Phosphopeptide fragmentation and analysis by mass spectrometry

The protein kinase complement of the human genome

Manning, G., Whyte, D. B., Martinez, R., Hunter, T., & Sudarsanam, S. (2002) · Science · doi:10.1126/science.1075762 · Cited by 8,145

Global, In Vivo, and Site-Specific Phosphorylation Dynamics in Signaling Networks

Olsen, J. V., Blagoev, B., Gnad, F., Macek, B., Kumar, C., Mortensen, P., & Mann, M. (2006) · Cell · doi:10.1016/j.cell.2006.09.026 · Cited by 3,499

Letter to the editors

Roepstorff, P., & Fohlman, J. (1984) · Biological Mass Spectrometry · doi:10.1002/bms.1200111109 · Cited by 2,633

Peptide and protein sequence analysis by electron transfer dissociation mass spectrometry

Syka, J. E. P., Coon, J. J., Schroeder, M. J., Shabanowitz, J., & Hunt, D. F. (2004) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0402700101 · Cited by 2,370

Electron Capture Dissociation of Multiply Charged Protein Cations. A Nonergodic Process

Zubarev, R. A., Kelleher, N. L., & McLafferty, F. W. (1998) · Journal of the American Chemical Society · doi:10.1021/ja973478k · Cited by 1,881

Phosphoproteome analysis by mass spectrometry and its application to Saccharomyces cerevisiae

Ficarro, S. B., McCleland, M. L., Stukenberg, P. T., Burke, D. J., Ross, M. M., Shabanowitz, J., Hunt, D. F., & White, F. M. (2002) · Nature Biotechnology · doi:10.1038/nbt0302-301 · Cited by 1,636

A probability-based approach for high-throughput protein phosphorylation analysis and site localization

Beausoleil, S. A., Villén, J., Gerber, S. A., Rush, J., & Gygi, S. P. (2006) · Nature Biotechnology · doi:10.1038/nbt1240 · Cited by 1,577

Large-scale characterization of HeLa cell nuclear phosphoproteins

Beausoleil, S. A., Jedrychowski, M., Schwartz, D., Elias, J. E., Villén, J., Li, J., Cohn, M. A., Cantley, L. C., & Gygi, S. P. (2004) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0404720101 · Cited by 1,375

Immunoaffinity profiling of tyrosine phosphorylation in cancer cells

Rush, J., Moritz, A., Lee, K. A., Guo, A., Goss, V. L., Spek, E. J., Zhang, H., Zha, X.-M., Polakiewicz, R. D., & Comb, M. J. (2005) · Nature Biotechnology · doi:10.1038/nbt1046 · Cited by 1,124

Fragmentation pathways of protonated peptides

Paizs, B., & Suhai, S. (2005) · Mass Spectrometry Reviews · doi:10.1002/mas.20024 · Cited by 1,118

Contributions of mass spectrometry to peptide and protein structure

Biemann, K. (1988) · Biological Mass Spectrometry · doi:10.1002/bms.1200160119 · Cited by 1,015

Mobile and localized protons: a framework for understanding peptide dissociation

Wysocki, V. H., Tsaprailis, G., Smith, L. L., & Breci, L. A. (2000) · Journal of Mass Spectrometry · doi:10.1002/1096-9888(200012)35:12<1399::aid-jms86>3.0.co;2-r · Cited by 997

Electron Capture Dissociation for Structural Characterization of Multiply Charged Protein Cations

Zubarev, R. A., Horn, D. M., Fridriksson, E. K., Kelleher, N. L., Kruger, N. A., Lewis, M. A., Carpenter, B. K., & McLafferty, F. W. (2000) · Analytical Chemistry · doi:10.1021/ac990811p · Cited by 986

Selective Isolation at the Femtomole Level of Phosphopeptides from Proteolytic Digests Using 2D-NanoLC-ESI-MS/MS and Titanium Oxide Precolumns

Pinkse, M. W. H., Uitto, P. M., Hilhorst, M. J., Ooms, B., & Heck, A. J. R. (2004) · Analytical Chemistry · doi:10.1021/ac0498617 · Cited by 891

Enrichment analysis of phosphorylated proteins as a tool for probing the phosphoproteome

