Protein Analysis by Shotgun/Bottom-up Proteomics

Cleavage of Structural Proteins during the Assembly of the Head of Bacteriophage T4

LAEMMLI, U. K. (1970) · Nature · doi:10.1038/227680a0 · Cited by 249,961 · see citing works

Controlling the False Discovery Rate: A Practical and Powerful Approach to Multiple Testing

Benjamini, Y., & Hochberg, Y. (1995) · Journal of the Royal Statistical Society Series B: Statistical Methodology · doi:10.1111/j.2517-6161.1995.tb02031.x · Cited by 109,482 · see citing works

Short-Term Effects of Nose-Only Cigarette Smoke Exposure on Glutathione Redox Homeostasis, Cytochrome P450 1A1/2 and Respiratory Enzyme Activities in Mice Tissues

Raza, H., John, A., & Nemmar, A. (2013) · Cellular Physiology and Biochemistry · doi:10.1159/000350087 · Cited by 47,311 · see citing works

Initial sequencing and analysis of the human genome

International Human Genome Sequencing Consortium, Whitehead Institute for Biomedical Research, C. F. G. R., Lander, E. S., Linton, L. M., Birren, B., Nusbaum, C., Zody, M. C., Baldwin, J., Devon, K., Dewar, K., et al. (2001) · Nature · doi:10.1038/35057062 · Cited by 24,216 · see citing works

High resolution two-dimensional electrophoresis of proteins.

O’Farrell, P. H. (1975) · Journal of Biological Chemistry · doi:10.1016/s0021-9258(19)41496-8 · Cited by 19,248 · see citing works

MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification

Cox, J., & Mann, M. (2008) · Nature Biotechnology · doi:10.1038/nbt.1511 · Cited by 14,855 · see citing works

The sequence of the human genome

Venter, J. C., Adams, M. D., Myers, E. W., Li, P. W., Mural, R. J., Sutton, G. G., Smith, H. O., Yandell, M., Evans, C. A., Holt, R. A., et al. (2001) · Science · doi:10.1126/science.1058040 · Cited by 13,909 · see citing works

Statistical significance for genomewide studies

Storey, J. D., & Tibshirani, R. (2003) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1530509100 · Cited by 9,692 · see citing works

Mass spectrometric sequencing of proteins silver-stained polyacrylamide gels.

Shevchenko, A., Wilm, M., Vorm, O., & Mann, M. F. (1996) · Analytical Chemistry · doi:10.1021/ac950914h · Cited by 9,047 · see citing works

The language of covalent histone modifications

Strahl, B. D., & Allis, C. D. (2000) · Nature · doi:10.1038/47412 · Cited by 8,679 · see citing works

Universal sample preparation method for proteome analysis

Wiśniewski, J. R., Zougman, A., Nagaraj, N., & Mann, M. (2009) · Nature Methods · doi:10.1038/nmeth.1322 · Cited by 8,352 · see citing works

Mass spectrometry-based proteomics

Aebersold, R., & Mann, M. (2003) · Nature · doi:10.1038/nature01511 · Cited by 6,955 · see citing works

The Sequence of the Human Genome

Venter, J., Adams, M., Myers, E., Li, P. W., Mural, R., Sutton, G., Smith, H., Yandell, M., Evans, C., Holt, R., et al. (2001) · Science · doi:10.1373/clinchem.2014.237016 · Cited by 6,779 · see citing works

Biomarkers and surrogate endpoints: Preferred definitions and conceptual framework

Biomarkers Definitions Working Group (2001) · Clinical Pharmacology & Therapeutics · doi:10.1067/mcp.2001.113989 · Cited by 6,771 · see citing works

An approach to correlate tandem mass spectral data of peptides with amino acid sequences in a protein database

Eng, J. K., McCormack, A. L., & Yates, J. R. (1994) · Journal of the American Society for Mass Spectrometry · doi:10.1016/1044-0305(94)80016-2 · Cited by 6,484 · see citing works

