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Smith JC, Figeys D. Recent developments in mass spectrometry-based quantitative phosphoproteomicsThis paper is one of a selection of papers published in this Special Issue, entitled CSBMCB — Systems and Chemical Biology, and has undergone the Journal's usual peer review process. Biochem Cell Biol 2008; 86:137-48. [DOI: 10.1139/o08-007] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Protein phosphorylation is a reversible post-translational modification that is involved in virtually all eukaryotic cellular processes and has been studied in great detail in recent years. Many developments in mass spectrometry (MS)-based proteomics have been successfully applied to study protein phosphorylation in highly complicated samples. Furthermore, the emergence of a variety of enrichment strategies has allowed some of the challenges associated with low phosphorylation stoichiometry and phosphopeptide copy number to be overcome. The dynamic nature of protein phosphorylation complicates its analysis; however, a number of methods have been developed to successfully quantitate phosphorylation changes in a variety of cellular systems. The following review details some of the most recent breakthroughs in the study of protein phosphorylation, or phosphoproteomics, using MS-based approaches. The majority of the focus is placed on detailing strategies that are currently used to conduct MS-based quantitative phosphoproteomics.
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Affiliation(s)
- Jeffrey C. Smith
- Ottawa Institute of Systems Biology, Faculty of Medicine, University of Ottawa, Ottawa, Ontario, Canada
| | - Daniel Figeys
- Ottawa Institute of Systems Biology, Faculty of Medicine, University of Ottawa, Ottawa, Ontario, Canada
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Lemeer S, Pinkse MWH, Mohammed S, van Breukelen B, den Hertog J, Slijper M, Heck AJR. Online Automated in Vivo Zebrafish Phosphoproteomics: From Large-Scale Analysis Down to a Single Embryo. J Proteome Res 2008; 7:1555-64. [DOI: 10.1021/pr700667w] [Citation(s) in RCA: 66] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Simone Lemeer
- Biomolecular Mass Spectrometry and Proteomics Group, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Sorbonnelaan 16, 3584 CA Utrecht, The Netherlands, and Hubrecht Institute, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
| | - Martijn W. H. Pinkse
- Biomolecular Mass Spectrometry and Proteomics Group, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Sorbonnelaan 16, 3584 CA Utrecht, The Netherlands, and Hubrecht Institute, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
| | - Shabaz Mohammed
- Biomolecular Mass Spectrometry and Proteomics Group, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Sorbonnelaan 16, 3584 CA Utrecht, The Netherlands, and Hubrecht Institute, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
| | - Bas van Breukelen
- Biomolecular Mass Spectrometry and Proteomics Group, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Sorbonnelaan 16, 3584 CA Utrecht, The Netherlands, and Hubrecht Institute, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
| | - Jeroen den Hertog
- Biomolecular Mass Spectrometry and Proteomics Group, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Sorbonnelaan 16, 3584 CA Utrecht, The Netherlands, and Hubrecht Institute, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
| | - Monique Slijper
- Biomolecular Mass Spectrometry and Proteomics Group, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Sorbonnelaan 16, 3584 CA Utrecht, The Netherlands, and Hubrecht Institute, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
| | - Albert J. R. Heck
- Biomolecular Mass Spectrometry and Proteomics Group, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Sorbonnelaan 16, 3584 CA Utrecht, The Netherlands, and Hubrecht Institute, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
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Mohammed S, Kraiczek K, Pinkse MWH, Lemeer S, Benschop JJ, Heck AJR. Chip-Based Enrichment and NanoLC−MS/MS Analysis of Phosphopeptides from Whole Lysates. J Proteome Res 2008; 7:1565-71. [DOI: 10.1021/pr700635a] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Shabaz Mohammed
- Biomolecular Mass Spectrometry and Proteomics Group, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Sorbonnelaan 16, 3584 CA Utrecht, The Netherlands, and Agilent Technologies R&D and Marketing GmbH & Company KG, Hewlett-Packard-Strasse 8, 76337 Waldbronn, Germany
| | - Karsten Kraiczek
- Biomolecular Mass Spectrometry and Proteomics Group, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Sorbonnelaan 16, 3584 CA Utrecht, The Netherlands, and Agilent Technologies R&D and Marketing GmbH & Company KG, Hewlett-Packard-Strasse 8, 76337 Waldbronn, Germany
| | - Martijn W. H. Pinkse
- Biomolecular Mass Spectrometry and Proteomics Group, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Sorbonnelaan 16, 3584 CA Utrecht, The Netherlands, and Agilent Technologies R&D and Marketing GmbH & Company KG, Hewlett-Packard-Strasse 8, 76337 Waldbronn, Germany
| | - Simone Lemeer
- Biomolecular Mass Spectrometry and Proteomics Group, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Sorbonnelaan 16, 3584 CA Utrecht, The Netherlands, and Agilent Technologies R&D and Marketing GmbH & Company KG, Hewlett-Packard-Strasse 8, 76337 Waldbronn, Germany
| | - Joris J. Benschop
- Biomolecular Mass Spectrometry and Proteomics Group, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Sorbonnelaan 16, 3584 CA Utrecht, The Netherlands, and Agilent Technologies R&D and Marketing GmbH & Company KG, Hewlett-Packard-Strasse 8, 76337 Waldbronn, Germany
| | - Albert J. R. Heck
- Biomolecular Mass Spectrometry and Proteomics Group, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Sorbonnelaan 16, 3584 CA Utrecht, The Netherlands, and Agilent Technologies R&D and Marketing GmbH & Company KG, Hewlett-Packard-Strasse 8, 76337 Waldbronn, Germany
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Miller ML, Hanke S, Hinsby AM, Friis C, Brunak S, Mann M, Blom N. Motif decomposition of the phosphotyrosine proteome reveals a new N-terminal binding motif for SHIP2. Mol Cell Proteomics 2008; 7:181-92. [PMID: 17938406 DOI: 10.1074/mcp.m700241-mcp200] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Advances in mass spectrometry-based proteomics have yielded a substantial mapping of the tyrosine phosphoproteome and thus provided an important step toward a systematic analysis of intracellular signaling networks in higher eukaryotes. In this study we decomposed an uncharacterized proteomics data set of 481 unique phosphotyrosine (Tyr(P)) peptides by sequence similarity to known ligands of the Src homology 2 (SH2) and the phosphotyrosine binding (PTB) domains. From 20 clusters we extracted 16 known and four new interaction motifs. Using quantitative mass spectrometry we pulled down Tyr(P)-specific binding partners for peptides corresponding to the extracted motifs. We confirmed numerous previously known interaction motifs and found 15 new interactions mediated by phosphosites not previously known to bind SH2 or PTB. Remarkably, a novel hydrophobic N-terminal motif ((L/V/I)(L/V/I)pY) was identified and validated as a binding motif for the SH2 domain-containing inositol phosphatase SHIP2. Our decomposition of the in vivo Tyr(P) proteome furthermore suggests that two-thirds of the Tyr(P) sites mediate interaction, whereas the remaining third govern processes such as enzyme activation and nucleic acid binding.