Oda, Y., Nagasu, T., & Chait, B. T. (2001) · Nature Biotechnology · doi:10.1038/86783 · Cited by 777

Quantitative Phosphoproteomics Applied to the Yeast Pheromone Signaling Pathway

Gruhler, A., Olsen, J. V., Mohammed, S., Mortensen, P., Færgeman, N. J., Mann, M., & Jensen, O. N. (2005) · Molecular & Cellular Proteomics · doi:10.1074/mcp.m400219-mcp200 · Cited by 763

A systematic approach to the analysis of protein phosphorylation

Zhou, H., Watts, J. D., & Aebersold, R. (2001) · Nature Biotechnology · doi:10.1038/86777 · Cited by 714

Quantitative Phosphoproteomics of Early Elicitor Signaling in Arabidopsis

Benschop, J. J., Mohammed, S., O'Flaherty, M., Heck, A. J. R., Slijper, M., & Menke, F. L. H. (2007) · Molecular & Cellular Proteomics · doi:10.1074/mcp.m600429-mcp200 · Cited by 676

The SCX/IMAC enrichment approach for global phosphorylation analysis by mass spectrometry

Villén, J., & Gygi, S. P. (2008) · Nature Protocols · doi:10.1038/nprot.2008.150 · Cited by 629

Analysis of phosphorylation sites on proteins from Saccharomyces cerevisiae by electron transfer dissociation (ETD) mass spectrometry

Chi, A., Huttenhower, C., Geer, L. Y., Coon, J. J., Syka, J. E. P., Bai, D. L., Shabanowitz, J., Burke, D. J., Troyanskaya, O. G., & Hunt, D. F. (2007) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0607084104 · Cited by 564

The role of electron capture dissociation in biomolecular analysis

Cooper, H. J., Håkansson, K., & Marshall, A. G. (2005) · Mass Spectrometry Reviews · doi:10.1002/mas.20014 · Cited by 514

Global proteomic profiling of phosphopeptides using electron transfer dissociation tandem mass spectrometry

Molina, H., Horn, D. M., Tang, N., Mathivanan, S., & Pandey, A. (2007) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0611217104 · Cited by 502

Mapping Sites of O-GlcNAc Modification Using Affinity Tags for Serine and Threonine Post-translational Modifications

Wells, L., Vosseller, K., Cole, R. N., Cronshaw, J. M., Matunis, M. J., & Hart, G. W. (2002) · Molecular & Cellular Proteomics · doi:10.1074/mcp.m200048-mcp200 · Cited by 420

Analysis of receptor signaling pathways by mass spectrometry: Identification of Vav-2 as a substrate of the epidermal and platelet-derived growth factor receptors

Pandey, A., Podtelejnikov, A. V., Blagoev, B., Bustelo, X. R., Mann, M., & Lodish, H. F. (2000) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.97.1.179 · Cited by 406

Performance Characteristics of Electron Transfer Dissociation Mass Spectrometry

Good, D. M., Wirtala, M., McAlister, G. C., & Coon, J. J. (2007) · Molecular & Cellular Proteomics · doi:10.1074/mcp.m700073-mcp200 · Cited by 396

Analysis of phosphorylated proteins and peptides by mass spectrometry

McLachlin, D. T., & Chait, B. T. (2001) · Current Opinion in Chemical Biology · doi:10.1016/s1367-5931(00)00250-7 · Cited by 382

A Neutral Loss Activation Method for Improved Phosphopeptide Sequence Analysis by Quadrupole Ion Trap Mass Spectrometry

Schroeder, M. J., Shabanowitz, J., Schwartz, J. C., Hunt, D. F., & Coon, J. J. (2004) · Analytical Chemistry · doi:10.1021/ac0497104 · Cited by 376

Supplemental Activation Method for High-Efficiency Electron-Transfer Dissociation of Doubly Protonated Peptide Precursors

Swaney, D. L., McAlister, G. C., Wirtala, M., Schwartz, J. C., Syka, J. E. P., & Coon, J. J. (2007) · Analytical Chemistry · doi:10.1021/ac061457f · Cited by 363

Characterization of phosphoproteins from electrophoretic gels by nanoscale Fe(III) affinity chromatography with off-line mass spectrometry analysis

