Cited by 271

The DOI matches its Crossref record; 125 of the 125 references it cites were found in a registry or an index.

Current trends in quantitative proteomics

Open access

Elliott, Monica H., Smith, Derek S., Parker, Carol E., Borchers, Christoph·2009·Journal of Mass Spectrometry

Open this paper in CoChat — free account

Abstract

It was inevitable that as soon as mass spectrometrists were able to tell biologists which proteins were in their samples, the next question would be how much of these proteins were present. This has turned out to be a much more challenging question. In this review, we describe the multiple ways that mass spectrometry has attempted to address this issue, both for relative quantitation and for absolute quantitation of proteins. There is no single method that will work for every problem or for every sample. What we present here is a variety of techniques, with guidelines that we hope will assist the researcher in selecting the most appropriate technique for the particular biological problem that needs to be addressed. We need to emphasize that this is a very active area of proteomics research—new quantitative methods are continuously being introduced and some ‘pitfalls’ of older methods are just being discovered. However, even though there is no perfect technique—and a better technique may be developed tomorrow—valuable information on biomarkers and pathways can be obtained using these currently available methods Copyright © 2009 John Wiley & Sons, Ltd.

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

Integrity signals

Registry

Crossref · 10.1002/jms.1692

Cites

125 of 125 references verified0 citation errors · 0 not checkable

Statistics

Claims the paper makes

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

Self-check

Percentages, sums and reported differences re-computed from the paper’s own numbers.

The self-check needs the paper’s full text.