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Affiliation(s)
- Martin Lee Miller
- Center for Biological Sequence Analysis, Technical University of Denmark, Kemitorvet, Building 208, DK-2800 Lyngby, Denmark
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Marcantonio M, Trost M, Courcelles M, Desjardins M, Thibault P. Combined enzymatic and data mining approaches for comprehensive phosphoproteome analyses: application to cell signaling events of interferon-gamma-stimulated macrophages. Mol Cell Proteomics 2007; 7:645-60. [PMID: 18006492 DOI: 10.1074/mcp.m700383-mcp200] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Protein phosphorylation is a central cell signaling event that underlies a broad spectrum of key physiological processes. Advances in affinity chromatography and mass spectrometry are now providing the ability to identify and quantitate thousands of phosphorylation sites simultaneously. Comprehensive phosphoproteome analyses present sizable analytical challenges in view of suppression effects of phosphopeptides and the variable quality of MS/MS spectra. This work presents an integrated enzymatic and data mining approach enabling the comprehensive detection of native and putative phosphopeptides following alkaline phosphatase digestion of titanium dioxide (TiO2)-enriched cell extracts. The correlation of retention times of more than 750 phospho- and dephosphopeptide pairs from J774 macrophage cell extracts indicated that removal of the phosphate groups can impart a gain or a loss in hydrophobicity that is partly explained by the formation of a salt bridge with proximal amino groups. Dephosphorylation also led to an average 2-fold increase in MS sensitivity that facilitated peptide sequencing. More importantly, alkaline phosphatase digestion enhanced the overall population of putative phosphopeptides from TiO2-enriched cell extracts providing a unique approach to profile multiphosphorylated cognates that would have remained otherwise undetected. The application of this approach is demonstrated for differential phosphoproteome analyses of mouse macrophages exposed to interferon-gamma for 5 min. TiO2 enrichment enabled the identification of 1143 phosphopeptides from 432 different proteins of which 125 phosphopeptides showed a 2-fold change upon interferon-gamma exposure. The use of alkaline phosphatase nearly doubled the number of putative phosphopeptides assignments leading to the observation of key interferon-gamma signaling events involved in vesicle trafficking, production of reactive oxygen species, and mRNA translation.
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Affiliation(s)
- Maria Marcantonio
- Institute for Research in Immunology and Cancer, Departments of Biochemistry, Université de Montréal, Station Centre-ville, Montréal H3C 3J7, Canada
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Gevaert K, Van Damme P, Ghesquière B, Impens F, Martens L, Helsens K, Vandekerckhove J. A la carte proteomics with an emphasis on gel-free techniques. Proteomics 2007; 7:2698-718. [PMID: 17640001 DOI: 10.1002/pmic.200700114] [Citation(s) in RCA: 72] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Since the introduction of the proteome term somewhat more than a decade ago the field of proteomics witnessed a rapid growth mainly fueled by instrumental analytical improvements. Of particular notice is the advent of a diverse set of gel-free proteomics techniques. In this review, we discuss several of these gel-free techniques both for monitoring protein concentration changes and protein modifications, in particular protein phosphorylation, glycosylation, and protein processing. Furthermore, different approaches for (multiplexed) gel-free proteome analysis are discussed.
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Affiliation(s)
- Kris Gevaert
- Department of Medical Protein Research, VIB, Ghent, Belgium.