Stensballe, A., Andersen, S., & Jensen, O. N. (2001) · PROTEOMICS · doi:10.1002/1615-9861(200102)1:2<207::aid-prot207>3.0.co;2-3 · Cited by 362

Electron-capture dissociation tandem mass spectrometry

Zubarev, R. A. (2004) · Current Opinion in Biotechnology · doi:10.1016/j.copbio.2003.12.002 · Cited by 360

Phosphorylation Analysis by Mass Spectrometry

Steen, H., Jebanathirajah, J. A., Rush, J., Morrice, N., & Kirschner, M. W. (2006) · Molecular & Cellular Proteomics · doi:10.1074/mcp.m500135-mcp200 · Cited by 349

Electron capture dissociation of singly and multiply phosphorylated peptides

Stensballe, A., Jensen, O. N., Olsen, J. V., Haselmann, K. F., & Zubarev, R. A. (2000) · Rapid Communications in Mass Spectrometry · doi:10.1002/1097-0231(20001015)14:19<1793::aid-rcm95>3.0.co;2-q · Cited by 348

State‐of‐the‐art in phosphoproteomics

Reinders, J., & Sickmann, A. (2005) · PROTEOMICS · doi:10.1002/pmic.200401289 · Cited by 346

Hydrophilic Interaction Chromatography Reduces the Complexity of the Phosphoproteome and Improves Global Phosphopeptide Isolation and Detection

McNulty, D. E., & Annan, R. S. (2008) · Molecular & Cellular Proteomics · doi:10.1074/mcp.m700543-mcp200 · Cited by 345

Toward a general mechanism of electron capture dissociation

Syrstad, E. A., & Turecček, F. (2005) · Journal of the American Society for Mass Spectrometry · doi:10.1016/j.jasms.2004.11.001 · Cited by 325

Phosphoprotein Isotope-Coded Affinity Tag Approach for Isolating and Quantitating Phosphopeptides in Proteome-Wide Analyses

Goshe, M. B., Conrads, T. P., Panisko, E. A., Angell, N. H., Veenstra, T. D., & Smith, R. D. (2001) · Analytical Chemistry · doi:10.1021/ac010081x · Cited by 318

Phosphopeptide/Phosphoprotein Mapping by Electron Capture Dissociation Mass Spectrometry

Shi, S. D.-H., Hemling, M. E., Carr, S. A., Horn, D. M., Lindh, I., & McLafferty, F. W. (2001) · Analytical Chemistry · doi:10.1021/ac000703z · Cited by 316

Improved peptide identification in proteomics by two consecutive stages of mass spectrometric fragmentation

Olsen, J. V., & Mann, M. (2004) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0405549101 · Cited by 313

Decision tree–driven tandem mass spectrometry for shotgun proteomics

Swaney, D. L., McAlister, G. C., & Coon, J. J. (2008) · Nature Methods · doi:10.1038/nmeth.1260 · Cited by 312

Phosphopeptide Analysis by Matrix-Assisted Laser Desorption Time-of-Flight Mass Spectrometry

Annan, R. S., & Carr, S. A. (1996) · Analytical Chemistry · doi:10.1021/ac960221g · Cited by 310

Selective Detection and Sequencing of Phosphopeptides at the Femtomole Level by Mass Spectrometry

Carr, S. A., Huddleston, M. J., & Annan, R. S. (1996) · Analytical Biochemistry · doi:10.1006/abio.1996.0313 · Cited by 305

Fragmentation of phosphopeptides in an ion trap mass spectrometer

DeGnore, J. P., & Qin, J. (1998) · Journal of the American Society for Mass Spectrometry · doi:10.1016/s1044-0305(98)00088-9 · Cited by 257

Selective detection of phosphopeptides in complex mixtures by electrospray liquid chromatography/mass spectrometry

Huddleston, M. J., Annan, R. S., Bean, M. F., & Carr, S. A. (1993) · Journal of the American Society for Mass Spectrometry · doi:10.1016/1044-0305(93)80049-5 · Cited by 242

Phosphospecific proteolysis for mapping sites of protein phosphorylation

Knight, Z. A., Schilling, B., Row, R. H., Kenski, D. M., Gibson, B. W., & Shokat, K. M. (2003) · Nature Biotechnology · doi:10.1038/nbt863 · Cited by 239

Statistical Characterization of the Charge State and Residue Dependence of Low-Energy CID Peptide Dissociation Patterns