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
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
The Human Plasma Proteome
Anderson, N. L., & Anderson, N. G. (2002) · Molecular & Cellular Proteomics · doi:10.1074/mcp.r200007-mcp200 · Cited by 4,414
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
Van Damme A.
Haine, M. M.-L., & Meeùs, N. (1986) · Cited by 3,464
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 2,500
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
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 1,819
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
Quantitative mass spectrometry in proteomics: a critical review
Bantscheff, M., Schirle, M., Sweetman, G., Rick, J., & Kuster, B. (2007) · Analytical and Bioanalytical Chemistry · doi:10.1007/s00216-007-1486-6 · Cited by 1,669
Mass spectrometry–based proteomics turns quantitative
Ong, S.-E., & Mann, M. (2005) · Nature Chemical Biology · doi:10.1038/nchembio736 · Cited by 1,572 · cited 5×
“to grow in the dialyzed serum required for SILAC due to the loss of essential growth factors.[1] The isotope distributions resulting from the combination of 13C and 15N can be difficult to interpret.”
BackgroundMethodInfluential
Absolute Quantification of Proteins by LCMSE
Silva, J. C., Gorenstein, M. V., Li, G.-Z., Vissers, J. P. C., & Geromanos, S. J. (2006) · Molecular & Cellular Proteomics · doi:10.1074/mcp.m500230-mcp200 · Cited by 1,529
Selected reaction monitoring for quantitative proteomics: a tutorial
Lange, V., Picotti, P., Domon, B., & Aebersold, R. (2008) · Molecular Systems Biology · doi:10.1038/msb.2008.61 · Cited by 1,407
Comparison of Label-free Methods for Quantifying Human Proteins by Shotgun Proteomics
Old, W. M., Meyer-Arendt, K., Aveline-Wolf, L., Pierce, K. G., Mendoza, A., Sevinsky, J. R., Resing, K. A., & Ahn, N. G. (2005) · Molecular & Cellular Proteomics · doi:10.1074/mcp.m500084-mcp200 · Cited by 1,206
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
Multi-site assessment of the precision and reproducibility of multiple reaction monitoring–based measurements of proteins in plasma
Addona, T. A., Abbatiello, S. E., Schilling, B., Skates, S. J., Mani, D. R., Bunk, D. M., Spiegelman, C. H., Zimmerman, L. J., Ham, A.-J. L., Keshishian, H., et al. (2009) · Nature Biotechnology · doi:10.1038/nbt.1546 · Cited by 1,037
Self-citation
Accurate quantitation of protein expression and site-specific phosphorylation
Oda, Y., Huang, K., Cross, F. R., Cowburn, D., & Chait, B. T. (1999) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.96.12.6591 · Cited by 1,006
Large-Scale Proteomic Analysis of the Human Spliceosome
Rappsilber, J., Ryder, U., Lamond, A. I., & Mann, M. (2002) · Genome Research · doi:10.1101/gr.473902 · Cited by 943
Unbiased quantitative proteomics of lipid rafts reveals high specificity for signaling factors
Foster, L. J., de Hoog, C. L., & Mann, M. (2003) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0631608100 · Cited by 834
Mass Spectrometric Quantitation of Peptides and Proteins Using Stable Isotope Standards and Capture by Anti-Peptide Antibodies (SISCAPA)
Anderson, N. L., Anderson, N. G., Haines, L. R., Hardie, D. B., Olafson, R. W., & Pearson, T. W. (2004) · Journal of Proteome Research · doi:10.1021/pr034086h · Cited by 804
Proteolytic 18O Labeling for Comparative Proteomics: Model Studies with Two Serotypes of Adenovirus
Yao, X., Freas, A., Ramirez, J., Demirev, P. A., & Fenselau, C. (2001) · Analytical Chemistry · doi:10.1021/ac001404c · Cited by 759
Computational prediction of proteotypic peptides for quantitative proteomics
Mallick, P., Schirle, M., Chen, S. S., Flory, M. R., Lee, H., Martin, D., Ranish, J., Raught, B., Schmitt, R., Werner, T., et al. (2007) · Nature Biotechnology · doi:10.1038/nbt1275 · Cited by 695
SILAC mouse for quantitative proteomics uncovers kindlin-3 as an essential factor for red blood cell function
Krüger, M., Moser, M., Ussar, S., Thievessen, I., Luber, C. A., Forner, F., Schmidt, S., Zanivan, S., Fässler, R., & Mann, M. (2008) · Cell · doi:10.1016/j.cell.2008.05.033 · Cited by 680
The absolute quantification strategy: a general procedure for the quantification of proteins and post-translational modifications
Kirkpatrick, D. S., Gerber, S. A., & Gygi, S. P. (2005) · Methods · doi:10.1016/j.ymeth.2004.08.018 · Cited by 559
Multiple reaction monitoring-based, multiplexed, absolute quantitation of 45 proteins in human plasma
Kuzyk, M. A., Smith, D., Yang, J., Cross, T. J., Jackson, A. M., Hardie, D. B., Anderson, N. L., & Borchers, C. H. (2009) · Molecular & Cellular Proteomics · doi:10.1074/mcp.m800540-mcp200 · Cited by 515
Self-citation
A novel strategy for quantitative proteomics using isotope‐coded protein labels
Schmidt, A., Kellermann, J., & Lottspeich, F. (2005) · PROTEOMICS · doi:10.1002/pmic.200400873 · Cited by 507
Normalization Approaches for Removing Systematic Biases Associated with Mass Spectrometry and Label-Free Proteomics
Callister, S. J., Barry, R. C., Adkins, J. N., Johnson, E. T., Qian, W.-J., Webb-Robertson, B.-J. M., Smith, R. D., & Lipton, M. S. (2006) · Journal of Proteome Research · doi:10.1021/pr050300l · Cited by 492