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Sines T, Granot-Attas S, Weisman-Welcher S, Elson A. Association of tyrosine phosphatase epsilon with microtubules inhibits phosphatase activity and is regulated by the epidermal growth factor receptor. Mol Cell Biol 2007; 27:7102-12. [PMID: 17709387 PMCID: PMC2168897 DOI: 10.1128/mcb.02096-06] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
Protein tyrosine phosphatases (PTPs) are key mediators that link physiological cues with reversible changes in protein structure and function; nevertheless, significant details concerning their regulation in vivo remain unknown. We demonstrate that PTPepsilon associates with microtubules in vivo and is inhibited by them in a noncompetitive manner. Microtubule-associated proteins, which interact strongly with microtubules in vivo, significantly increase binding of PTPepsilon to tubulin in vitro and further reduce phosphatase activity. Conversely, disruption of microtubule structures in cells reduces their association with PTPepsilon, alters the subcellular localization of the phosphatase, and increases its specific activity. Activation of the epidermal growth factor receptor (EGFR) increases the PTPepsilon-microtubule association in a manner dependent upon EGFR-induced phosphorylation of PTPepsilon at Y638 and upon microtubule integrity. These events are transient and occur with rapid kinetics similar to EGFR autophosphorylation, suggesting that activation of the EGFR transiently down-regulates PTPepsilon activity near the receptor by promoting the PTPepsilon-microtubule association. Tubulin also inhibits the tyrosine phosphatase PTP1B but not receptor-type PTPmu or the unrelated alkaline phosphatase. The data suggest that reversible association with microtubules is a novel, physiologically regulated mechanism for regulation of tyrosine phosphatase activity in cells.
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Affiliation(s)
- Tal Sines
- Department of Molecular Genetics, The Weizmann Institute of Science, Rehovot 76100, Israel
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58
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Tang LY, Deng N, Wang LS, Dai J, Wang ZL, Jiang XS, Li SJ, Li L, Sheng QH, Wu DQ, Li L, Zeng R. Quantitative phosphoproteome profiling of Wnt3a-mediated signaling network: indicating the involvement of ribonucleoside-diphosphate reductase M2 subunit phosphorylation at residue serine 20 in canonical Wnt signal transduction. Mol Cell Proteomics 2007; 6:1952-67. [PMID: 17693683 DOI: 10.1074/mcp.m700120-mcp200] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The complexity of canonical Wnt signaling comes not only from the numerous components but also from multiple post-translational modifications. Protein phosphorylation is one of the most common modifications that propagates signals from extracellular stimuli to downstream effectors. To investigate the global phosphorylation regulation and uncover novel phosphoproteins at the early stages of canonical Wnt signaling, HEK293 cells were metabolically labeled with two stable isotopic forms of lysine and were stimulated for 0, 1, or 30 min with purified Wnt3a. After phosphoprotein enrichment and LC-MS/MS analysis, 1057 proteins were identified in all three time points. In total 287 proteins showed a 1.5-fold or greater change in at least one time point. In addition to many known Wnt signaling transducers, other phosphoproteins were identified and quantitated, implicating their involvement in canonical Wnt signaling. k-Means clustering analysis showed dynamic patterns for the differential phosphoproteins. Profile pattern and interaction network analysis of the differential phosphoproteins implicated the possible roles for those unreported components in Wnt signaling. Moreover 100 unique phosphorylation sites were identified, and 54 of them were quantitated in the three time points. Site-specific phosphopeptide quantitation revealed that Ser-20 phosphorylation on RRM2 increased upon 30-min Wnt3a stimulation. Further studies with mutagenesis, the Wnt reporter gene assay, and RNA interference indicated that RRM2 functioned downstream of beta-catenin as an inhibitor of Wnt signaling and that Ser-20 phosphorylation of RRM2 counteracted its inhibition effect. Our systematic profiling of dynamic phosphorylation changes responding to Wnt3a stimulation not only presented a comprehensive phosphorylation network regulated by canonical Wnt signaling but also found novel molecules and phosphorylation involved in Wnt signaling.
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Affiliation(s)
- Liu-Ya Tang
- State Key Laboratory of Molecular Biology, Shangai 200031, China
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59
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Fournier ML, Gilmore JM, Martin-Brown SA, Washburn MP. Multidimensional Separations-Based Shotgun Proteomics. Chem Rev 2007; 107:3654-86. [PMID: 17649983 DOI: 10.1021/cr068279a] [Citation(s) in RCA: 143] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Smith JC, Duchesne MA, Tozzi P, Ethier M, Figeys D. A Differential Phosphoproteomic Analysis of Retinoic Acid-Treated P19 Cells. J Proteome Res 2007; 6:3174-86. [PMID: 17622165 DOI: 10.1021/pr070122r] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
External stimuli trigger internal signaling events within a cell that may represent either a temporary or permanent shift in the phosphorylation state of its proteome. Numerous reports have elucidated phosphorylation sites from a variety of biological samples and more recent studies have monitored the temporal dynamics of protein phosphorylation as a given system is perturbed. Understanding which proteins are phosphorylated as well as when they are phosphorylated may indicate novel functional roles within a system and allow new therapeutic avenues to be explored. To elucidate the dynamics of protein phosphorylation within differentiating murine P19 embryonal carcinoma cells, we induced P19 cells to differentiate using all-trans-retinoic acid and developed a strategy that combines isotopically labeled methyl esterification, immobilized metal affinity chromatography, mass spectrometric analysis, and a rigorous and unique data evaluation approach. We present the largest differential phosphoproteomic analysis using isotopically labeled methyl esterification to date, identifying a total of 472 phosphorylation sites on 151 proteins; 56 of these proteins had altered abundances following treatment with retinoic acid and approximately one-third of these have been previously associated with cellular differentiation. A series of bioinformatic tools were used to extract information from the data and explore the implications of our findings. This study represents the first global gel-free analysis that elucidates protein phosphorylation dynamics during cellular differentiation.
