and function of host cell nucleoli in addition to coding for a number of nucleolar targeted viral proteins. Here we have used unbiased proteomic methods, including high throughput mass spectrometry coupled with Stable Isotope Labeling of Amino acids in Cell culture (SILAC) and traditional two dimensional (2-D) gel electrophoresis to identify quantitative changes in the protein composition of the nucleolus during adenovirus infection. 2-D gel analysis revealed changes in six proteins. By c...
Source: Molecular and Cellular Proteomics : MCP - October 6, 2009 Category: Molecular Biology Authors: Lam YW, Evans VC, Heesom KJ, Lamond AI, Matthews DA Tags: Mol Cell Proteomics Source Type: journals

The mycobacterium bovis BCG phagosome proteome.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Mycobacterium tuberculosis and Mycobacterium bovis BCG alter the maturation of their phagosomes and reside within a compartment that resists acidification and fusion with lysosomes. To define the molecular composition of this compartment, we developed a novel method for obtaining highly purified phagosomes from BCG infected human macrophages and analyzed the phagosomes by Western immunoblotting and mass spectrometry-based proteomics. Our purification procedure revealed that BCG grown on artificial medium become less dense after growth in macrophages. By Western immunoblotting, LAMP-2, Niemann Pick protein C1, and synta...
Source: Molecular and Cellular Proteomics : MCP - October 6, 2009 Category: Molecular Biology Authors: Lee BY, Jethwaney D, Schilling B, Clemens DL, Gibson BW, Horwitz MA Tags: Mol Cell Proteomics Source Type: journals

Finding Chimeras: A bioinformatic strategy for identification of cross-linked peptides.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Chemical cross-linking, followed by identification of the cross-linked residues, is a powerful approach to probe the topologies and interacting surfaces of protein assemblies. In this work, we demonstrate a new bioinformatic approach using multiple program modules within the software package 'Protein Prospector' that greatly facilitates the discovery of cross-linked peptides in chemical cross-linking studies. Examples are given for how this approach has been used for defining interfaces in heterodimeric and homodimeric protein complexes, both of which provide results in close agreement with crystal structures, verifyin...
Source: Molecular and Cellular Proteomics : MCP - October 5, 2009 Category: Molecular Biology Authors: Chu F, Baker PR, Burlingame AL, Chalkley RJ Tags: Mol Cell Proteomics Source Type: journals

Quantitative nano-proteomics for protein complexes (QNanoPX) related to estrogen transcriptional action.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
We developed an integrated proteomics approach using a chemically functionalized gold nanoparticle (AuNP) as a novel probe for affinity purification in order to analyze a large protein complex in vivo. We then applied this approach to globally map the transcriptional activation complex of the estrogen response element (ERE). This approach was designated as Quantitative Nano-Proteomics for Protein complexes (QNanoPX). In this approach, the positive AuNP-ERE probes were functionalized with polyethylene glycol (PEG) and the consensus sequence of ERE and negative AuNP-PEG probes were functionalized with PEG without the ERE...
Source: Molecular and Cellular Proteomics : MCP - October 4, 2009 Category: Molecular Biology Authors: Cheng PC, Chang HK, Chen SH Tags: Mol Cell Proteomics Source Type: journals

Proteome-scale characterization of human s-acylated proteins in lipid raft-enriched and non-raft membranes.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Protein S-acylation (palmitoylation), a reversible post-translational modification, is critically involved in regulating protein subcellular localization, activity, stability, and multimeric complex assembly. However, proteome-scale characterization of S-acylation has lagged far behind that of phosphorylation, and global analysis of the localization of S-acylated proteins within different membrane domains has not been reported. Here we describe a novel proteomic approach, designated Palmitoyl Protein Identification and Site Characterization (PalmPISC), for proteome-scale enrichment and characterization of S-acylated pr...
Source: Molecular and Cellular Proteomics : MCP - October 1, 2009 Category: Molecular Biology Authors: Yang W, Di Vizio D, Kirchner M, Steen H, Freeman MR Tags: Mol Cell Proteomics Source Type: journals