A novel genetic system to detect protein–protein interactions

Fields, S., & Song, O.-K. (1989) · Nature · doi:10.1038/340245a0 · Cited by 6,152 · see citing works

The Genome Sequence of Drosophila melanogaster

Adams, M. D., Celniker, S., Holt, R. A., Evans, C. A., Gocayne, J. D., Amanatides, P. G., Scherer, S. E., Li, P. W., Hoskins, R. A., Galle, R. F., et al. (2000) · Science · doi:10.1126/science.287.5461.2185 · Cited by 5,902 · see citing works

Stable isotope labeling by amino acids in cell culture, SILAC, as a simple and accurate approach to expression proteomics

Ong, S.-E., Blagoev, B., Kratchmarova, I., Kristensen, D. B., Steen, H., Pandey, A., & Mann, M. (2002) · Molecular & Cellular Proteomics · doi:10.1074/mcp.m200025-mcp200 · Cited by 5,574 · see citing works

Andromeda: A Peptide Search Engine Integrated into the MaxQuant Environment

Cox, J., Neuhauser, N., Michalski, A., Scheltema, R. A., Olsen, J. V., & Mann, M. (2011) · Journal of Proteome Research · doi:10.1021/pr101065j · Cited by 5,350 · see citing works

Empirical statistical model to estimate the accuracy of peptide identifications made by MS/MS and database search.

Keller, A., Nesvizhskii, A., Kolker, E., & Aebersold, R. (2002) · Analytical Chemistry · doi:10.1021/ac025747h · Cited by 4,970 · see citing works

A statistical model for identifying proteins by tandem mass spectrometry.

Nesvizhskii, A., Keller, A., Kolker, E., & Aebersold, R. (2003) · Analytical Chemistry · doi:10.1021/ac0341261 · Cited by 4,902 · see citing works

Large-scale analysis of the yeast proteome by multidimensional protein identification technology

Washburn, M. P., Wolters, D. A., & Yates, J. R. (2001) · Nature Biotechnology · doi:10.1038/85686 · Cited by 4,759 · see citing works

Functional organization of the yeast proteome by systematic analysis of protein complexes

Gavin, A., Böesche, M., Krause, R., Grandi, P., Marzioch, M., Bauer, A., Schultz, J., Rick, J. M., Michon, A., Cruciat, C., et al. (2002) · Nature · doi:10.1038/415141a · Cited by 4,729 · see citing works

A comprehensive analysis of protein–protein interactions in Saccharomyces cerevisiae

Uetz, P., Giot, L., Cagney, G., Mansfield, T. A., Judson, R. S., Knight, J. R., Lockshon, D., Narayan, V., Srinivasan, M., Pochart, P., et al. (2000) · Nature · doi:10.1038/35001009 · Cited by 4,706 · see citing works

Skyline: an open source document editor for creating and analyzing targeted proteomics experiments

MacLean, B., Tomazela, D. M., Shulman, N., Chambers, M., Finney, G. L., Frewen, B., Kern, R., Tabb, D. L., Liebler, D. C., & MacCoss, M. J. (2010) · Bioinformatics · doi:10.1093/bioinformatics/btq054 · Cited by 4,697 · see citing works

Quantitative analysis of complex protein mixtures using isotope-coded affinity tags

Gygi, S. P., Rist, B., Gerber, S. A., Turecek, F., Gelb, M. H., & Aebersold, R. (1999) · Nature Biotechnology · doi:10.1038/13690 · Cited by 4,683 · see citing works

Genome Sequence of the Nematode C. elegans : A Platform for Investigating Biology

Berg, J. (1998) · Science · doi:10.1126/science.282.5396.2012 · Cited by 4,458 · see citing works

The Human Plasma Proteome

Anderson, N. L., & Anderson, N. G. (2002) · Molecular & Cellular Proteomics · doi:10.1074/mcp.r200007-mcp200 · Cited by 4,414 · see citing works