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Affiliation(s)
- Jeffrey C Smith
- Ottawa Institute of Systems Biology and Biochemistry, Microbiology and Immunology Department, Faculty of Medicine, University of Ottawa, 451 Smyth Road, Ottawa, Ontario K1H 8M5, Canada
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Grant MM, Scheel-Toellner D, Griffiths HR. Contributions to our understanding of T cell physiology through unveiling the T cell proteome. Clin Exp Immunol 2007; 149:9-15. [PMID: 17488298 PMCID: PMC1942030 DOI: 10.1111/j.1365-2249.2007.03395.x] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Since the sequencing of the human genome was completed, attention has turned to examining the functionality of the molecular machinery, in particular of protein expression. Differential proteome analysis by two-dimensional electrophoresis has been adopted to study changes in T cell proteomes during T cell activation, and this work is increasing our understanding of the complexity of signals elicited across multiple pathways. The purpose of this review is to summarize the available evidence in the application of proteomic techniques and methodologies to understand T cell receptor activation from lipid raft and cytoskeletal rearrangements, through to signalling cascades, transcription factor modulation and changes in protein expression patterns. These include post-translational modifications, which are not encoded by the genome.
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Affiliation(s)
- M M Grant
- School of Dentistry, The University of Birmingham, St Chads Queensway, Birmingham, UK.
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Azarkan M, Huet J, Baeyens-Volant D, Looze Y, Vandenbussche G. Affinity chromatography: A useful tool in proteomics studies. J Chromatogr B Analyt Technol Biomed Life Sci 2007; 849:81-90. [PMID: 17113368 DOI: 10.1016/j.jchromb.2006.10.056] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2006] [Revised: 09/26/2006] [Accepted: 10/27/2006] [Indexed: 11/22/2022]
Abstract
Separation or fractionation of a biological sample in order to reduce its complexity is often a prerequisite to qualitative or quantitative proteomic approaches. Affinity chromatography is an efficient protein separation method based on the interaction between target proteins and specific immobilized ligands. The large range of available ligands allows to separate a complex biological extract in different protein classes or to isolate the low abundance species such as post-translationally modified proteins. This method plays an essential role in the isolation of protein complexes and in the identification of protein-protein interaction networks. Affinity chromatography is also required for quantification of protein expression by using isotope-coded affinity tags.
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Affiliation(s)
- Mohamed Azarkan
- Laboratoire de Chimie Générale (CP: 609), Faculté de Médecine, Université Libre de Bruxelles, Campus Erasme, 808, route de Lennik, B-1070 Bruxelles, Belgium
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Rennefahrt UEE, Deacon SW, Parker SA, Devarajan K, Beeser A, Chernoff J, Knapp S, Turk BE, Peterson JR. Specificity profiling of Pak kinases allows identification of novel phosphorylation sites. J Biol Chem 2007; 282:15667-78. [PMID: 17392278 DOI: 10.1074/jbc.m700253200] [Citation(s) in RCA: 104] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
The p21-activated kinases (Paks) serve as effectors of the Rho family GTPases Rac and Cdc42. The six human Paks are divided into two groups based on sequence similarity. Group I Paks (Pak1 to -3) phosphorylate a number of substrates linking this group to regulation of the cytoskeleton and both proliferative and anti-apoptotic signaling. Group II Paks (Pak4 to -6) are thought to play distinct functional roles, yet their few known substrates are also targeted by Group I Paks. To determine if the two groups recognize distinct target sequences, we used a degenerate peptide library method to comprehensively characterize the consensus phosphorylation motifs of Group I and II Paks. We find that Pak1 and Pak2 exhibit virtually identical substrate specificity that is distinct from that of Pak4. Based on structural comparisons and mutagenesis, we identified two key amino acid residues that mediate the distinct specificities of Group I and II Paks and suggest a structural basis for these differences. These results implicate, for the first time, residues from the small lobe of a kinase in substrate selectivity. Finally, we utilized the Pak1 consensus motif to predict a novel Pak1 phosphorylation site in Pix (Pak-interactive exchange factor) and demonstrate that Pak1 phosphorylates this site both in vitro and in cultured cells. Collectively, these results elucidate the specificity of Pak kinases and illustrate a general method for the identification of novel sites phosphorylated by Paks.
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Affiliation(s)
- Ulrike E E Rennefahrt
- Division of Basic Science, Fox Chase Cancer Center, Philadelphia, Pennsylvania 19111, USA
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64
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Hsiao HH, Hsieh HY, Chou CC, Lin SY, Wang AHJ, Khoo KH. Concerted Experimental Approach for Sequential Mapping of Peptides and Phosphopeptides Using C18-Functionalized Magnetic Nanoparticles. J Proteome Res 2007; 6:1313-24. [PMID: 17348702 DOI: 10.1021/pr0604817] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
An integrated analytical approach for the enrichment, detection, and sequencing of phosphopeptides using matrix-assisted laser desorption/ionization (MALDI) tandem mass spectrometry (MS) was developed. On the basis of C18-functionalized Fe3O4 nanoparticles, the enrichment method was designed not only to specifically trap phosphopeptides, but also nonphosphorylated peptides, both of which can be subsequently desorbed selectively and directly for MALDI-MS analysis without an elution step. Peptide binding is afforded by the C18-derivatization, whereas the highly selective capture of phosphopeptides is based on higher binding affinity afforded by additional metal chelating interaction between the Fe3O4 nanoparticles and the phosphate groups. Upon binding, the initial aqueous wash allows desalting, while a second and a third wash with high acetonitrile content coupled with diluted sulfuric acid and ammonia removes most of the bound nonphosphorylated peptides. Selective or sequential mapping of the peptides and phosphopeptides can, thus, be effected by spotting the washed nanoparticles onto the MALDI target plate along with judicious choice of matrices. The inclusion of phosphoric acid in a 2,5-dihydroxybenzoic acid matrix allows the desorption and detection of phosphopeptides, whereas an alpha-cyano-4-hydroxy-cinnamic acid matrix with formic acid allows only the desorption of nonphosphorylated peptides. The method used to enrich phosphopeptides prior to MS applications is more sensitive and tolerable to sodium dodecyl sulfate than IMAC. We have demonstrated the applicability of C18-functionalized Fe3O4 nanoparticles in the detection of in vitro phosphorylation sites on the myelin basic protein, and at least 17 phosphopeptides were identified, including one previously uncharacterized site.