Quantitative Atlas of Membrane Transporter Proteins: Development and Application of a Highly Sensitive Simultaneous LC/MS/MS Method Combined with Novel In-silico Peptide Selection Criteria
Kamiie, J., Ohtsuki, S., Iwase, R., Ohmine, K., Katsukura, Y., Yanai, K., Sekine, Y., Uchida, Y., Ito, S., & Terasaki, T. (2008) · Pharmaceutical Research · doi:10.1007/s11095-008-9532-4 · Cited by 478
Precision proteomics: The case for high resolution and high mass accuracy
Mann, M., & Kelleher, N. L. (2008) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0800788105 · Cited by 450
Label-Free Protein Quantification Using LC-Coupled Ion Trap or FT Mass Spectrometry: Reproducibility, Linearity, and Application with Complex Proteomes
Wang, G., Wu, W. W., Zeng, W., Chou, C.-L., & Shen, R.-F. (2006) · Journal of Proteome Research · doi:10.1021/pr050406g · Cited by 423
Direct proteomic mapping of the lung microvascular endothelial cell surface in vivo and in cell culture
Durr, E., Yu, J., Krasinska, K. M., Carver, L. A., Yates, J. R., Testa, J. E., Oh, P., & Schnitzer, J. E. (2004) · Nature Biotechnology · doi:10.1038/nbt993 · Cited by 420
Metabolic labeling of C. elegans and D. melanogaster for quantitative proteomics
Krijgsveld, J., Ketting, R. F., Mahmoudi, T., Johansen, J., Artal-Sanz, M., Verrijzer, C. P., Plasterk, R. H. A., & Heck, A. J. R. (2003) · Nature Biotechnology · doi:10.1038/nbt848 · Cited by 408
Technical, Experimental, and Biological Variations in Isobaric Tags for Relative and Absolute Quantitation (iTRAQ)
Gan, C. S., Chong, P. K., Pham, T. K., & Wright, P. C. (2007) · Journal of Proteome Research · doi:10.1021/pr060474i · Cited by 404
A quantitative analysis software tool for mass spectrometry–based proteomics
Park, S. K., Venable, J. D., Xu, T., & Yates, J. R. (2008) · Nature Methods · doi:10.1038/nmeth.1195 · Cited by 401
Quantification of C‐reactive protein in the serum of patients with rheumatoid arthritis using multiple reaction monitoring mass spectrometry and 13C‐labeled peptide standards
Kuhn, E., Wu, J., Karl, J., Liao, H., Zolg, W., & Guild, B. (2004) · PROTEOMICS · doi:10.1002/pmic.200300670 · Cited by 398
Metabolic Labeling of Mammalian Organisms with Stable Isotopes for Quantitative Proteomic Analysis
Wu, C. C., MacCoss, M. J., Howell, K. E., Matthews, D. E., & Yates, J. R. (2004) · Analytical Chemistry · doi:10.1021/ac049208j · Cited by 386 · cited 1×
“[59] Yates and collaborators also showed that metabolic labeling of an entire organism was possible in mammals (in this case, a rat[60]), but this is usually prohibitively expensive.”
Background
Significance Analysis of Spectral Count Data in Label-free Shotgun Proteomics
Choi, H., Fermin, D., & Nesvizhskii, A. I. (2008) · Molecular & Cellular Proteomics · doi:10.1074/mcp.m800203-mcp200 · Cited by 364
A Quantitative Study of the Effects of Chaotropic Agents, Surfactants, and Solvents on the Digestion Efficiency of Human Plasma Proteins by Trypsin
Proc, J. L., Kuzyk, M. A., Hardie, D. B., Yang, J., Smith, D. S., Jackson, A. M., Parker, C. E., & Borchers, C. H. (2010) · Journal of Proteome Research · doi:10.1021/pr100656u · Cited by 353
Self-citation
Isotope dilution--mass spectrometric quantification of specific proteins: model application with apolipoprotein A-I
Barr, J. R., Maggio, V. L., Patterson, D. G., Cooper, G. R., Henderson, L. O., Turner, W. E., Smith, S. J., Hannon, W. H., Needham, L. L., & Sampson, E. J. (1996) · Clinical Chemistry · doi:10.1093/clinchem/42.10.1676 · Cited by 347
Multiple reaction monitoring for quantitative biomarker analysis in proteomics and metabolomics☆
Kitteringham, N. R., Jenkins, R. E., Lane, C. S., Elliott, V. L., & Park, B. K. (2009) · Journal of Chromatography B · doi:10.1016/j.jchromb.2008.11.013 · Cited by 343
Protein identification methods in proteomics
Gevaert, K., & Vandekerckhove, J. (2000) · Electrophoresis · doi:10.1002/(sici)1522-2683(20000401)21:6<1145::aid-elps1145>3.0.co;2-z · Cited by 338
SuperHirn – a novel tool for high resolution LC‐MS‐based peptide/protein profiling
Mueller, L. N., Rinner, O., Schmidt, A., Letarte, S., Bodenmiller, B., Brusniak, M., Vitek, O., Aebersold, R., & Müller, M. (2007) · PROTEOMICS · doi:10.1002/pmic.200700057 · Cited by 308
Mass Spectrometric Analysis of Protein Mixtures at Low Levels Using Cleavable 13C-Isotope-coded Affinity Tag and Multidimensional Chromatography
Hansen, K. C., Schmitt-Ulms, G., Chalkley, R. J., Hirsch, J., Baldwin, M. A., & Burlingame, A. L. (2003) · Molecular & Cellular Proteomics · doi:10.1074/mcp.m300021-mcp200 · Cited by 297
Use of Artificial Neural Networks for the Accurate Prediction of Peptide Liquid Chromatography Elution Times in Proteome Analyses
Petritis, K., Kangas, L. J., Ferguson, P. L., Anderson, G. A., Paša-Tolić, L., Lipton, M. S., Auberry, K. J., Strittmatter, E. F., Shen, Y., Zhao, R., et al. (2003) · Analytical Chemistry · doi:10.1021/ac0205154 · Cited by 294
Utility of Accurate Mass Tags for Proteome-Wide Protein Identification
Conrads, T. P., Anderson, G. A., Veenstra, T. D., Paša-Tolić, L., & Smith, R. D. (2000) · Analytical Chemistry · doi:10.1021/ac0002386 · Cited by 281