Multiplexed protein quantitation in Saccharomyces cerevisiae using amine-reactive isobaric tagging reagents

Ross, P. L., Huang, Y. N., Marchese, J. N., Williamson, B., Parker, K., Hattan, S., Khainovski, N., Pillai, S., Dey, S., Daniels, S., et al. (2004) · Molecular & Cellular Proteomics · doi:10.1074/mcp.m400129-mcp200 · Cited by 4,401 · see citing works

Lysine acetylation targets protein complexes and co-regulates major cellular functions

Choudhary, C., Kumar, C., Gnad, F., Nielsen, M. L., Rehman, M., Walther, T. C., Olsen, J. V., & Mann, M. (2009) · Science · doi:10.1126/science.1175371 · Cited by 4,040 · see citing works

Target-decoy search strategy for increased confidence in large-scale protein identifications by mass spectrometry

Elias, J. E., & Gygi, S. P. (2007) · Nature Methods · doi:10.1038/nmeth1019 · Cited by 3,925 · see citing works

Oncogenic kinase signalling.

Blume-Jensen, P., & Hunter, T. (2001) · Nature · doi:10.1038/35077225 · Cited by 3,738 · see citing works

Mechanisms Underlying Ubiquitination

Pickart, C. M. (2001) · Annual Review of Biochemistry · doi:10.1146/annurev.biochem.70.1.503 · Cited by 3,731 · see citing works

Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry

Ho, Y., Gruhler, A., Heilbut, A. M., Bader, G. D., Moore, L., Adams, S., Millar, A., Taylor, P. P., Bennett, K. L., Boutilier, K., et al. (2002) · Nature · doi:10.1038/415180a · Cited by 3,573 · see citing works

A comprehensive two-hybrid analysis to explore the yeast protein interactome

Ito, T., Chiba, T., Ozawa, R., Yoshida, M., Hattori, M., & Sakaki, Y. (2001) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.061034498 · Cited by 3,566 · see citing works

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

Olsen, J. V., Blagoev, B., Gnad, F., Maček, B., Kumar, C., Mortensen, P., & Mann, M. (2006) · Cell · doi:10.1016/j.cell.2006.09.026 · Cited by 3,484 · see citing works

Widespread changes in protein synthesis induced by microRNAs

Selbach, M., Schwanhäusser, B., Thierfelder, N., Fang, Z., Khanin, R., & Rajewsky, N. (2008) · Nature · doi:10.1038/nature07228 · Cited by 3,429 · see citing works

Towards a proteome-scale map of the human protein–protein interaction network

Rual, J.-F. M., Venkatesan, K., Hao, T., Hirozane-Kishikawa, T., Dricot, A., Li, N., Berriz, G. F., Gibbons, F. D., Dreze, M., Ayivi-Guedehoussou, N., et al. (2005) · Nature · doi:10.1038/nature04209 · Cited by 2,937 · see citing works

Global landscape of protein complexes in the yeast Saccharomyces cerevisiae

Krogan, N. J., Cagney, G., Yu, H., Zhong, G., Guo, X., Ignatchenko, A., Li, J., Pu, S., Datta, N., Tikuisis, A., et al. (2006) · Nature · doi:10.1038/nature04670 · Cited by 2,915 · see citing works

Targeted Data Extraction of the MS/MS Spectra Generated by Data-independent Acquisition: A New Concept for Consistent and Accurate Proteome Analysis

Gillet, L. C., Navarro, P., Tate, S., Röst, H., Selevsek, N., Reiter, L., Bonner, R., & Aebersold, R. (2012) · Molecular & Cellular Proteomics · doi:10.1074/mcp.o111.016717 · Cited by 2,877 · see citing works

A generic protein purification method for protein complex characterization and proteome exploration

Rigaut, G., Shevchenko, A., Rutz, B., Wilm, M., Mann, M., & Séraphin, B. (1999) · Nature Biotechnology · doi:10.1038/13732 · Cited by 2,707 · see citing works