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Affiliation(s)
- He-Hsuan Hsiao
- National Core Facilities for Proteomics Research, Academia Sinica, Taipei 115, Taiwan
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65
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Hanoulle X, Van Damme J, Staes A, Martens L, Goethals M, Vandekerckhove J, Gevaert K. A new functional, chemical proteomics technology to identify purine nucleotide binding sites in complex proteomes. J Proteome Res 2007; 5:3438-45. [PMID: 17137346 DOI: 10.1021/pr060313e] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Adenine nucleotides are small, abundant molecules that bind numerous proteins involved in pivotal cellular processes. These nucleotides are co-factors or substrates for enzymes, regulators of protein function, or structural binding motifs. The identification of nucleotide-binding sites on a proteome-wide scale is tempting in view of the high number of nucleotide-binding proteins, their large in vivo concentration differences, and the various functions they exert. Here, we report on a functional, chemical, gel-free proteomics technology that allows the identification of protein adenine nucleotide-binding site(s) in cell lysates. Our technology uses a synthetic ATP analogue, 5'-p-fluorosulfonylbenzoyladenosine (FSBA), as an affinity/activity-based probe for nucleotide-binding sites. When applied on a cellular level, 185 different FSBA-labeled sites in a human Jurkat cell lysate were identified. Functional and structural aspects of the use of FSBA on a proteome-wide scale are discussed.
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Affiliation(s)
- Xavier Hanoulle
- Department of Medical Protein Research and Biochemistry, Flanders Interuniversity Institute for Biotechnology and Faculty of Medicine and Health Sciences, Ghent University, A. Baertsoenkaai 3, B-9000 Ghent, Belgium
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Abstract
Acute myeloid leukemia (AML) is a frequent hematological malignancy. Despite enormous therapeutic efforts that range from various cytotoxic agents to allogeneic stem cell transplantation, overall survival of patients with AML remains unsatisfying. The poor survival rates are mainly due to therapy-related mortality, failure of induction chemotherapy and early relapses. Therefore, novel therapeutic agents that are more efficient and better tolerated are eagerly sought after. For existing therapeutic strategies, there is a lack of markers that are capable of reliably predicting prognosis or the therapeutic response prior to treatment. There is hope that elucidation of the AML-specific proteome will prompt the discovery of novel therapeutic targets and biomarkers in AML. Modern mass-spectrometry instrumentation has achieved excellent performance in terms of sensitivity, resolution and mass accuracy; however, so far, the contribution of proteomics to the care of patients with AML is virtually zero. This might be partly because mass spectrometry instrumentation and protein fractionation still lack true high-throughput capabilities with highest levels of reproducibility, thus hampering large-scale translational studies with clinical samples. Since mass-spectrometry instruments are very intricate devices, their successful operation will hinge on the willingness and ability of mass-spectrometry experts and clinical researchers to adopt new views, learn from each other and cooperate in order to ultimately benefit the patient suffering from AML. This review highlights some clinical problems circumventing the treatment of patients with AML. Furthermore, it provides a brief overview of the technical background of standard proteomics approaches and describes opportunities, challenges and pitfalls of proteomic studies with regards to AML.
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Affiliation(s)
- Akos Czibere
- Heinrich Heine University, Department of Hematology, Oncology and Clinical Immunlogy, Moorenstr. 5, 40225 Düsseldorf, Germany.
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67
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Ahn NG, Shabb JB, Old WM, Resing KA. Achieving in-depth proteomics profiling by mass spectrometry. ACS Chem Biol 2007; 2:39-52. [PMID: 17243782 DOI: 10.1021/cb600357d] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Proteomics addresses the important goal of determining the chemistry and composition of proteins in biological samples. Mass-spectrometry-based strategies have been highly successful in identifying and profiling proteins in complex mixtures; however, although depth of sampling continues to improve, a general recognition exists that no study has yet achieved complete protein coverage in any tissue, cell type, subcellular component, or fluid. The development of new approaches for comprehensively surveying highly complex protein mixtures, distinguishing protein isoforms, quantifying changes in protein abundance between different samples, and mapping post-translational modifications are areas of active research. These will be needed to achieve the "systems-wide" protein profiling goals of defining molecular responses to cell perturbations and obtaining biomarker information for disease detection, prognosis, and responses to therapy. We review recent progress in approaching these problems and present examples of successful applications and the outlook for the future.
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Affiliation(s)
- Natalie G Ahn
- Department of Chemistry and Biochemistry, University of Colorado, Boulder, Colorado 80309, USA.