Quantitation and Facilitated de Novo Sequencing of Proteins by Isotopic N-Terminal Labeling of Peptides with a Fragmentation-Directing Moiety
Münchbach, M., Quadroni, M., Miotto, G., & James, P. (2000) · Analytical Chemistry · doi:10.1021/ac000265w · Cited by 280
Retooling Leishmania metabolism: from sand fly gut to human macrophage
Rosenzweig, D., Smith, D., Opperdoes, F., Stern, S., Olafson, R. W., & Zilberstein, D. (2008) · The FASEB Journal · doi:10.1096/fj.07-9254com · Cited by 274
Self-citation
A Comparison of Labeling and Label-Free Mass Spectrometry-Based Proteomics Approaches
Patel, V. J., Thalassinos, K., Slade, S. E., Connolly, J. B., Crombie, A., Murrell, J. C., & Scrivens, J. H. (2009) · Journal of Proteome Research · doi:10.1021/pr900080y · Cited by 258
Absolute Quantification of the Model Biomarker Prostate-Specific Antigen in Serum by LC−MS/MS Using Protein Cleavage and Isotope Dilution Mass Spectrometry
Barnidge, D. R., Goodmanson, M. K., Klee, G. G., & Muddiman, D. C. (2004) · Journal of Proteome Research · doi:10.1021/pr049963d · Cited by 253
Controlling Deuterium Isotope Effects in Comparative Proteomics
Zhang, R., Sioma, C. S., Thompson, R. A., Xiong, L., & Regnier, F. E. (2002) · Analytical Chemistry · doi:10.1021/ac025614w · Cited by 238
Protein Profiling with Cleavable Isotope-coded Affinity Tag (cICAT) Reagents
Li, J., Steen, H., & Gygi, S. P. (2003) · Molecular & Cellular Proteomics · doi:10.1074/mcp.m300070-mcp200 · Cited by 218
A label‐free quantification method by MS/MS TIC compared to SILAC and spectral counting in a proteomics screen
Asara, J. M., Christofk, H. R., Freimark, L. M., & Cantley, L. C. (2008) · PROTEOMICS · doi:10.1002/pmic.200700426 · Cited by 218
A database of mass spectrometric assays for the yeast proteome
Picotti, P., Lam, H., Campbell, D., Deutsch, E. W., Mirzaei, H., Ranish, J., Domon, B., & Aebersold, R. (2008) · Nature Methods · doi:10.1038/nmeth1108-913 · Cited by 211
Prevention of Amino Acid Conversion in SILAC Experiments with Embryonic Stem Cells
Bendall, S. C., Hughes, C., Stewart, M. H., Doble, B., Bhatia, M., & Lajoie, G. A. (2008) · Molecular & Cellular Proteomics · doi:10.1074/mcp.m800113-mcp200 · Cited by 205
Quantitative proteomics using stable isotope labeling with amino acids in cell culture
Harsha, H. C., Molina, H., & Pandey, A. (2008) · Nature Protocols · doi:10.1038/nprot.2008.2 · Cited by 202
Comparative LC‐MS: A landscape of peaks and valleys
America, A. H. P., & Cordewener, J. H. G. (2008) · PROTEOMICS · doi:10.1002/pmic.200700694 · Cited by 191
VIPER: an advanced software package to support high-throughput LC-MS peptide identification
Monroe, M. E., Tolić, N., Jaitly, N., Shaw, J. L., Adkins, J. N., & Smith, R. D. (2007) · Bioinformatics · doi:10.1093/bioinformatics/btm281 · Cited by 189
PhosphoPep—a phosphoproteome resource for systems biology research in Drosophila Kc167 cells
Bodenmiller, B., Malmstrom, J., Gerrits, B., Campbell, D., Lam, H., Schmidt, A., Rinner, O., Mueller, L. N., Shannon, P. T., Pedrioli, P. G., et al. (2007) · Molecular Systems Biology · doi:10.1038/msb4100182 · Cited by 187
Coupling immunoaffinity techniques with MS for quantitative analysis of low-abundance protein biomarkers
Ackermann, B. L., & Berna, M. J. (2007) · Expert Review of Proteomics · doi:10.1586/14789450.4.2.175 · Cited by 179
Multiple Reaction Monitoring of mTRAQ-Labeled Peptides Enables Absolute Quantification of Endogenous Levels of a Potential Cancer Marker in Cancerous and Normal Endometrial Tissues
DeSouza, L. V., Taylor, A. M., Li, W., Minkoff, M. S., Romaschin, A. D., Colgan, T. J., & Siu, K. W. M. (2008) · Journal of Proteome Research · doi:10.1021/pr800312m · Cited by 172
The APEX Quantitative Proteomics Tool: Generating protein quantitation estimates from LC-MS/MS proteomics results
Braisted, J. C., Kuntumalla, S., Vogel, C., Marcotte, E. M., Rodrigues, A. R., Wang, R., Huang, S.-T., Ferlanti, E. S., Saeed, A. I., Fleischmann, R. D., et al. (2008) · BMC Bioinformatics · doi:10.1186/1471-2105-9-529 · Cited by 169
Quantitative Proteome Analysis of Human Plasma following in Vivo Lipopolysaccharide Administration Using 16O/18O Labeling and the Accurate Mass and Time Tag Approach
Qian, W.-J., Monroe, M. E., Liu, T., Jacobs, J. M., Anderson, G. A., Shen, Y., Moore, R. J., Anderson, D. J., Zhang, R., Calvano, S. E., et al. (2005) · Molecular & Cellular Proteomics · doi:10.1074/mcp.m500045-mcp200 · Cited by 164
Proteolytic 18O Labeling for Comparative Proteomics: Evaluation of Endoprotease Glu-C as the Catalytic Agent
Reynolds, K. J., Yao, X., & Fenselau, C. (2002) · Journal of Proteome Research · doi:10.1021/pr0100016 · Cited by 156
PatternLab for proteomics: a tool for differential shotgun proteomics
Carvalho, P. C., Fischer, J. D. S. D. G., Chen, E. I., Yates, J. R., & Barbosa, V. C. (2008) · BMC Bioinformatics · doi:10.1186/1471-2105-9-316 · Cited by 152
Expediting the Development of Targeted SRM Assays: Using Data from Shotgun Proteomics to Automate Method Development
Prakash, A., Tomazela, D. M., Frewen, B., MacLean, B., Merrihew, G., Peterman, S., & MacCoss, M. J. (2009) · Journal of Proteome Research · doi:10.1021/pr801028b · Cited by 147