Binding partner switching on microtubules and aurora-B in the mitosis to cytokinesis transition.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
The cytoskeleton globally reorganizes between mitosis (M-phase) and cytokinesis (C-phase), which presumably requires extensive regulatory changes. To reveal these, we undertook a comparative proteomic analysis of cells tightly drug-synchronized in each phase. We identified 25 proteins that bind selectively to microtubules in C-phase, and identified several novel binding partners including NUSAP. C-phase selective microtubule binding of many of these proteins depended on activity of Aurora kinases, as assayed by treatment with the drug VX680. Aurora-B binding partners switched dramatically between M-phase to C-phase, an...
Source: Molecular and Cellular Proteomics : MCP - September 27, 2009 Category: Molecular Biology Authors: Ozlu N, Monigatti F, Renard BY, Field CM, Steen H, Mitchison TJ, Steen JJ Tags: Mol Cell Proteomics Source Type: journals

Cks proteins protect mitochondrial genome integrity by interacting with mitochondrial single-stranded DNA binding protein.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Cks (cyclin-dependent kinase subunit) proteins interact with cyclin-dependent kinases (Cdks) with high affinity. Mammalian Cks1 and Cks2 bind Cdk1 and Cdk2 and partake in the control of cell cycle progression. We identified Cks-interacting proteins by affinity purification followed by mass spectrometry in the human lymphocytic cell line, Ramos. Apart from known interactors, such as Cdks, we identified a novel Cdk-dependent interaction between Cks proteins and the mitochondrial single-stranded DNA-binding protein (mtSSB). mtSSB binds both Cks1 and Cks2 and undergoes Cdk-dependent phosphorylation. mtSSB is known to parti...
Source: Molecular and Cellular Proteomics : MCP - September 27, 2009 Category: Molecular Biology Authors: Radulovic M, Crane E, Crawford M, Godovac Zimmermann J, Yu VP Tags: Mol Cell Proteomics Source Type: journals

Bladder cancer associated protein: a potential prognostic biomarker in human bladder cancer.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
It is becoming increasingly clear that no single marker will have the sensitivity and specificity necessary to be used on its own for diagnosis/prognosis of tumors. Inter-patient and intra-tumor heterogeneity provide overwhelming odds against the existence of such an ideal marker. With this in mind our laboratory has been applying a long-term systematic approach to identify multiple biomarkers that can be used for clinical purposes. As a result of these studies, we have identified and reported several candidate biomarker proteins that are deregulated in bladder cancer. Following the conceptual biomarker development pha...
Source: Molecular and Cellular Proteomics : MCP - September 24, 2009 Category: Molecular Biology Authors: Moreira JM, Ohlsson G, Gromov P, Simon R, Sauter G, Celis JE, Gromova I Tags: Mol Cell Proteomics Source Type: journals

Identification of five candidate lung cancer biomarkers by proteomic analysis of conditioned media of four lung cancer cell lines.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Detection of lung cancer at an early stage is necessary for successful therapy and improved survival rates. We performed a bottom-up proteomic analysis employing a two-dimensional LC-MS/MS strategy on the conditioned media (CM) of 4 lung cancer cell lines of different histological backgrounds [non-small cell lung cancer: H23 (adenocarcinoma), H520 (squamous cell carcinoma), H460 (large cell carcinoma) and small cell lung cancer (H1688)] to identify secreted or membrane-bound proteins that could be useful as novel lung cancer biomarkers. Proteomic analysis of the four CM allowed identification of 1,830 different protein...
Source: Molecular and Cellular Proteomics : MCP - September 22, 2009 Category: Molecular Biology Authors: Planque C, Kulasingan V, Smith CR, Reckamp K, Goodglick L, Diamandis EP Tags: Mol Cell Proteomics Source Type: journals

In depth qualitative and quantitative profiling of tyrosine phosphorylation using a combination of phosphopeptide immuno-affinity purification and stable isotope dimethyl labeling.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Several mass spectrometry based assays have emerged for the quantitative profiling of cellular tyrosine phosphorylation. Ideally, these methods should reveal the exact sites of tyrosine phosphorylation, be quantitative and not cost-prohibitive. The latter is often an issue as typically several milligrams of (stable isotope labeled) starting protein material is required to enable the detection of low abundant phosphotyrosine peptides. Here, we adopted and refined a peptide centric immuno-affinity purification approach for the quantitative analysis of tyrosine phosphorylation by combining it with a cost-effective stable ...
Source: Molecular and Cellular Proteomics : MCP - September 20, 2009 Category: Molecular Biology Authors: Boersema PJ, Foong LY, Ding VM, Lemeer S, van Breukelen B, Philp R, Boekhorst J, Snel B, den Hertog J, Choo AB, Heck AJ Tags: Mol Cell Proteomics Source Type: journals