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Emadali A, Metrakos PP, Kalantari F, Boutros T, Boismenu D, Chevet E. Proteomic analysis of tyrosine phosphorylation during human liver transplantation. Proteome Sci 2007; 5:1. [PMID: 17199894 PMCID: PMC1769479 DOI: 10.1186/1477-5956-5-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2006] [Accepted: 01/02/2007] [Indexed: 12/31/2022] Open
Abstract
Background Ischemia-reperfusion (I/R) causes a dramatic reprogramming of cell metabolism during liver transplantation and can be linked to an alteration of the phosphorylation level of several cellular proteins. Over the past two decades, it became clear that tyrosine phosphorylation plays a pivotal role in a variety of important signalling pathways and was linked to a wide spectrum of diseases. Functional profiling of the tyrosine phosphoproteome during liver transplantation is therefore of great biological significance and is likely to lead to the identification of novel targets for drug discovery and provide a basis for novel therapeutic strategies. Results Using liver biopsies collected during the early phases of organ procurement and transplantation, we aimed at characterizing the global patterns of tyrosine phosphorylation during hepatic I/R. A proteomic approach, based on the purification of tyrosine phosphorylated proteins followed by their identification using mass spectrometry, allowed us to identify Nck-1, a SH2/SH3 adaptor, as a potential regulator of I/R injury. Using immunoblot, cell fractionation and immunohistochemistry, we demonstrate that Nck-1 phosphorylation, expression and localization were affected in liver tissue upon I/R. In addition, mass spectrometry identification of Nck-1 binding partners during the course of the transplantation also suggested a dynamic interaction between Nck-1 and actin during I/R. Conclusion Taken together, our data suggest that Nck-1 may play a role in I/R-induced actin reorganization, which was previously reported to be detrimental for the hepatocytes of the transplanted graft. Nck-1 could therefore represent a target of choice for the design of new organ preservation strategies, which could consequently help to reduce post-reperfusion liver damages and improve transplantation outcomes.
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Affiliation(s)
- Anouk Emadali
- Department of Surgery, McGill University, Montreal, Quebec, Canada
- CEA/Grenoble, Grenoble, France
| | - Peter P Metrakos
- Department of Surgery, McGill University, Montreal, Quebec, Canada
| | - Fariba Kalantari
- Department of Surgery, McGill University, Montreal, Quebec, Canada
| | - Tarek Boutros
- Department of Surgery, McGill University, Montreal, Quebec, Canada
| | - Daniel Boismenu
- Genome Québec Innovation Centre, McGill University, Montreal, Quebec, Canada
| | - Eric Chevet
- Department of Surgery, McGill University, Montreal, Quebec, Canada
- Genome Québec Innovation Centre, McGill University, Montreal, Quebec, Canada
- Departement of Medecine, McGill University, Montreal, Quebec, Canada
- Department of Anatomy and Cell Biology, McGill University, Montreal, Quebec, Canada
- Team AVENIR, INSERM E362, Université Bordeaux 2, Bordeaux, France
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69
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Bodenmiller B, Mueller LN, Pedrioli PGA, Pflieger D, Jünger MA, Eng JK, Aebersold R, Tao WA. An integrated chemical, mass spectrometric and computational strategy for (quantitative) phosphoproteomics: application to Drosophila melanogaster Kc167 cells. MOLECULAR BIOSYSTEMS 2007; 3:275-86. [PMID: 17372656 DOI: 10.1039/b617545g] [Citation(s) in RCA: 65] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Current methods for phosphoproteome analysis have several limitations. First, most methods for phosphopeptide enrichment lack the specificity to truly purify phosphopeptides. Second, fragmentation spectra of phosphopeptides, in particular those of phosphoserine and phosphothreonine containing peptides, are often dominated by the loss of the phosphate group(s) and therefore lack the information required to identify the peptide sequence and the site of phosphorylation, and third, sequence database search engines and statistical models for data validation are not optimized for the specific fragmentation properties of phosphorylated peptides. Consequently, phosphoproteomic data are characterized by large and unknown rates of false positive and false negative phosphorylation sites. Here we present an integrated chemical, mass spectrometric and computational strategy to improve the efficiency, specificity and confidence in the identification of phosphopeptides and their site(s) of phosphorylation. Phosphopeptides were isolated with high specificity through a simple derivatization procedure based on phosphoramidate chemistry. Identification of phosphopeptides, their site(s) of phosphorylation and the corresponding phosphoproteins was achieved by the optimization of the mass spectrometric data acquisition procedure, the computational tools for database searching and the data post processing. The strategy was applied to the mapping of phosphorylation sites of a purified transcription factor, dFOXO and for the global analysis of protein phosphorylation of Drosophila melanogaster Kc167 cells.
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Affiliation(s)
- Bernd Bodenmiller
- Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
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70
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Ndassa YM, Orsi C, Marto JA, Chen S, Ross MM. Improved immobilized metal affinity chromatography for large-scale phosphoproteomics applications. J Proteome Res 2006; 5:2789-99. [PMID: 17022650 DOI: 10.1021/pr0602803] [Citation(s) in RCA: 101] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Dysregulated protein phosphorylation is a primary culprit in multiple physiopathological states. Hence, although analysis of signaling cascades on a proteome-wide scale would provide significant insight into both normal and aberrant cellular function, such studies are simultaneously limited by sheer biological complexity and concentration dynamic range. In principle, immobilized metal affinity chromatography (IMAC) represents an ideal enrichment method for phosphoproteomics. However, anecdotal evidence suggests that this technique is not widely and successfully applied beyond analysis of simple standards, gel bands, and targeted protein immunoprecipitations. Here, we report significant improvements in IMAC-based methodology for enrichment of phosphopeptides from complex biological mixtures. Moreover, we provide detailed explanation for key variables that in our hands most influenced the outcome of these experiments. Our results indicate 5- to 10-fold improvement in recovery of singly- and multiply phosphorylated peptide standards in addition to significant improvement in the number of high-confidence phosphopeptide sequence assignments from global analysis of cellular lysate. In addition, we quantitatively track phosphopeptide recovery as a function of phosphorylation state, and provide guidance for impedance-matching IMAC column capacity with anticipated phosphopeptide content of complex mixtures. Finally, we demonstrate that our improved methodology provides for identification of phosphopeptide distributions that closely mimic physiological conditions.