SISCAPA Peptide Enrichment on Magnetic Beads Using an In-line Bead Trap Device
Anderson, N. L., Jackson, A., SMITH, D. S. H., Hardie, D. B., Borchers, C. H., & Pearson, T. W. (2009) · Molecular & Cellular Proteomics · doi:10.1074/mcp.m800446-mcp200 · Cited by 143
Self-citation
Differential expression analysis of Escherichia coli proteins using a novel software for relative quantitation of LC‐MS/MS data
Johansson, C., Samskog, J., Sundström, L., Wadensten, H., Björkesten, L., & Flensburg, J. (2006) · PROTEOMICS · doi:10.1002/pmic.200500921 · Cited by 130
Site-Specific Mass Tagging with Stable Isotopes in Proteins for Accurate and Efficient Protein Identification
Chen, X., Smith, L. M., & Bradbury, E. M. (2000) · Analytical Chemistry · doi:10.1021/ac9911600 · Cited by 117
Review of a current role of mass spectrometry for proteome research
Chen, C. (2008) · Analytica Chimica Acta · doi:10.1016/j.aca.2008.06.017 · Cited by 111
Stable Isotope Labeling by Amino Acids in Cell Culture (SILAC) and Quantitative Comparison of the Membrane Proteomes of Self-renewing and Differentiating Human Embryonic Stem Cells
Prokhorova, T. A., Rigbolt, K. T. G., Johansen, P. T., Henningsen, J., Kratchmarova, I., Kassem, M. S., & Blagoev, B. (2009) · Molecular & Cellular Proteomics · doi:10.1074/mcp.m800287-mcp200 · Cited by 110
Current chemical tagging strategies for proteome analysis by mass spectrometry.
Leitner, A., & Lindner, W. (2004) · Journal of chromatography. B, Analytical technologies in the biomedical and life sciences · doi:10.1016/j.jchromb.2004.09.057 · Cited by 110
Spectral Index for Assessment of Differential Protein Expression in Shotgun Proteomics
Fu, X., Gharib, S. A., Green, P. S., Aitken, M. L., Frazer, D. A., Park, D. R., Vaisar, T., & Heinecke, J. W. (2008) · Journal of Proteome Research · doi:10.1021/pr070271+ · Cited by 108
MRMaid, the Web-based Tool for Designing Multiple Reaction Monitoring (MRM) Transitions
Mead, J. A., Bianco, L., Ottone, V., Barton, C., Kay, R. G., Lilley, K. S., Bond, N. J., & Bessant, C. (2008) · Molecular & Cellular Proteomics · doi:10.1074/mcp.m800192-mcp200 · Cited by 108
Implications of 15N‐metabolic labeling for automated peptide identification in Arabidopsis thaliana
Nelson, C. J., Huttlin, E. L., Hegeman, A., Harms, A., & Sussman, M. (2007) · Proteomics · doi:10.1002/pmic.200600832 · Cited by 106
N‐Terminal peptide labeling strategy for incorporation of isotopic tags: a method for the determination of site‐specific absolute phosphorylation stoichiometry
Zhang, X., Jin, Q. K., Carr, S. A., & Annan, R. S. (2002) · Rapid Communications in Mass Spectrometry · doi:10.1002/rcm.864 · Cited by 104
Endometrial Carcinoma Biomarker Discovery and Verification Using Differentially Tagged Clinical Samples with Multidimensional Liquid Chromatography and Tandem Mass Spectrometry
DeSouza, L. V., Grigull, J., Ghanny, S., et al. (2007) · Molecular & Cellular Proteomics · doi:10.1074/mcp.m600378-mcp200 · Cited by 104
Quantitative mass spectrometry-based techniques for clinical use: Biomarker identification and quantification☆
Simpson, K., Whetton, A. D., & Dive, C. (2008) · Journal of Chromatography B · doi:10.1016/j.jchromb.2008.11.023 · Cited by 94
Stable isotopic labeling in proteomics
Gevaert, K., Impens, F., Ghesquière, B., Damme, P. V., Lambrechts, A., & Vandekerckhove, J. (2008) · Proteomics · doi:10.1002/pmic.200800421 · Cited by 91
MRMer, an Interactive Open Source and Cross-platform System for Data Extraction and Visualization of Multiple Reaction Monitoring Experiments
Martin, D. B., Holzman, T., May, D., Peterson, A. C., Eastham, A., Eng, J. K., & McIntosh, M. W. (2008) · Molecular & Cellular Proteomics · doi:10.1074/mcp.m700504-mcp200 · Cited by 88
Quantitative proteomics as a new piece of the systems biology puzzle.
Bachi, A., & Bonaldi, T. (2008) · Journal of Proteomics · doi:10.1016/j.jprot.2008.07.001 · Cited by 87
Quantitative Protein Profiling by Mass Spectrometry Using Label-Free Proteomics
Haqqani, A. S., Kelly, J. F., & Stanimirovic, D. B. (2008) · Methods in molecular biology · doi:10.1007/978-1-59745-188-8_17 · Cited by 87
Absolute Quantification of Potential Cancer Markers in Clinical Tissue Homogenates Using Multiple Reaction Monitoring on a Hybrid Triple Quadrupole/Linear Ion Trap Tandem Mass Spectrometer
DeSouza, L. V., Romaschin, A. D., Colgan, T. J., & Siu, K. W. M. (2009) · Analytical Chemistry · doi:10.1021/ac802726a · Cited by 86
An immunoaffinity tandem mass spectrometry (iMALDI) assay for detection of Francisella tularensis
Jian, J., Parker, C. E., Fuller, J. R., Kawula, T. H., & Borchers, C. H. (2007) · Analytica Chimica Acta · doi:10.1016/j.aca.2007.10.025 · Cited by 82
Self-citation
Quantitative proteomics to study mitogen-activated protein kinases
Blagoev, B., & MANN, M. (2006) · Methods · doi:10.1016/j.ymeth.2006.08.001 · Cited by 80
MaRiMba: A Software Application for Spectral Library-Based MRM Transition List Assembly
Sherwood, C. A., Eastham, A., Lee, L. W., Peterson, A. C., Eng, J. K., Shteynberg, D. D., Mendoza, L., Deutsch, E. W., Risler, J., Tasman, N., et al. (2009) · Journal of Proteome Research · doi:10.1021/pr900010h · Cited by 80