Huang, Y., Triscari, J. M., Tseng, G. C., Pasa-Tolic, L., Lipton, M. S., Smith, R. D., & Wysocki, V. H. (2005) · Analytical Chemistry · doi:10.1021/ac0480949 · Cited by 227

Improved β-Elimination-Based Affinity Purification Strategy for Enrichment of Phosphopeptides

McLachlin, D. T., & Chait, B. T. (2003) · Analytical Chemistry · doi:10.1021/ac034989u · Cited by 225

Electron Capture Dissociation Initiates a Free Radical Reaction Cascade

Leymarie, N., Costello, C. E., & O'Connor, P. B. (2003) · Journal of the American Chemical Society · doi:10.1021/ja028831n · Cited by 220

Application of electron transfer dissociation (ETD) for the analysis of posttranslational modifications

Wiesner, J., Premsler, T., & Sickmann, A. (2008) · PROTEOMICS · doi:10.1002/pmic.200800329 · Cited by 219

NCα Bond Dissociation Energies and Kinetics in Amide and Peptide Radicals. Is the Dissociation a Non-ergodic Process?

Tureček, F. (2003) · Journal of the American Chemical Society · doi:10.1021/ja021323t · Cited by 205

Phosphoric Acid as a Matrix Additive for MALDI MS Analysis of Phosphopeptides and Phosphoproteins

Kjellström, S., & Jensen, O. N. (2004) · Analytical Chemistry · doi:10.1021/ac0400257 · Cited by 194

Analysis of Protein Phosphorylation by a Combination of Elastase Digestion and Neutral Loss Tandem Mass Spectrometry

Schlosser, A., Pipkorn, R., Bossemeyer, D., & Lehmann, W. D. (2001) · Analytical Chemistry · doi:10.1021/ac000826j · Cited by 176

Implementation of Electron-Transfer Dissociation on a Hybrid Linear Ion Trap−Orbitrap Mass Spectrometer

McAlister, G. C., Phanstiel, D., Good, D. M., Berggren, W. T., & Coon, J. J. (2007) · Analytical Chemistry · doi:10.1021/ac070020k · Cited by 173

Highly Robust, Automated, and Sensitive Online TiO2-Based Phosphoproteomics Applied To Study Endogenous Phosphorylation in Drosophila melanogaster

Pinkse, M. W. H., Mohammed, S., Gouw, J. W., van Breukelen, B., Vos, H. R., & Heck, A. J. R. (2008) · Journal of Proteome Research · doi:10.1021/pr700605z · Cited by 168

Advances in the Analysis of Protein Phosphorylation

Paradela, A., & Albar, J. P. (2008) · Journal of Proteome Research · doi:10.1021/pr7006544 · Cited by 164

Identification of Phosphorylation Sites in Proteins Separated by Polyacrylamide Gel Electrophoresis

Zhang, X., Herring, C. J., Romano, P. R., Szczepanowska, J., Brzeska, H., Hinnebusch, A. G., & Qin, J. (1998) · Analytical Chemistry · doi:10.1021/ac971207m · Cited by 162

Electron Transfer versus Proton Transfer in Gas-Phase Ion/Ion Reactions of Polyprotonated Peptides

Gunawardena, H. P., He, M., Chrisman, P. A., Pitteri, S. J., Hogan, J. M., Hodges, B. D. M., & McLuckey, S. A. (2005) · Journal of the American Chemical Society · doi:10.1021/ja0526057 · Cited by 160

Evaluation of Gas-Phase Rearrangement and Competing Fragmentation Reactions on Protein Phosphorylation Site Assignment Using Collision Induced Dissociation-MS/MS and MS3

Palumbo, A. M., & Reid, G. E. (2008) · Analytical Chemistry · doi:10.1021/ac801768s · Cited by 159

Identification and Characterization of Posttranslational Modifications of Proteins by MALDI Ion Trap Mass Spectrometry

Qin, J., & Chait, B. T. (1997) · Analytical Chemistry · doi:10.1021/ac970489n · Cited by 157

Electrospray tandem mass spectrometric studies of phosphopeptides and phosphopeptide analogues

Tholey, A., Reed, J., & Lehmann, W. D. (1999) · Journal of Mass Spectrometry · Cited by 152