ACETYLATION AND METHYLATION OF HISTONES AND THEIR POSSIBLE ROLE IN THE REGULATION OF RNA SYNTHESIS

Allfrey, V. G., Faulkner, R. D., & Mirsky, A. E. (1964) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.51.5.786 · Cited by 2,649 · see citing works

Signaling—2000 and Beyond

Hunter, T. (2000) · Cell · doi:10.1016/s0092-8674(00)81688-8 · Cited by 2,586 · see citing works

TANDEM: matching proteins with tandem mass spectra

Craig, R., & Beavis, R. C. (2004) · Bioinformatics · doi:10.1093/bioinformatics/bth092 · Cited by 2,553 · see citing works

Proteome survey reveals modularity of the yeast cell machinery

Gavin, A., Aloy, P., Grandi, P., Krause, R., Böesche, M., Marzioch, M., Rau, C., Jensen, L. J., Bastuck, S., Dümpelfeld, B., et al. (2006) · Nature · doi:10.1038/nature04532 · Cited by 2,544 · see citing works

A Model for Random Sampling and Estimation of Relative Protein Abundance in Shotgun Proteomics

Liu, H., Sadygov, R. G., & Yates, J. R. (2004) · Analytical Chemistry · doi:10.1021/ac0498563 · Cited by 2,486 · see citing works

Semi-supervised learning for peptide identification from shotgun proteomics datasets

Käll, L., Canterbury, J. D., Weston, J., Noble, W. S., & MacCoss, M. J. (2007) · Nature Methods · doi:10.1038/nmeth1113 · Cited by 2,424 · see citing works

A Human Protein-Protein Interaction Network: A Resource for Annotating the Proteome

Stelzl, U., Worm, U., Lalowski, M. M., Haenig, C., Brembeck, F. H., Goehler, H., Strödicke, M., Zenkner, M., Schoenherr, A., Koeppen, S., et al. (2005) · Cell · doi:10.1016/j.cell.2005.08.029 · Cited by 2,389 · see citing works

Tandem Mass Tags: A Novel Quantification Strategy for Comparative Analysis of Complex Protein Mixtures by MS/MS

Thompson, A., Schäfer, J., Kuhn, K., Kienle, S., Schwarz, J., Schmidt, G., Neumann, T., & Hamon, C. (2003) · Analytical Chemistry · doi:10.1021/ac0262560 · Cited by 2,386 · see citing works

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 · see citing works

A Protein Interaction Map of Drosophila melanogaster

Giot, L., Bader, J. S., Brouwer, C., Chaudhuri, A., Kuang, B., Li, Y., Hao, Y. L., Ooi, C., Godwin, B., Vitols, E., et al. (2003) · Science · doi:10.1126/science.1090289 · Cited by 2,266 · see citing works

Direct analysis of protein complexes using mass spectrometry

Link, A. J., Eng, J. K., Schieltz, D. M., Carmack, E., Mize, G. J., Morris, D. R., Garvik, B. M., & Yates, J. R. (1999) · Nature Biotechnology · doi:10.1038/10890 · Cited by 2,218 · see citing works

Difference gel electrophoresis. A single gel method for detecting changes in protein extracts

Ünlü, M., Morgan, M. E., & Minden, J. S. (1997) · Electrophoresis · doi:10.1002/elps.1150181133 · Cited by 2,180 · see citing works

Exponentially Modified Protein Abundance Index (emPAI) for Estimation of Absolute Protein Amount in Proteomics by the Number of Sequenced Peptides per Protein

Ishihama, Y., Oda, Y., Tabata, T., Sato, T., Nagasu, T., Rappsilber, J., & Mann, M. (2005) · Molecular & Cellular Proteomics · doi:10.1074/mcp.m500061-mcp200 · Cited by 2,055 · see citing works

Integrated Genomic and Proteomic Analyses of a Systematically Perturbed Metabolic Network