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Affiliation(s)
- Yasmine M Ndassa
- Biophysics Program, Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Dana-Farber Cancer Institute, Boston, Massachusetts 02115, USA
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71
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Morandell S, Stasyk T, Grosstessner-Hain K, Roitinger E, Mechtler K, Bonn GK, Huber LA. Phosphoproteomics strategies for the functional analysis of signal transduction. Proteomics 2006; 6:4047-56. [PMID: 16791829 DOI: 10.1002/pmic.200600058] [Citation(s) in RCA: 107] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Protein phosphorylation is a key regulatory mechanism of cellular signalling processes. The analysis of phosphorylated proteins and the characterisation of phosphorylation sites under different biological conditions are some of the most challenging tasks in current proteomics research. Reduction of the sample complexity is one major step for the analysis of low-abundance kinase substrates, which can be achieved by various subcellular fractionation techniques. One strategy is the enrichment of phosphorylated proteins or peptides by immunoprecipitation or chromatography, e.g. immobilised metal affinity chromatography, prior to analysis. 2-DE gels are powerful tools for the analysis of phosphoproteins when combined with new multiplexing techniques like DIGE, phosphospecific stains, autoradiography or immunoblotting. In addition, several gel-free methods combining chromatography with highly sensitive MS have been successfully applied for the analysis of complex phosphoproteomes. Recently developed approaches like KESTREL or 'chemical genetics' and also protein microarrays offer new possibilities for the identification of specific kinase targets. This review summarises various strategies for the analyses of phosphoproteins with a special focus on the identification of novel kinase substrates.
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Affiliation(s)
- Sandra Morandell
- Division Cell Biology, Biocenter, Innsbruck Medical University, Innsbruck, Austria
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72
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Schmelzle K, White FM. Phosphoproteomic approaches to elucidate cellular signaling networks. Curr Opin Biotechnol 2006; 17:406-14. [PMID: 16806894 DOI: 10.1016/j.copbio.2006.06.004] [Citation(s) in RCA: 116] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2006] [Revised: 05/01/2006] [Accepted: 06/07/2006] [Indexed: 01/21/2023]
Abstract
Protein phosphorylation is crucial in the regulation of signaling pathways that control various biological responses. Recent progress in diverse methodologies to investigate protein phosphorylation in complex biological samples has resulted in more rapid, detailed and quantitative analyses of signaling networks. In particular, advances in mass spectrometry (MS) have enabled the identification and quantification of thousands of both known and novel phosphorylation sites. Initial MS-based information can be complemented with a variety of recently developed and improved phosphoproteomic techniques. These include multiplexed microbead or kinase activity assays, flow cytometry based single-cell analysis, protein microarrays and interaction studies. The combination of multiple approaches, coupled with phenotypic response measurements, computational modeling and biochemical manipulations, will ultimately reveal the mechanistic regulation of signaling networks.
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Affiliation(s)
- Katrin Schmelzle
- Biological Engineering Division, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
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73
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Wang Y, Li R, Du D, Zhang C, Yuan H, Zeng R, Chen Z. Proteomic analysis reveals novel molecules involved in insulin signaling pathway. J Proteome Res 2006; 5:846-55. [PMID: 16602692 DOI: 10.1021/pr050391m] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The binding of insulin to its receptor triggers a signaling cascade regulated by protein complexes via tyrosine phosphorylation events on a multitude of associated proteins. To search novel phosphotyrosine proteins or associated proteins involved in insulin signaling pathway, we employed a method in which Rat1 cells stably expressing the human insulin receptor were stimulated with or without insulin and sub-fractionated prior to enrichment of phosphotyrosine proteins by immunoprecipitation and analysis by LC-MS/MS. Bioinformatic analysis and manual confirmation of peptide phosphorylation site assignments led to identification of 35 phosphotyrosine sites derived from 31 protein groups. Over 50% of these proteins were reported for the first time as tyrosine phosphorylated, including gigaxonin, XIAP and CDK10. In addition, we also found that calcium/calmodulin-dependent protein serine kinase (CASK), a key protein in protein-targeting and vesicle transport in neurons, forms a complex with two unidentified phosphotyrosine proteins pp100 and pp95 in response to insulin-stimulation, though CASK is not itself tyrosine phosphorylated. Furthermore, insulin was able to decrease CASK nuclear location, as well as down-regulate the expression of CASK targeted genes. Our results imply CASK as a novel joint knot connecting CASK-mediated pathways with the insulin signaling. Our data provide a wealth of information potentially paving the way to identify new components in the insulin signaling network.