A Proteomics Grade Electron Transfer Dissociation-Enabled Hybrid Linear Ion Trap-Orbitrap Mass Spectrometer

McAlister, G. C., Berggren, W. T., Griep‐Raming, J., Horning, S. R., Makarov, A., Phanstiel, D., Stafford, G. C., Swaney, D. L., Syka, J. E. P., Zabrouskov, V., et al. (2008) · Journal of Proteome Research · doi:10.1021/pr800264t · Cited by 146

Straightforward ladder sequencing of peptides using a Lys-N metalloendopeptidase

Taouatas, N., Drugan, M. M., Heck, A. J. R., & Mohammed, S. (2008) · Nature Methods · doi:10.1038/nmeth.1204 · Cited by 141

An Approach to Locate Phosphorylation Sites in a Phosphoprotein: Mass Mapping by Combining Specific Enzymatic Degradation with Matrix-Assisted Laser Desorption/Ionization Mass Spectrometry

Liao, P., Leykam, J. F., Andrews, P., Gage, D. A., & Allison, J. (1994) · Analytical Biochemistry · doi:10.1006/abio.1994.1224 · Cited by 140

An Integrated, Directed Mass Spectrometric Approach for In-depth Characterization of Complex Peptide Mixtures

Schmidt, A., Gehlenborg, N., Bodenmiller, B., Mueller, L. N., Campbell, D., Mueller, M., Aebersold, R. H., & Domon, B. (2008) · Molecular & Cellular Proteomics · doi:10.1074/mcp.m700498-mcp200 · Cited by 140

On-Line LC−MS Approach Combining Collision-Induced Dissociation (CID), Electron-Transfer Dissociation (ETD), and CID of an Isolated Charge-Reduced Species for the Trace-Level Characterization of Proteins with Post-Translational Modifications

Wu, S., Hühmer, A. F. R., Hao, Z., & Karger, B. L. (2007) · Journal of Proteome Research · doi:10.1021/pr070313u · Cited by 136

Implementation of Ion/Ion Reactions in a Quadrupole/Time-of-Flight Tandem Mass Spectrometer

Xia, Y., Chrisman, P. A., Erickson, D. E., Liu, J., Liang, X., Londry, F. A., Yang, M. J., & McLuckey, S. A. (2006) · Analytical Chemistry · doi:10.1021/ac0606296 · Cited by 128

Electron-Transfer Ion/Ion Reactions of Doubly Protonated Peptides: Effect of Elevated Bath Gas Temperature

Pitteri, S. J., Chrisman, P. A., & McLuckey, S. A. (2005) · Analytical Chemistry · doi:10.1021/ac050666h · Cited by 124

Highly Efficient Phosphopeptide Enrichment by Calcium Phosphate Precipitation Combined with Subsequent IMAC Enrichment

Zhang, X., Ye, J., Jensen, O. N., & Roepstorff, P. (2007) · Molecular & Cellular Proteomics · doi:10.1074/mcp.m700278-mcp200 · Cited by 121

Improved low‐energy electron injection systems for high rate electron capture dissociation in Fourier transform ion cyclotron resonance mass spectrometry

Tsybin, Y. O., Håkansson, P., Budnik, B., Haselmann, K. F., Kjeldsen, F., Gorshkov, M. V., & Zubarev, R. A. (2001) · Rapid Communications in Mass Spectrometry · doi:10.1002/rcm.448 · Cited by 115

Comprehensive Comparison of Collision Induced Dissociation and Electron Transfer Dissociation

Molina, H., Matthiesen, R., Kandasamy, K., & Pandey, A. (2008) · Analytical Chemistry · doi:10.1021/ac8007785 · Cited by 110

Automated Identification and Quantification of Protein Phosphorylation Sites by LC/MS on a Hybrid Triple Quadrupole Linear Ion Trap Mass Spectrometer

Williamson, B. L., Marchese, J., & Morrice, N. A. (2005) · Molecular & Cellular Proteomics · doi:10.1074/mcp.m500210-mcp200 · Cited by 108

Mechanistic Insights into the Multistage Gas-Phase Fragmentation Behavior of Phosphoserine- and Phosphothreonine-Containing Peptides