Ideker, T., Thorsson, V., Ranish, J. A., Christmas, R., Buhler, J., Eng, J. K., Bumgarner, R., Goodlett, D. R., Aebersold, R., & Hood, L. (2001) · Science · doi:10.1126/science.292.5518.929 · Cited by 2,050 · see citing works

Hydrophilic-interaction chromatography for the separation of peptides, nucleic acids and other polar compounds

Alpert, A. J. (1990) · Journal of Chromatography A · doi:10.1016/s0021-9673(00)96972-3 · Cited by 1,974 · see citing works

Regulation of cellular metabolism by protein lysine acetylation

Zhao, S., Xu, W., Jiang, W., Yu, W., Lin, Y., Zhang, T., Yao, J., Zhou, L., Zeng, Y., Li, H., et al. (2010) · Science · doi:10.1126/science.1179689 · Cited by 1,910 · see citing works

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 · see citing works

Analytical Properties of the Nanoelectrospray Ion Source

Wilm, M. S., & Mann, M. (1996) · Analytical Chemistry · doi:10.1021/ac9509519 · Cited by 1,871 · see citing works

Protein biomarker discovery and validation: the long and uncertain path to clinical utility

Rifai, N., Gillette, M. A., & Carr, S. A. (2006) · Nature Biotechnology · doi:10.1038/nbt1235 · Cited by 1,867 · see citing works

An Automated Multidimensional Protein Identification Technology for Shotgun Proteomics

Wolters, D. A., Washburn, M. P., & Yates, J. R. (2001) · Analytical Chemistry · doi:10.1021/ac010617e · Cited by 1,821 · see citing works

Absolute quantification of proteins and phosphoproteins from cell lysates by tandem MS

Gerber, S. A., Rush, J., Stemman, O., Kirschner, M. W., & Gygi, S. P. (2003) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0832254100 · Cited by 1,733 · see citing works

Quantitative mass spectrometry in proteomics: a critical review

Bantscheff, M., Schirle, M., Sweetman, G. M. A., Rick, J. M., & Küster, B. (2007) · Analytical and Bioanalytical Chemistry · doi:10.1007/s00216-007-1486-6 · Cited by 1,659 · see citing works

Biomarkers in Cancer Staging, Prognosis and Treatment Selection

Ludwig, J. A., & Weinstein, J. N. (2005) · Nature reviews. Cancer · doi:10.1038/nrc1739 · Cited by 1,655 · see citing works

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 · see citing works

A Map of the Interactome Network of the Metazoan C. elegans

Li, S., Armstrong, C. M., Bertin, N., Ge, H., Milstein, S., Boxem, M., Vidalain, P., Han, J.-D. J., Chesneau, A., Hao, T., et al. (2004) · Science · doi:10.1126/science.1091403 · Cited by 1,628 · see citing works

Scansite 2.0: proteome-wide prediction of cell signaling interactions using short sequence motifs

Obenauer, J. C. (2003) · Nucleic Acids Research · doi:10.1093/nar/gkg584 · Cited by 1,602 · see citing works

A proteomics approach to understanding protein ubiquitination

Peng, J., Schwartz, D., Elias, J. E., Thoreen, C. C., Cheng, D., Marsischky, G., Roelofs, J., Finley, D. J., & Gygi, S. P. (2003) · Nature Biotechnology · doi:10.1038/nbt849 · Cited by 1,601 · see citing works

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 · see citing works

Mass spectrometry–based proteomics turns quantitative

Ong, S.-E., & Mann, M. (2005) · Nature Chemical Biology · doi:10.1038/nchembio736 · Cited by 1,572 · see citing works

Parts per Million Mass Accuracy on an Orbitrap Mass Spectrometer via Lock Mass Injection into a C-trap