Unbiased quantitation of Escherichia coli membrane proteome using phase-transfer surfactants.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
We developed a sample preparation protocol for rapid and unbiased analysis of the membrane proteome using an alimentary canal-mimicking system in which proteases are activated in the presence of bile salts. In this rapid and unbiased protocol, immobilized trypsin is used in the presence of deoxycholate and lauroylsarcocine to increase digestion efficiency, as well as to increase the solubility of the membrane proteins. Using 22.5 microgram of E. coli whole cell lysate, we quantitatively demonstrated that membrane proteins were extracted and digested at the same level as soluble proteins without any solubility-related b...
Source: Molecular and Cellular Proteomics : MCP - September 17, 2009 Category: Molecular Biology Authors: Masuda T, Saito N, Tomita M, Ishihama Y Tags: Mol Cell Proteomics Source Type: journals

Defining elastic fiber interactions by molecular fishing: an affinity purification and mass spectrometry approach.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
We describe an affinity purification and mass spectrometry strategy that has provided new insights into the molecular interactions of elastic fibers, essential extracellular assemblies that provide elastic recoil in dynamic tissues. Using cell culture models, we have defined primary and secondary elastic fiber interaction networks by identifying molecular interactions with the elastic fiber molecules, fibrillin-1, MAGP-1, fibulin-5 and lysyl oxidase. The sensitivity and validity of our method was confirmed by identification of known interactions with the bait proteins. Our study has revealed novel extracellular protein int...
Source: Molecular and Cellular Proteomics : MCP - September 14, 2009 Category: Molecular Biology Authors: Cain SA, McGovern A, Small E, Ward LJ, Baldock C, Shuttleworth A, Kielty CM Tags: Mol Cell Proteomics Source Type: journals

Systematic comparative protein expression profiling of clear cell renal cell carcinoma: A pilot study based on the separation of tissue specimen by two-dimensional electrophoresis.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Proteome-based technologies represent powerful tools for the analysis of protein expression profiles including the identification of potential cancer candidate biomarkers. Thus, we here provide a comprehensive protein expression map for clear cell renal cell carcinoma established by systematic comparative two-dimensional gel electrophoresis based protein expression profiling of 16 paired tissue systems comprised of ccRCC lesions and corresponding tumor-adjacent renal epithelium using overlapping narrow pH gradients. This approach led to the mapping of 348 distinct spots corresponding to 248 different protein identities...
Source: Molecular and Cellular Proteomics : MCP - September 13, 2009 Category: Molecular Biology Authors: Lichtenfels R, Dressler SP, Zobawa M, Recktenwald CV, Ackermann A, Atkins D, Kersten M, Hesse A, Puttkammer M, Lottspeich F, Seliger B Tags: Mol Cell Proteomics Source Type: journals

IDEAL-Q: An automated tool for label-free quantitation analysis using an efficient peptide alignment approach and spectral data validation.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
In this paper, we present a fully automated tool, called IDEAL-Q, for label-free quantitation analysis. It accepts raw data in the standard mzXML format as well as search results from major search engines, including Mascot, SEQUEST, and X!Tandem, as input data. To quantify as many identified peptides as possible, IDEAL-Q uses an efficient algorithm to predict the elution time of a peptide unidentified in a specific LC-MS/MS run, but identified in other runs. Then, the predicted elution time is used to detect peak clusters of the assigned peptide. Detected peptide peaks are processed by statistical and computational met...
Source: Molecular and Cellular Proteomics : MCP - September 12, 2009 Category: Molecular Biology Authors: Tsou CC, Tasi CF, Tsui YH, Sudhir PR, Wang YT, Chen YJ, Chen JY, Sung TY, Hsu WL Tags: Mol Cell Proteomics Source Type: journals

In vitro and in vivo protein-bound tyrosine nitration characterized by diagonal chromatography.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
A new proteomics technique for analyzing 3-nitrotyrosine-containing peptides is presented here. This technique is based on the COFRADIC (combined fractional diagonal chromatography) peptide isolation procedures by which specific classes of peptides are isolated following a series of identical reverse-phase HPLC separation steps. Dithionite is here used to reduce 3-nitrotyrosine to 3-aminotyrosine peptides which thereby become more hydrophilic. Our COFRADIC technique was first applied to characterize tyrosine nitration in tetranitromethane-modified BSA and further led to a high quality list of 335 tyrosine nitration sit...
Source: Molecular and Cellular Proteomics : MCP - September 8, 2009 Category: Molecular Biology Authors: Ghesquière B, Colaert N, Helsens K, Dejager L, Vanhaute C, Verleysen K, Kas K, Timmerman E, Goethals M, Libert C, Vandekerckhove J, Gevaert K Tags: Mol Cell Proteomics Source Type: journals