Palumbo, A. M., Tepe, J. J., & Reid, G. E. (2008) · Journal of Proteome Research · doi:10.1021/pr0705136 · Cited by 106

Peptide Sequencing and Characterization of Post-Translational Modifications by Enhanced Ion-Charging and Liquid Chromatography Electron-Transfer Dissociation Tandem Mass Spectrometry

Kjeldsen, F., Giessing, A. M. B., Ingrell, C. R., et al. (2007) · Analytical Chemistry · doi:10.1021/ac701700g · Cited by 104

Leaving group and gas phase neighboring group effects in the side chain losses from protonated serine and its derivatives

Reid, G. E., Simpson, R. J., & O’Hair, R. A. J. (2000) · Journal of the American Society for Mass Spectrometry · doi:10.1016/s1044-0305(00)00189-6 · Cited by 93

SLoMo: Automated Site Localization of Modifications from ETD/ECD Mass Spectra

Bailey, C. M., Sweet, S. M. M., Cunningham, D. L., Zeller, M., Heath, J. K., & Cooper, H. J. (2009) · Journal of Proteome Research · doi:10.1021/pr800917p · Cited by 91

PhosphoScore: An Open-Source Phosphorylation Site Assignment Tool for MSn Data

Ruttenberg, B. E., Pisitkun, T., Knepper, M. A., & Hoffert, J. D. (2008) · Journal of Proteome Research · doi:10.1021/pr800169k · Cited by 87

Large Scale Localization of Protein Phosphorylation by Use of Electron Capture Dissociation Mass Spectrometry

Sweet, S. M. M., Bailey, C. M., Cunningham, D. L., Heath, J. K., & Cooper, H. J. (2009) · Molecular & Cellular Proteomics · doi:10.1074/mcp.m800451-mcp200 · Cited by 85

Evaluation of the utility of neutral‐loss‐dependent MS3 strategies in large‐scale phosphorylation analysis

Villén, J., Beausoleil, S. A., & Gygi, S. P. (2008) · PROTEOMICS · doi:10.1002/pmic.200800283 · Cited by 83

Secondary fragmentation of linear peptides in electron capture dissociation

Cooper, H. J., Hudgins, R. R., Håkansson, K., & Marshall, A. G. (2003) · International Journal of Mass Spectrometry · doi:10.1016/s1387-3806(03)00202-1 · Cited by 82

Strong Cation Exchange-based Fractionation of Lys-N-generated Peptides Facilitates the Targeted Analysis of Post-translational Modifications

Taouatas, N., Altelaar, M. A. F., Drugan, M. M., Helbig, A. O., Mohammed, S., & Heck, A. J. R. (2008) · Molecular & Cellular Proteomics · doi:10.1074/mcp.m800285-mcp200 · Cited by 79

Online Automated in Vivo Zebrafish Phosphoproteomics: From Large-Scale Analysis Down to a Single Embryo

Lemeer, S., Pinkse, M. W. H., Mohammed, S., van Breukelen, B., den Hertog, J., Slijper, M., & Heck, A. J. R. (2008) · Journal of Proteome Research · doi:10.1021/pr700667w · Cited by 78

Enhancement of the Efficiency of Phosphoproteomic Identification by Removing Phosphates after Phosphopeptide Enrichment

Ishihama, Y., Wei, F., Aoshima, K., Sato, T., Kuromitsu, J., & Oda, Y. (2007) · Journal of Proteome Research · doi:10.1021/pr060452w · Cited by 77

Effects of Cation Charge-Site Identity and Position on Electron-Transfer Dissociation of Polypeptide Cations

Xia, Y., Gunawardena, H. P., Erickson, D. E., & McLuckey, S. A. (2007) · Journal of the American Chemical Society · doi:10.1021/ja0736764 · Cited by 75

Comparison of MS2-Only, MSA, and MS2/MS3 Methodologies for Phosphopeptide Identification

Ulintz, P., Yocum, A. K., Bodenmiller, B., Aebersold, R. H., Andrews, P., & Nesvizhskii, A. I. (2008) · Journal of Proteome Research · doi:10.1021/pr800535h · Cited by 74

Combined Enzymatic and Data Mining Approaches for Comprehensive Phosphoproteome Analyses