Olsen, J. V., de Godoy, L. M. F., Li, G., Maček, B., Mortensen, P., Pesch, R., Makarov, A., Lange, O., Horning, S. R., & Mann, M. (2005) · Molecular & Cellular Proteomics · doi:10.1074/mcp.t500030-mcp200 · Cited by 1,513 · see citing works

Highly Selective Enrichment of Phosphorylated Peptides from Peptide Mixtures Using Titanium Dioxide Microcolumns

Larsen, M. R., Thingholm, T. E., Jensen, O. N., Roepstorff, P., & Jørgensen, T. J. D. (2005) · Molecular & Cellular Proteomics · doi:10.1074/mcp.t500007-mcp200 · Cited by 1,478 · see citing works

Cycling of O-linked β-N-acetylglucosamine on nucleocytoplasmic proteins

Hart, G. W., Housley, M. P., & Slawson, C. (2007) · Nature · doi:10.1038/nature05815 · Cited by 1,418 · see citing works

Protein S-nitrosylation: a physiological signal for neuronal nitric oxide

Jaffrey, S. R., Erdjument‐Bromage, H., Ferris, C. D., Tempst, P., & Snyder, S. H. (2001) · Nature Cell Biology · doi:10.1038/35055104 · Cited by 1,402 · see citing works

Selected reaction monitoring for quantitative proteomics: a tutorial

Lange, V., Picotti, P., Domon, B., & Aebersold, R. H. (2008) · Molecular Systems Biology · doi:10.1038/msb.2008.61 · Cited by 1,396 · see citing works

Identification and quantification of N-linked glycoproteins using hydrazide chemistry, stable isotope labeling and mass spectrometry

Zhang, H., Li, X., Martin, D. B., & Aebersold, R. H. (2003) · Nature Biotechnology · doi:10.1038/nbt827 · Cited by 1,389 · see citing works

Large-scale characterization of HeLa cell nuclear phosphoproteins

Beausoleil, S. A., Jedrychowski, M. P., 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 1,376 · see citing works

DTASelect and Contrast: Tools for Assembling and Comparing Protein Identifications from Shotgun Proteomics

Tabb, D. L., McDonald, W. H., & Yates, J. R. (2002) · Journal of Proteome Research · doi:10.1021/pr015504q · Cited by 1,369 · see citing works

Multiplex peptide stable isotope dimethyl labeling for quantitative proteomics

Boersema, P. J., Raijmakers, R., Lemeer, S., Mohammed, S., & Heck, A. J. R. (2009) · Nature Protocols · doi:10.1038/nprot.2009.21 · Cited by 1,359 · see citing works

The Orbitrap: a new mass spectrometer

Hu, Q., Noll, R. J., Li, H., Makarov, A., Hardman, M., & Cooks, R. G. (2005) · Journal of Mass Spectrometry · doi:10.1002/jms.856 · Cited by 1,338 · see citing works

Protein mapping by combined isoelectric focusing and electrophoresis of mouse tissues

Klose, J. (1975) · Human Genetics · doi:10.1007/bf00281458 · Cited by 1,204 · see citing works

Interaction network containing conserved and essential protein complexes in Escherichia coli

Butland, G., Peregrín-Alvarez, J. M., Li, J., Yang, W., Yang, X., Canadien, V., Starostine, A., Richards, D., Beattie, B., Krogan, N., et al. (2005) · Nature · doi:10.1038/nature03239 · Cited by 1,201 · see citing works

Protein sequencing by tandem mass spectrometry.