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Affiliation(s)
- Yiguo Wang
- Key Laboratory of Proteomics, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 320 Yue Yang Road, Shanghai 200031, China
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74
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Kim JE, White FM. Quantitative analysis of phosphotyrosine signaling networks triggered by CD3 and CD28 costimulation in Jurkat cells. THE JOURNAL OF IMMUNOLOGY 2006; 176:2833-43. [PMID: 16493040 DOI: 10.4049/jimmunol.176.5.2833] [Citation(s) in RCA: 89] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
The mechanism by which stimulation of coreceptors such as CD28 contributes to full activation of TCR signaling pathways has been intensively studied, yet quantitative measurement of costimulation effects on functional TCR signaling networks has been lacking. In this study, phosphotyrosine networks triggered by CD3, CD28, or CD3 and CD28 costimulation were analyzed by site-specific quantitative phosphoproteomics, resulting in identification of 101 tyrosine and 3 threonine phosphorylation sites and quantification of 87 sites across four cell states. As expected, CD3 stimulation induced phosphorylation of CD3 chains and upstream components of TCR pathways such as Zap70, while CD28 stimulation induced phosphorylation of CD28, Vav-1, and other adaptor proteins including downstream of tyrosine kinase 1, Grb2-associated protein 2 (Grap2), and Wiskott-Aldrich syndrome protein. CD3 and CD28 costimulation induced a complex response including decreased threonine phosphorylation in the ERK1 and ERK2 activation loops and increased phosphorylation of selected tyrosine sites on ERK1/2, p38, phospholipase C-gamma, Src homology 2 domain-containing transforming protein 1, Grap2, and Vav-1, potentiating T cell activation. Hierarchical clustering and self-organizing maps were used to identify modules of coregulated phosphorylation sites within the network. Quantitative information in our study suggests quantitative and qualitative contribution by costimulation of CD28 on CD3-stimulated TCR signaling networks via enhanced phosphorylation of phospholipase C-gamma/Src homology 2 domain-containing transforming protein 1/Grap2/Vav-1 and their effects on downstream components including MAPKs.
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Affiliation(s)
- Ji-Eun Kim
- Biological Engineering Division, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
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75
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Moser K, White FM. Phosphoproteomic analysis of rat liver by high capacity IMAC and LC-MS/MS. J Proteome Res 2006; 5:98-104. [PMID: 16396499 DOI: 10.1021/pr0503073] [Citation(s) in RCA: 135] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Proper liver function is crucial for metabolism control and to clear toxic substances from the bloodstream. Many small-molecule therapeutics accumulate in the liver, negatively impacting liver function and often resulting in hepatotoxicity and cell death. Several analytical methods are currently utilized to evaluate hepatotoxicity and monitor liver function. To date, none of these methods have specifically targeted protein phosphorylation-mediated signal transduction pathways which should be altered in response to toxic effects of small molecule therapeutics. To develop novel assays to probe specific signaling pathways in the liver, identification and quantification of specific protein phosphorylation sites in this complex organ is necessary. Here, we have utilized an optimized immobilized metal affinity chromatography (IMAC) protocol to enrich phosphorylated peptides from a tryptic digest of proteins isolated from whole liver lysate. LC-MS/MS analysis of IMAC-enriched peptides resulted in the identification of more than 300 phosphorylation sites from over 200 proteins in rat liver, a significant advance over previously published analyses of the liver phosphoproteome. Previously characterized phosphorylation sites and potentially novel sites were identified in the current study, including sites on proteins implicated in metabolism regulation, transcription, translation, and canonical signaling pathways. Moreover, protein phosphorylation analysis was performed without prior fractionation of the sample, enabling analysis of small sample amounts while minimizing analysis time, potentially allowing for high-throughput assays to be performed with this methodology. From these data, it appears that this methodology can be used to identify new phosphorylation sites and, in combination with a stable isotope-labeling step, to investigate the effects of liver diseases, cancer and evaluate potential toxicology of new drug substances.
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Affiliation(s)
- Katrin Moser
- Biological Engineering Division, MIT, Cambridge, Massachusetts 02139, USA
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76
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Tao WA, Wollscheid B, O'Brien R, Eng JK, Li XJ, Bodenmiller B, Watts JD, Hood L, Aebersold R. Quantitative phosphoproteome analysis using a dendrimer conjugation chemistry and tandem mass spectrometry. Nat Methods 2005; 2:591-8. [PMID: 16094384 DOI: 10.1038/nmeth776] [Citation(s) in RCA: 257] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2005] [Accepted: 06/20/2005] [Indexed: 01/19/2023]
Abstract
We present a robust and general method for the identification and relative quantification of phosphorylation sites in complex protein mixtures. It is based on a new chemical derivatization strategy using a dendrimer as a soluble polymer support and tandem mass spectrometry (MS/MS). In a single step, phosphorylated peptides are covalently conjugated to a dendrimer in a reaction catalyzed by carbodiimide and imidazole. Modified phosphopeptides are released from the dendrimer via acid hydrolysis and analyzed by MS/MS. When coupled with an initial antiphosphotyrosine protein immunoprecipitation step and stable-isotope labeling, in a single experiment, we identified all known tyrosine phosphorylation sites within the immunoreceptor tyrosine-based activation motifs (ITAM) of the T-cell receptor (TCR) CD3 chains, and previously unknown phosphorylation sites on total 97 tyrosine phosphoproteins and their interacting partners in human T cells. The dynamic changes in phosphorylation were quantified in these proteins.
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Affiliation(s)
- W Andy Tao
- The Bindley Bioscience Center and Department of Biochemistry, Purdue University, West Lafayette, Indiana 47907, USA
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