Predicting Intensity Ranks of Peptide Fragment Ions
Frank, A. M. (2009) · Journal of Proteome Research · doi:10.1021/pr800677f · Cited by 76
Computational methods for the comparative quantification of proteins in label-free LCn-MS experiments
Wong, J. W. H., Sullivan, M. J., & Cagney, G. (2007) · Briefings in Bioinformatics · doi:10.1093/bib/bbm046 · Cited by 76
Semi-supervised LC/MS alignment for differential proteomics
Fischer, B., Grossmann, J., Röth, V., Gruissem, W., Baginsky, S., & Buhmann, J. M. (2006) · Bioinformatics · doi:10.1093/bioinformatics/btl219 · Cited by 74
Corra: Computational framework and tools for LC-MS discovery and targeted mass spectrometry-based proteomics
Brusniak, M., Bodenmiller, B., Campbell, D. S., Cooke, K., Eddes, J. S., Garbutt, A., Lau, H., Letarte, S., Mueller, L. N., Sharma, V., et al. (2008) · BMC Bioinformatics · doi:10.1186/1471-2105-9-542 · Cited by 73
Systematic Characterization of Nuclear Proteome during Apoptosis
Hwang, S., Lundgren, D. H., Mayya, V., Rezaul, K., Cowan, A. E., Eng, J. K., & Han, D. K. M. (2006) · Molecular & Cellular Proteomics · doi:10.1074/mcp.m500162-mcp200 · Cited by 72
Quantitative proteomics of intracellular Porphyromonas gingivalis
Xia, Q., Wang, T., Taub, F., Park, Y., Capestany, C. A., Lamont, R. J., & Hackett, M. (2007) · PROTEOMICS · doi:10.1002/pmic.200700543 · Cited by 67
Development of an immuno tandem mass spectrometry (iMALDI) assay for EGFR diagnosis
Jian, J., Parker, C. E., Hoadley, K. A., Perou, C. M., Boysen, G., & Borchers, C. H. (2007) · PROTEOMICS - CLINICAL APPLICATIONS · doi:10.1002/prca.200700009 · Cited by 65
Self-citation
Significance analysis of microarray for relative quantitation of LC/MS data in proteomics
Roxas, B. A., & Li, Q.-B. (2008) · BMC Bioinformatics · doi:10.1186/1471-2105-9-187 · Cited by 63
Mortalin is regulated by APOE in hippocampus of AD patients and by human APOE in TR mice
Osorio, C., Sullivan, P. M., Dong, H., Mace, B. E., Ervin, J. F., Strittmatter, W. J., & Álzate, Ó. (2006) · Neurobiology of Aging · doi:10.1016/j.neurobiolaging.2006.08.011 · Cited by 62
Label-Free Comparative Analysis of Proteomics Mixtures Using Chromatographic Alignment of High-Resolution μLC−MS Data
Finney, G. L., Blackler, A. R., Hoopmann, M. R., Canterbury, J. D., Wu, C. C., & MacCoss, M. J. (2008) · Analytical Chemistry · doi:10.1021/ac701649e · Cited by 61
A label‐free internal standard method for the differential analysis of bioactive lupin proteins using nano HPLC‐Chip coupled with Ion Trap mass spectrometry
Brambilla, F., Resta, D., Isak, I., Zanotti, M., & Arnoldi, A. (2008) · PROTEOMICS · doi:10.1002/pmic.200800317 · Cited by 60
ProteinQuant Suite: a bundle of automated software tools for label‐free quantitative proteomics
Mann, B. F., Maděra, M., Sheng, Q., Tang, H., Mechref, Y. S., & Novotný, M. V. (2008) · Rapid Communications in Mass Spectrometry · doi:10.1002/rcm.3781 · Cited by 57
ProtQuant: a tool for the label-free quantification of MudPIT proteomics data
Bridges, S. M., Magee, G. B., Wang, N., Williams, W. P., Burgess, S. C., & Nanduri, B. (2007) · BMC Bioinformatics · doi:10.1186/1471-2105-8-s7-s24 · Cited by 57
Playing tag with quantitative proteomics
Iliuk, A. B., Galan, J. A., & Tao, W. A. (2008) · Analytical and Bioanalytical Chemistry · doi:10.1007/s00216-008-2386-0 · Cited by 55
Large-Scale Multiplexed Quantitative Discovery Proteomics Enabled by the Use of an 18 O-Labeled “Universal” Reference Sample
Qian, W., Liu, T., Petyuk, V., Gritsenko, M. A., Petritis, B. O., Polpitiya, A. D., Kaushal, A., Xiao, W., Finnerty, C. C., Jeschke, M. G., et al. (2008) · Journal of Proteome Research · doi:10.1021/pr800467r · Cited by 55
Quantitative Analysis of Isotope Distributions In Proteomic Mass Spectrometry Using Least-Squares Fourier Transform Convolution
Sperling, E., Bunner, A. E., Sykes, M. T., & Williamson, J. R. (2008) · Analytical Chemistry · doi:10.1021/ac800080v · Cited by 54
A New Algorithm Using Cross-Assignment for Label-Free Quantitation with LC−LTQ-FT MS
Andreev, V. P., Li, L., Cao, L., Gu, Y., Rejtar, T., Wu, S.-L., & Karger, B. L. (2007) · Journal of Proteome Research · doi:10.1021/pr0606880 · Cited by 49
The Effects of Shared Peptides on Protein Quantitation in Label-Free Proteomics by LC/MS/MS
Jin, S., Daly, D. S., Springer, D. L., & Miller, J. H. (2007) · Journal of Proteome Research · doi:10.1021/pr0704175 · Cited by 49
Comparison of a Label-Free Quantitative Proteomic Method Based on Peptide Ion Current Area to the Isotope Coded Affinity Tag Method
Ryu, S., Gallis, B. M., Goo, Y. A., Shaffer, S. A., Radulovic, D., & Goodlett, D. R. (2008) · Cancer Informatics · doi:10.4137/cin.s385 · Cited by 49
Mass Spectrometric Characterization of a Discontinuous Epitope of the HIV Envelope Protein HIV-gp120 Recognized by the Human Monoclonal Antibody 1331A
Hochleitner, E. O., Górny, M. K., Zolla‐Pazner, S., & Tomer, K. B. (2000) · The Journal of Immunology · doi:10.4049/jimmunol.164.8.4156 · Cited by 46
Mass Spectrometry Reveals Specific and Global Molecular Transformations during Viral Infection