From PKA to HCN: The cAMP-capture compound mass spectrometry as a novel tool for targeting cAMP binding proteins.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
We present here the design, synthesis, and application of a new Capture Compound to target and identify cAMP binding proteins in complex protein mixtures. Starting with modest amounts of total protein mixture (65 microg-500 microg), we demonstrate that the cAMP Capture Compounds (cAMP-CCs) can be used to isolate bona fide cAMP binding proteins from lysates of Escherichia coli, mammalian HepG2 cells, and subcellular fractions of mammalian brain, respectively. The identified proteins captured by the cAMP-CC range from soluble cAMP binding proteins, such as the catabolite gene activator protein from E. coli and regulatory sub...
Source: Molecular and Cellular Proteomics : MCP - September 8, 2009 Category: Molecular Biology Authors: Luo Y, Blex C, Baessler O, Glinski M, Dreger M, Sefkow M, Köster H Tags: Mol Cell Proteomics Source Type: journals

A proteomic study of the response to salinity and drought stress in an introgression strain of bread wheat.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
The effect of drought and salinity stress on the seedlings of the somatic hybrid wheat cv. Shanrong No. 3 (SR3) and its parent bread wheat cv. Jinan 177 (JN177) was investigated using two dimensional gel electrophoresis and mass spectrometry. Out of a set of 93 (root) and 65 (leaf) differentially expressed proteins (DEPs), 34 (root) and six (leaf) DEPs were cultivar-specific. The remaining DEPs were salinity/drought stress responsive, but not cultivar-specific. Many of the DEPs were expressed under both drought and salinity stress. The amounts of stress responsive DEPs between SR3 and JN177 were almost equivalent, wher...
Source: Molecular and Cellular Proteomics : MCP - September 2, 2009 Category: Molecular Biology Authors: Peng Z, Wang M, Li F, Lv H, Li C, Xia G Tags: Mol Cell Proteomics Source Type: journals

The Moscow HUPO Human Proteome Project Workshop.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
PMID: 19734150 [PubMed - as supplied by publisher] (Source: Molecular and Cellular Proteomics : MCP)
Source: Molecular and Cellular Proteomics : MCP - August 31, 2009 Category: Molecular Biology Authors: Archakov A, Bergeron JJ, Khlunov A, Lisitsa A, Paik YK Tags: Mol Cell Proteomics Source Type: journals

Measuring proteome dynamics in vivo: As easy as adding water?Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
In this report, we demonstrate the potential of quantifying proteome dynamics by coupling the administration of stable isotopes with mass spectrometric assays. Although the direct administration of a labeled amino acid(s) is typically used to measure protein synthesis we explain the application of labeled water, comparing 2H2O vs. H218O for measuring albumin biosynthesis in vivo. This application emphasizes two distinct advantages of using labeled water over a labeled amino acid(s). First, in long-term studies (e.g. days or weeks) it is not practical to continuously administer a labeled amino acid(s), however, in the prese...
Source: Molecular and Cellular Proteomics : MCP - August 31, 2009 Category: Molecular Biology Authors: Rachdaoui N, Austin L, Kramer E, Previs MJ, Anderson VE, Kasumov T, Previs SF Tags: Mol Cell Proteomics Source Type: journals

Identification of cardiac myosin binding protein C as a candidate biomarker of myocardial infarction by proteomic analysis.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Acute myocardial infarction (AMI) is a common cause of death for which effective treatments are available providing diagnosis is rapid. The current diagnostic gold standards are circulating cardiac troponins I and T. However, their slow release delays diagnosis and their persistence limit their utility in the identification of reinfarction. The aim was to identify candidate biomarkers of AMI. Isolated mouse hearts were perfused with oxygenated protein-free buffer and coronary effluent collected after ischemia or during matched normoxic perfusion. Effluents were analysed using proteomic approaches based on 1D or 2D init...
Source: Molecular and Cellular Proteomics : MCP - August 30, 2009 Category: Molecular Biology Authors: Jacquet S, Yin X, Sicard P, Clark J, Skanaganayagam GS, Mayr M, Marber MS Tags: Mol Cell Proteomics Source Type: journals