Hunt, D. F., Yates, J. R., Shabanowitz, J., Winston, S., & Hauer, C. (1986) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.83.17.6233 · Cited by 1,189 · see citing works

Absolute protein expression profiling estimates the relative contributions of transcriptional and translational regulation

Lu, P., Vogel, C., Wang, R., Yao, X., & Marcotte, E. M. (2007) · Nature Biotechnology · doi:10.1038/nbt1270 · Cited by 1,139 · see citing works

Immunoaffinity profiling of tyrosine phosphorylation in cancer cells

Rush, A. J., Moritz, A., Lee, K. A., Guo, A., Goss, V. L., Spek, E. J., Zhang, H., Zha, X., Polakiewicz, R. D., & Comb, M. J. (2004) · Nature Biotechnology · doi:10.1038/nbt1046 · Cited by 1,126 · see citing works

Quantitative Proteomics Reveals the Function of Unconventional Ubiquitin Chains in Proteasomal Degradation

Xu, P., Duong, D. M., Seyfried, N. T., Cheng, D., Xie, Y., Robert, J., Rush, A. J., Hochstrasser, M., Finley, D. J., & Peng, J. (2009) · Cell · doi:10.1016/j.cell.2009.01.041 · Cited by 1,125 · see citing works

Molecular analysis of genetic differences between Mycobacterium bovis BCG and virulent M. bovis

Mahairas, G. G., Sabo, P. J., Hickey, M. J., Singh, D. C., & Stover, C. K. (1996) · Journal of Bacteriology · doi:10.1128/jb.178.5.1274-1282.1996 · Cited by 1,103 · see citing works

Covalent histone modifications — miswritten, misinterpreted and mis-erased in human cancers

Chi, P., Allis, C. D., & Wang, G. G. (2010) · Nature reviews. Cancer · doi:10.1038/nrc2876 · Cited by 1,099 · see citing works

Role of Accurate Mass Measurement (±10 ppm) in Protein Identification Strategies Employing MS or MS/MS and Database Searching

Clauser, K. R., Baker, P. R., & Burlingame, A. L. (1999) · Analytical Chemistry · doi:10.1021/ac9810516 · Cited by 1,084 · see citing works

Proteomics by Mass Spectrometry: Approaches, Advances, and Applications

Yates, J. R., Ruse, C. I., & Nakorchevsky, A. (2009) · Annual Review of Biomedical Engineering · doi:10.1146/annurev-bioeng-061008-124934 · Cited by 1,078 · see citing works

PEAKS DB: De Novo Sequencing Assisted Database Search for Sensitive and Accurate Peptide Identification

Zhang, J., Xin, L., Shan, B., Chen, W., Xie, M., Yuen, D., Zhang, W., Zhang, Z., Lajoie, G., & Ma, B. (2011) · Molecular & Cellular Proteomics · doi:10.1074/mcp.m111.010587 · Cited by 1,073 · see citing works

GlycoWorkbench: A Tool for the Computer-Assisted Annotation of Mass Spectra of Glycans

Ceroni, A., Maaß, K., Geyer, H., Geyer, R., Dell, A., & Haslam, S. M. (2008) · Journal of Proteome Research · doi:10.1021/pr7008252 · Cited by 1,059 · see citing works

Quantitative chemical proteomics reveals mechanisms of action of clinical ABL kinase inhibitors

Bantscheff, M., Eberhard, D., Abraham, Y., Bastuck, S., Böesche, M., Hobson, S., Mathieson, T., Perrin, J., Raida, M., Rau, C., et al. (2007) · Nature Biotechnology · doi:10.1038/nbt1328 · Cited by 1,036 · see citing works

Interpretation of Shotgun Proteomic Data

Nesvizhskii, A. I., & Aebersold, R. (2005) · Molecular & Cellular Proteomics · doi:10.1074/mcp.r500012-mcp200 · Cited by 1,025 · see citing works

Accurate quantitation of protein expression and site-specific phosphorylation.

Oda, Y., Huang, K., Cross, F., Cowburn, D., & Chait, B. (1999) · Proceedings of the National Academy of Sciences of the United States of America · doi:10.1073/pnas.96.12.6591 · Cited by 1,011 · see citing works

MS3 eliminates ratio distortion in isobaric multiplexed quantitative proteomics

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Ion Activation Methods for Peptides and Proteins

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Proteomics Research in Cardiovascular Medicine and Biomarker Discovery

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Top Down Proteomics

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Advancements in Top-Down Proteomics

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