Go, E. P., Wikoff, W. R., Shen, Z., O’Maille, G., Morita, H., Conrads, T. P., Nordstrom, A., Trauger, S. A., Uritboonthai, W., Lucas, D. A., et al. (2006) · Journal of Proteome Research · doi:10.1021/pr060215t · Cited by 46
The development of multiple reaction monitoring assays for liver‐derived plasma proteins
McKay, M. J., Sherman, J., Laver, M., Baker, M. S., Clarke, S. J., & Molloy, M. P. (2007) · PROTEOMICS - CLINICAL APPLICATIONS · doi:10.1002/prca.200700305 · Cited by 44
Determination of serum cortisol by thermospray liquid chromatography/mass spectrometry: Comparison with gas chromatography/mass spectrometry
Gaskell, S. J., Rollins, K., Smith, R. W., et al. (1987) · Journal of Mass Spectrometry · doi:10.1002/bms.1200141205 · Cited by 43
Pseudo Internal Standard Approach for Label-Free Quantitative Proteomics
Tabata, T., Sato, T., Kuromitsu, J., & Oda, Y. (2007) · Analytical Chemistry · doi:10.1021/ac701628m · Cited by 42
Quantification of Isotopically Overlapping Deamidated and 18O-Labeled Peptides Using Isotopic Envelope Mixture Modeling
Dasari, S., Wilmarth, P. A., Reddy, A. P., Robertson, L. J. G., Nagalla, S. R., & David, L. L. (2009) · Journal of Proteome Research · doi:10.1021/pr801054w · Cited by 41
MRM screening/biomarker discovery with linear ion trap MS: a library of human cancer-specific peptides
Xu, Y., & Lazar, I. M. (2009) · BMC Cancer · doi:10.1186/1471-2407-9-96 · Cited by 40
Peak intensity prediction in MALDI-TOF mass spectrometry: A machine learning study to support quantitative proteomics
Timm, W., Scherbart, A., Böcker, S., Kohlbacher, O., & Nattkemper, T. W. (2008) · BMC Bioinformatics · doi:10.1186/1471-2105-9-443 · Cited by 40
Quantitation of human glutathione S‐transferases in complex matrices by liquid chromatography/tandem mass spectrometry with signature peptides
Zhang, F., Bartels, M. J., & Stott, W. T. (2004) · Rapid Communications in Mass Spectrometry · doi:10.1002/rcm.1364 · Cited by 40
Inverse 15 N‐metabolic labeling/mass spectrometry for comparative proteomics and rapid identification of protein markers/targets
Wang, Y. K., Ma, Z., Quinn, D. F., & Fu, E. W. (2002) · Rapid Communications in Mass Spectrometry · doi:10.1002/rcm.725 · Cited by 38
Implementation of a data repository-driven approach for targeted proteomics experiments by multiple reaction monitoring
Walsh, G. M., Lin, S., Evans, D. M., Khosrovi-Eghbal, A., Beavis, R. C., & Kast, J. (2008) · Journal of Proteomics · doi:10.1016/j.jprot.2008.11.015 · Cited by 37
Comparison of two label-free global quantitation methods, APEX and 2D gel electrophoresis, applied to the Shigella dysenteriae proteome
Kuntumalla, S., Braisted, J. C., Huang, S.-T., Parmar, P. P., Clark, D. J., Alami, H., Zhang, Q., Donohue-Rolfe, A., Tzipori, S., Fleischmann, R. D., et al. (2009) · Proteome Science · doi:10.1186/1477-5956-7-22 · Cited by 35
Reproducibility Assessment of Relative Quantitation Strategies for LC−MS Based Proteomics
Kim, Y. J., Zhan, P., Feild, B. J., et al. (2007) · Analytical Chemistry · doi:10.1021/ac070200u · Cited by 35
Two-dimensional electrophoretic/chromatographic separations combined with electrospray ionization FTICR mass spectrometry for high throughput proteome analysis
Gao, H., Shen, Y., Veenstra, T. D., Harkewicz, R., Anderson, G., Bruce, J. E., Paša‐Tolić, L., & Smith, R. (2000) · Journal of Microcolumn Separations · Cited by 29
Protein abundance ratios for global studies of prokaryotes
Xia, Q., Hendrickson, E. L., Wang, T., Lamont, R. J., Leigh, J. A., & Hackett, M. (2007) · PROTEOMICS · doi:10.1002/pmic.200700267 · Cited by 26
An assessment of false discovery rates and statistical significance in label-free quantitative proteomics with combined filters
Li, Q., & Roxas, B. P. (2009) · BMC Bioinformatics · doi:10.1186/1471-2105-10-43 · Cited by 23
Erratum to: Ringo – an R/Bioconductor package for analyzing ChIP-chip readouts
Toedling, J., Skylar, O., Krueger, T., Fischer, J. J., Sperling, S., & Huber, W. K. (2007) · BMC Bioinformatics · doi:10.1186/1471-2105-8-443 · Cited by 20
Automated Calculation of Unique PeptideSequencesforUnambiguous Identification of HighlyHomologousProteins byMassSpectrometry
Kohl, M., Redlich, G., Eisenacher, M., Schnabel, A., Meyer, H. E., Marcus, K., & Stephan, C. (2008) · Journal of Proteomics & Bioinformatics · doi:10.4172/jpb.1000003 · Cited by 16
Differential Plasma Glycoproteome of p19ARF Skin Cancer Mouse Model Using the Corra Label-Free LC-MS Proteomics Platform
Letarte, S., Brusniak, M., Campbell, D. S., Eddes, J. S., Kemp, C. J., Lau, H., Mueller, L. N., Schmidt, A., Shannon, P. T., Kelly‐Spratt, K. S., et al. (2008) · Clinical Proteomics · doi:10.1007/s12014-008-9018-8 · Cited by 11
Range Charts for Agreement in Measurement Comparison Studies, With Application to Replicate Mass Spectrometry Experiments
Koziol, J. A., Feng, A. C., Yu, J., Griffin, N. M., & Schnitzer, J. E. (2008) · Journal of Proteomics & Bioinformatics · doi:10.4172/jpb.1000036 · Cited by 4
Chapter 17 Mass Spectrometry-Driven Approaches to Quantitative Proteomics and Beyond
Oeljeklaus, S., Barbour, J., Meyer, H., & Warscheid, B. (2008) · Comprehensive analytical chemistry · doi:10.1016/s0166-526x(08)00217-1 · Cited by 2