"ChopNspice", a mass-spectrometric approach that allows identification of endogenous SUMO-conjugated peptides.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conjugation of SUMO to substrates is involved in a large number of cellular processes. Typically, SUMO is conjugated to lysine residues within a SUMO consensus site; however, an increasing number of proteins are sumoylated on non-consensus sites. To appreciate the functional consequences of sumoylation, the identification of SUMO attachment sites is of critical importance. Discovery of SUMO acceptor sites is usually performed by a laborious mutagenesis approach or using mass spectrometry (MS). In MS, identification of SUMO acceptor sites in higher eukaryotes is hampered by the large tryptic fragments of SUMO1 and SUMO2...
Source: Molecular and Cellular Proteomics : MCP - August 30, 2009 Category: Molecular Biology Authors: Hsiao HH, Meulmeester E, Frank BT, Melchior F, Urlaub H Tags: Mol Cell Proteomics Source Type: journals

Proteome, phosphoproteome and hydroxyproteome of liver mitochondria in diabetic rats at early pathogenic stages.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
It has been proposed that mitochondrial dysfunction is involved in the pathogenesis of type 2 diabetes (T2D). To dissect the underlying mechanisms, we performed a multiplexed proteomics study on liver mitochondria isolated from a spontaneous diabetic rat model before/after they are rendered diabetic. All together we identified 1091 mitochondrial proteins, 228 phosphoproteins and 355 hydroxyproteins. Mitochondrial proteins were found to undergo expression changes in a highly correlated fashion during T2D development. For example, proteins involved in ss-oxidation, TCA cycle, oxidative phosphorylation (OXPHOS) and other ...
Source: Molecular and Cellular Proteomics : MCP - August 22, 2009 Category: Molecular Biology Authors: Deng WJ, Nie S, Dai J, Wu JR, Zeng R Tags: Mol Cell Proteomics Source Type: journals

Recombinant surface proteomics as a tool to analyze humoral immune responses in bovines infected by Mycoplasma mycoides subsp. mycoides SC.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
In conclusion, a toolbox with recombinant proteins and a flexible suspension array assay that allows multiplex analysis of humoral immune responses to M mycoides SC, has been created. PMID: 19696080 [PubMed - as supplied by publisher] (Source: Molecular and Cellular Proteomics : MCP)
Source: Molecular and Cellular Proteomics : MCP - August 19, 2009 Category: Molecular Biology Authors: Hamsten C, Neiman M, Schwenk JM, Hamsten M, March JB, Persson A Tags: Mol Cell Proteomics Source Type: journals

Phosphoproteomics of Klebsiella pneumoniae NTUH-K2044 reveals a tight link between tyrosine phosphorylation and virulence.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Encapsulated Klebsiella pneumoniae (K. pneumoniae) is the predominant causative agent of pyogenic liver abscess, an emerging infectious disease often complicates with metastatic meningitis or endophthalmitis. The capsular polysaccharide on K. pneumoniae surface was determined as the key to virulence. Although the regulation of capsular polysaccharide biosynthesis is largely unclear, it was found protein tyrosine kinases and phosphatases are involved. Therefore, the identification and characterization of such kinases, phosphatases and their substrates would advance our knowledge of the underlying mechanism in capsule fo...
Source: Molecular and Cellular Proteomics : MCP - August 19, 2009 Category: Molecular Biology Authors: Lin MH, Hsu TL, Lin SY, Pan YJ, Jan JT, Wang JT, Khoo KH, Wu SH Tags: Mol Cell Proteomics Source Type: journals

Enrichment and site-mapping of O-Linked N-Acetylglucosamine by a combination of chemical/enzymatic tagging, photochemical cleavage, and electron transfer dissociation (ETD) mass spectrometry.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Numerous cellular processes are regulated by the reversible addition of either phosphate or N-acetylglucosamine (O-GlcNAc) to nuclear and cytoplasmic proteins. While sensitive methods exist for the enrichment and identification of protein phosphorylation sites, those for the enrichment of O-GlcNAc containing peptides are lacking. Reported here is highly efficient methodology for enrichment and characterization of O-GlcNAc sites from complex samples. In this method, O-GlcNAc modified peptides are tagged with a novel biotinylation reagent, enriched by affinity chromatography, released from the solid support by photochemi...
Source: Molecular and Cellular Proteomics : MCP - August 18, 2009 Category: Molecular Biology Authors: Wang Z, Udeshi ND, O'Malley M, Shabanowitz J, Hunt DF, Hart GW Tags: Mol Cell Proteomics Source Type: journals