Marcantonio, M., Trost, M., Courcelles, M., Desjardins, M., & Thibault, P. (2007) · Molecular & Cellular Proteomics · doi:10.1074/mcp.m700383-mcp200 · Cited by 67

Motif-Specific Sampling of Phosphoproteomes

Ruse, C. I., McClatchy, D. B., Lu, B., Cociorva, D., Motoyama, A., Park, S. K., & Yates, J. R. (2008) · Journal of Proteome Research · doi:10.1021/pr800147u · Cited by 60

Comparative Phosphoproteomics of Zebrafish Fyn/Yes Morpholino Knockdown Embryos*S

Lemeer, S., Jopling, C., Gouw, J., Mohammed, S., Heck, A., Slijper, M., & den Hertog, J. (2008) · Molecular & Cellular Proteomics · doi:10.1074/mcp.m800081-mcp200 · Cited by 58

An Automated Platform for Analysis of Phosphoproteomic Datasets: Application to Kidney Collecting Duct Phosphoproteins

Hoffert, J. D., Wang, G., Pisitkun, T., Shen, R., & Knepper, M. A. (2007) · Journal of Proteome Research · doi:10.1021/pr0701153 · Cited by 57

A Data-Mining Scheme for Identifying Peptide Structural Motifs Responsible for Different MS/MS Fragmentation Intensity Patterns

Huang, Y., Tseng, G. C., Yuan, S., Paša‐Tolić, L., Lipton, M. S. W., Smith, R. D., & Wysocki, V. H. (2007) · Journal of Proteome Research · doi:10.1021/pr070106u · Cited by 57

Straightforward and de Novo Peptide Sequencing by MALDI-MS/MS Using a Lys-N Metalloendopeptidase

Boersema, P. J., Taouatas, N., Altelaar, M. A. F., Gouw, J. W., Ross, P. L., Pappin, D., Heck, A. J. R., & Mohammed, S. (2008) · Molecular & Cellular Proteomics · doi:10.1074/mcp.m800249-mcp200 · Cited by 53

Multiplexed Proteomics Mapping of Yeast RNA Polymerase II and III Allows Near-Complete Sequence Coverage and Reveals Several Novel Phosphorylation Sites

Mohammed, S., Lorenzen, K., Kerkhoven, R., van Breukelen, B., Vannini, A., Cramer, P., & Heck, A. J. R. (2008) · Analytical Chemistry · doi:10.1021/ac7024283 · Cited by 50

Fast Multiple Electron Capture Dissociation in a Linear Radio Frequency Quadrupole Ion Trap

Satake, H., Hasegawa, H., Hirabayashi, A., Hashimoto, Y., Baba, T., & Masuda, K. (2007) · Analytical Chemistry · doi:10.1021/ac071462z · Cited by 47

Taking aim at shotgun phosphoproteomics

Hoffert, J. D., & Knepper, M. A. (2007) · Analytical Biochemistry · doi:10.1016/j.ab.2007.11.023 · Cited by 47

Performance of a quadrupole ion trap mass spectrometer adapted for ion/ion reaction studies

Reid, G. E., Wells, J. M., Badman, E. R., & McLuckey, S. A. (2002) · International Journal of Mass Spectrometry · doi:10.1016/s1387-3806(02)00984-3 · Cited by 45

Metal Oxide-Based Enrichment Combined with Gas-Phase Ion-Electron Reactions for Improved Mass Spectrometric Characterization of Protein Phosphorylation

Kweon, H. K., & Håkansson, K. (2008) · Journal of Proteome Research · doi:10.1021/pr070386d · Cited by 45

Investigating MS2/MS3 Matching Statistics

Ulintz, P., Bodenmiller, B., Andrews, P., Aebersold, R. H., & Nesvizhskii, A. I. (2007) · Molecular & Cellular Proteomics · doi:10.1074/mcp.m700128-mcp200 · Cited by 40

PhosphoScan: A Probability-Based Method for Phosphorylation Site Prediction Using MS2/MS3 Pair Information

Wan, Y., Cripps, D., Thomas, S. N., Campbell, P., Ambulos, N. P., Chen, T., & Yang, A. J. (2008) · Journal of Proteome Research · doi:10.1021/pr700773p · Cited by 34

Studies on the dephosphorylation of phosphotyrosine-containing peptides during post-source decay in matrix-assisted laser desorption/ionization

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