Bioanalytical Chemistry of Cytokines–a Review
Stenken, J. A., & Poschenrieder, A. J. (2015) · Analytica Chimica Acta · doi:10.1016/j.aca.2014.10.009 · Cited by 302
Simultaneous Quantification of Apolipoprotein A-I and Apolipoprotein B by Liquid-Chromatography–Multiple- Reaction–Monitoring Mass Spectrometry
Agger, S. A., Marney, L. C., & Hoofnagle, A. N. (2010) · Clinical Chemistry · doi:10.1373/clinchem.2010.152264 · Cited by 143
CE‐MS‐based proteomics in biomarker discovery and clinical application
Pontillo, C., Filip, S., Borràs, D. M., Mullen, W., Vlahou, A., & Mischak, H. (2015) · PROTEOMICS – Clinical Applications · doi:10.1002/prca.201400115 · Cited by 77
A practical data processing workflow for multi-OMICS projects
Kohl, M., Megger, D. A., Trippler, M., Meckel, H., Ahrens, M., Bracht, T., Weber, F., Hoffmann, A.-C., Baba, H. A., Sitek, B., et al. (2014) · Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics · doi:10.1016/j.bbapap.2013.02.029 · Cited by 60
“) strategies (for review see [56–58]).”
Capillary electrophoresis with Orbitrap-Velos mass spectrometry detection
Wojcik, R., Li, Y., MacCoss, M. J., & Dovichi, N. J. (2012) · Talanta · doi:10.1016/j.talanta.2011.10.048 · Cited by 43

See all 271

Authors: Elliott, M. H., Smith, D. S., Parker, C. E., & Borchers, C.
Venue: Journal of Mass Spectrometry
Publisher: Wiley
Published: 2009-12
Volume: 44
Issue: 12
Pages: 1637-1660
ISSN: 1076-5174 (ISSN-L)
1096-9888
DOI: 10.1002/jms.1692
OpenAlex: W2022794640
Cited by: 271
References: 125
FWCI: 15.28
Type: journal article
Language: en
Open access: bronze

About these checks

Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.

Statistics and arithmetic are recomputed, not judged.

Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.

What counts as a claim ›How we measure confidence ›How we check this ›

Are you an author, or do you see a problem with this page? Request a review

Data sources

Bibliographic data: Semantic Scholar, OpenAlex, Crossref.

Contains information from the Semantic Scholar Academic Graph Datasets, made available under the ODC Attribution License (ODC-BY 1.0).

Semantic Scholar’s data is described in: Kinney, R., et al. (2023). The Semantic Scholar Open Data Platform. arXiv:2301.10140.

Current trends in quantitative proteomics

Abstract

Overview

Integrity signals

Verification

Claims the paper makes

Self-check

Citations

Cites

Cited by

Metadata

Record

About these checks

Data sources