Report: A community standard format for the representation of protein affinity reagents.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
ntecchi-Palazzi L, Palcy S, Rodriguez H, Schweinsberg S, Sievert V, Stoevesandt O, Taussig MJ, Uhlen M, Wingren C, Gold L, Hermjakob H Protein affinity reagents (PARs), most commonly antibodies, are essential reagents for protein characterization in basic research, biotechnology and diagnostics, as well as the fastest growing class of therapeutics. Large numbers of PARs are available commercially; however their quality is often uncertain. In addition, currently available PARs cover only a fraction of the human proteome, and their cost is prohibitive for proteome-scale applications. This situation has triggered several ...
Source: Molecular and Cellular Proteomics : MCP - August 12, 2009 Category: Molecular Biology Authors: Gloriam DE, Orchard S, Bertinetti D, Bjorling E, Bongcam-Rudloff E, Bourbeillon J, Bradbury AR, de Daruvar A, Dubel S, Frank R, Gibson TJ, Haslam N, Herberg FW, Hiltke T, Hoheisel JD, Kerrien S, Koegl M, Konthur Z, Korn B, Landegren U, van der Maarel S, M Tags: Mol Cell Proteomics Source Type: journals

Concurrent quantification of proteome and phosphoproteome to reveal system-wide association of protein phosphorylation and gene expression.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
In this study, we combined quantitative labeling with multiple dimensional liquid chromatography mass spectrometry to monitor proteome and phosphoproteome in the initial period of adipocytes differentiation. For a specific protein, its phosphorylation level may be regulated by kinase or phosphatase without involvement of gene expression, or as an accompanied phenomenon with the alteration of its gene expression. Concurrent quantification of phosphopeptides and non-phosphorylated peptides make it possible to differentiate cellular phosphorylation changes at these two levels. Furthermore, on the system level, certain protein...
Source: Molecular and Cellular Proteomics : MCP - August 11, 2009 Category: Molecular Biology Authors: Wu YB, Dai J, Yang XL, Li SJ, Zhao SL, Tang JS, Zheng GY, Li YX, Wu JR, Zeng R Tags: Mol Cell Proteomics Source Type: journals

Affinity-enrichment and characterization of mucin core 1-type glycopeptides from bovine serum.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
We report the unambiguous identification of 21 novel glycosylation sites. We also detail the limitations of the enrichment method as well as the ETD analysis. PMID: 19674964 [PubMed - as supplied by publisher] (Source: Molecular and Cellular Proteomics : MCP)
Source: Molecular and Cellular Proteomics : MCP - August 11, 2009 Category: Molecular Biology Authors: Darula Z, Medzihradszky KF Tags: Mol Cell Proteomics Source Type: journals

iTRAQ based proteomic profiling reveals increased metabolic activity and cellular crosstalk in angiogenic compared to invasive Glioblastoma phenotype.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
In conclusion, we describe molecular profiles that reflect the change from an invasive to an angiogenic brain tumor phenotype. The identified proteins could be further exploited as biomarkers or therapeutic targets for malignant gliomas. PMID: 19674965 [PubMed - as supplied by publisher] (Source: Molecular and Cellular Proteomics : MCP)
Source: Molecular and Cellular Proteomics : MCP - August 11, 2009 Category: Molecular Biology Authors: Rajcevic U, Petersen K, Knol JC, Loos M, Bougnaud S, Klychnikov O, Li KW, Pham TV, Wang J, Miletic H, Peng Z, Bjerkvig R, Jimenez CR, Niclou SP Tags: Mol Cell Proteomics Source Type: journals

O-GlcNAc modification of insulin receptor substrate-1 (IRS-1) occurs in close proximity to multiple SH2 domain binding motifs.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Insulin receptor substrate 1 (IRS-1) is a highly phosphorylated adaptor protein critical to insulin and IGF-1 receptor signaling. Ser/Thr kinases impact the metabolic and mitogenic effects elicited by insulin and IGF-1 through feedback and feedforward regulation at the level of IRS-1. S/T residues of IRS-1 are also O-GlcNAc modified which may influence the phosphorylation status of the protein. To facilitate the understanding of the functional effects of O-GlcNAc modification on IRS-1 mediated signaling, we have identified the sites of O-GlcNAc modification of rat and human IRS-1. Tandem mass spectrometric analysis of ...
Source: Molecular and Cellular Proteomics : MCP - August 10, 2009 Category: Molecular Biology Authors: Klein AL, Berkaw MN, Buse MG, Ball LE Tags: Mol Cell Proteomics Source Type: journals

Glucose-Regulated Protein 78 Is an Intracellular Antiviral Factor against Hepatitis B Virus.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
In conclusion, the present study demonstrates for the first time that GRP78 functions as an endogenous anti-HBV factor via IFN-ss1-OAS-RNase L pathway in hepatocytes. Induction of hepatic GRP78 may provide a novel therapeutic approach in treating HBV infection. PMID: 19671925 [PubMed - as supplied by publisher] (Source: Molecular and Cellular Proteomics : MCP)
Source: Molecular and Cellular Proteomics : MCP - August 10, 2009 Category: Molecular Biology Authors: Ma Y, Yu J, Chan HL, Chen YC, Wang H, Chen Y, Chan CY, Go MY, Tsai SN, Ngai SM, To KF, Tong JH, He QY, Sung JJ, Kung HF, Cheng CH, He ML Tags: Mol Cell Proteomics Source Type: journals

Label-free quantitative proteomics analysis of etiolated maize seedling leaves during greening.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
To better understand light regulation of C4 plant maize development, we investigated dynamic proteomic differences between green seedlings (control), etiolated seedlings, and etiolated seedlings illuminated for 6 or 12 h using a label-free quantitative proteomic approach based on nanoscale ultra-performance liquid chromatography-ESI-MSE. Among more than 400 proteins identified, 73 significantly altered during etiolated maize seedlings greening. Of these 73 proteins, 25 were identified as membrane proteins which seldom had been identified with 2 DE methods, indicating the power of our label-free method for membrane prot...
Source: Molecular and Cellular Proteomics : MCP - August 6, 2009 Category: Molecular Biology Authors: Shen Z, Li P, Ni RJ, Ritchie M, Yang CP, Liu GF, Ma W, Liu GJ, Ma L, Li SJ, Wei ZG, Wang HX, Wang BC Tags: Mol Cell Proteomics Source Type: journals

A mixed-integer linear optimization framework for the identification and quantification of targeted post-translational modifications of highly modified proteins using multiplexed ETD tandem mass spectrometry.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
There is significant interest in the identification of hyper-modified proteins, such as histones. We have recently developed chromatography that is particularly suited for LC-MS ETD analysis of highly modified polypeptides. This work presents a novel mixed-integer linear optimization (MILP) computational framework which utilizes both ETD tandem mass spectrometry and the corresponding chromatography to identify and quantify the modified protein forms present within an entire LC-MS dataset. For a given primary sequence, the entire set of post-translational modifications that satisfy a precursor mass are enumerated by sol...
Source: Molecular and Cellular Proteomics : MCP - August 6, 2009 Category: Molecular Biology Authors: Dimaggio PA, Young NL, Baliban RC, Garcia BA, Floudas CA Tags: Mol Cell Proteomics Source Type: journals

The mouse C2C12 myoblast cell surface N-linked glycoproteome: Identification, glycosite occupancy, and membrane orientation.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Endogenous regeneration and repair mechanisms are responsible for replacing dead and damaged cells to maintain or enhance tissue and organ function, and one of the best examples of endogenous repair mechanisms involves skeletal muscle. Although the molecular mechanisms that regulate the differentiation of satellite cells and myoblasts towards myofibers are not fully understood, cell surface proteins that sense and respond to their environment play an important role. The cell surface capturing technology (CSC-technology) was used here to uncover the cell surface N-linked glycoprotein subproteome of myoblasts and to iden...
Source: Molecular and Cellular Proteomics : MCP - August 3, 2009 Category: Molecular Biology Authors: Gundry RL, Raginski K, Tarasova Y, Tchernyshyov I, Bausch-Fluck D, Elliott ST, Boheler KR, Van Eyk JE, Wollscheid B Tags: Mol Cell Proteomics Source Type: journals

High-throughput characterization of combinatorial histone codes.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
We present a novel method utilizing "salt-less" pH gradient weak cation exchange-hydrophilic interaction liquid chromatography (WCX-HILIC) directly coupled to electron transfer dissociation (ETD) mass spectrometry for the automated on-line high-throughput characterization of hyper-modified combinatorial Histone Codes. This technique, performed on a low resolution mass spectrometer, displays an improvement over existing methods with approximately 100-fold reduction in sample requirements and analysis time. The scheme presented is capable of identifying all of the major combinatorial Histone Codes present in a sample in a 2-...
Source: Molecular and Cellular Proteomics : MCP - August 3, 2009 Category: Molecular Biology Authors: Young NL, Dimaggio PA, Plazas-Mayorca MD, Baliban RC, Floudas CA, Garcia BA Tags: Mol Cell Proteomics Source Type: journals

Global effects of kinase inhibitors on signaling networks revealed by quantitative phosphoproteomics.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Aberrant signaling causes many diseases and manipulating signaling pathways with kinase inhibitors has emerged as a promising area of drug research. Most kinase inhibitors target the conserved ATP-binding pocket, therefore specificity is a major concern. Proteomics has previously been used to identify the direct targets of kinase inhibitors upon affinity purification from cellular extracts. Here we introduce a complementary approach to evaluate the effect of kinase inhibitors on the entire cell signaling network. We employ triple labeling SILAC to compare cellular phosphorylation levels for control, EGF growth factor s...
Source: Molecular and Cellular Proteomics : MCP - August 2, 2009 Category: Molecular Biology Authors: Pan C, Olsen JV, Daub H, Mann M Tags: Mol Cell Proteomics Source Type: journals

Proteomic analysis of microtubule associated proteins during macrophage activation.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Classical activation of macrophages induces a wide range of signaling and vesicle trafficking events to produce a more aggressive cellular phenotype. The microtubule (MT) cytoskeleton is crucial for the regulation of immune responses. In the current study, we used a large scale proteomics approach to analyze the change in protein composition of the MT associated protein (MAP) network by macrophage stimulation with the inflammatory cytokine, IFN-gamma, and the endotoxin, lipopolysaccharide (LPS). Overall, the analysis identified 409 proteins that bound directly or indirectly to MTs. Out of these, 52 were up regulated tw...
Source: Molecular and Cellular Proteomics : MCP - August 1, 2009 Category: Molecular Biology Authors: Patel PC, Fisher KH, Yang EC, Deane CM, Harrison RE Tags: Mol Cell Proteomics Source Type: journals

Differential 14-3-3-affinity capture reveals new downstream targets of PI 3-kinase signaling.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
We devised a strategy of 14-3-3 affinity capture and release, isotope-differential (D0/D4) dimethyl labeling of tryptic digests, and phosphopeptide characterization, to identify novel targets of insulin/IGF1/PI 3-kinase signaling. Notably, four known insulin-regulated proteins (PFK-2, PRAS40, AS160 and MYO1C) had high D0/D4 values meaning that they were more highly represented amongst 14-3-3-binding proteins from insulin-stimulated than unstimulated cells. Amongst novel candidates, insulin-receptor substrate 2 (IRS2), the pro-apoptotic CCDC6, E3 ubiquitin ligase ZNRF2 and signaling adapter SASH1 were confirmed to bind ...
Source: Molecular and Cellular Proteomics : MCP - July 31, 2009 Category: Molecular Biology Authors: Dubois F, Vandermoere F, Gernez A, Murphy J, Toth R, Chen S, Geraghty KM, Morrice NA, Mackintosh C Tags: Mol Cell Proteomics Source Type: journals

Quantitative phosphokinome analysis of the Met pathway activated by the invasin InlB from listeria monocytogenes.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Stimulated by its physiological ligand HGF, the transmembrane receptor tyrosine kinase Met activates a signalling machinery that leads to mitogenic, motogenic and morphogenic responses. Remarkably, the food-borne human pathogen Listeria monocytogenes also promotes autophosphorylation of Met through its virulence factor InlB and subsequently exploits Met signalling to induce phagocytosis into a broad range of host cells. Although the interaction between InlB and Met has been studied in detail, the signalling specificity of components involved in InlB-triggered cellular responses remains poorly characterized. The analysi...
Source: Molecular and Cellular Proteomics : MCP - July 28, 2009 Category: Molecular Biology Authors: Reinl T, Nimtz M, Hundertmark C, Johl T, Kéri G, Wehland J, Daub H, Jänsch L Tags: Mol Cell Proteomics Source Type: journals

Outside the unusual cell wall of hyperthermophilic archaeon Aeropyrum pernix.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
In contrast to the extensively studied eukaryal and bacterial protein secretion systems, comparatively less is known about how and which proteins cross the archaeal cell membrane. In order to identify secreted proteins of the hyperthermophilic archaeon Aeropyrum pernix K1 we used a proteomic approach to analyze the extracellular and cell surface protein fractions. The experimentally obtained data comprising 107 proteins were compared to the in silico predicted secretome. Due to the lack of signal peptide and cellular localization prediction tools specific for archaeal species, programs trained on eukaryotic and/or gram...
Source: Molecular and Cellular Proteomics : MCP - July 27, 2009 Category: Molecular Biology Authors: Palmieri G, Cannio R, Fiume I, Rossi M, Pocsfalvi G Tags: Mol Cell Proteomics Source Type: journals