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

Nature Biotechnology

Volumn 26, Issue 12, 2008, Pages 1367-1372

  Cox, Jürgen ^a   Mann, Matthias ^a  

^a MAX PLANCK INSTITUTE OF BIOCHEMISTRY   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACIDS; ANIMAL CELL CULTURE; GRAPH THEORY; HIGH PERFORMANCE LIQUID CHROMATOGRAPHY; ISOTOPES; MAMMALS; MASS SPECTROMETRY; MOLECULAR BIOLOGY; ORGANIC ACIDS; PROTEINS; THREE DIMENSIONAL; TOPOLOGY;

CORRELATION ANALYSES; EFFICIENT ANALYSES; HIGH RESOLUTIONS; MAMMALIAN CELLS; MASS ACCURACIES; MASS MEASUREMENTS; PEPTIDE IDENTIFICATIONS; PEPTIDE PAIRS; PROTEIN QUANTIFICATIONS; PROTEOME; PROTEOMICS; RAW DATUMS; ROBUST IDENTIFICATIONS; SIGNAL INTENSITIES;

AMINES;

AMINO ACID; ISOTOPE;

ALGORITHM; ARTICLE; CONTROLLED STUDY; CORRELATION ANALYSIS; HUMAN; HUMAN CELL; MAMMAL CELL; MASS SPECTROMETRY; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEOMICS; QUANTITATIVE ANALYSIS; SIGNAL TRANSDUCTION;

ALGORITHMS; COMPUTATIONAL BIOLOGY; DATABASES, PROTEIN; HELA CELLS; HUMANS; MASS SPECTROMETRY; PEPTIDES; PROTEINS; PROTEOME; PROTEOMICS;

MAMMALIA;

EID: 57449099865     PISSN: 10870156     EISSN: 15461696     Source Type: Journal    
DOI: 10.1038/nbt.1511     Document Type: Article

References (43)

1. Allison, D.B., Cui, X., Page, G.P. & Sabripour, M. Microarray data analysis: from disarray to consolidation and consensus. Nat. Rev. Genet. 7, 55-65 (2006).
2. Patterson, S.D. & Aebersold, R.H. Proteomics: the first decade and beyond. Nat. Genet. 33 Suppl, 311-323 (2003).
3. Nesvizhskii, A.I., Vitek, O. & Aebersold, R. Analysis and validation of proteomic data generated by tandem mass spectrometry. Nat. Methods 4, 787-797 (2007).
4. Aebersold, R. & Mann, M. Mass spectrometry-based proteomics. Nature 422, 198-207 (2003).
5. Steen, H. & Mann, M. The ABC's (and XYZ's) of peptide sequencing. Nat. Rev. Mol. Cell Biol. 5, 699-711 (2004).
6. Sadygov, R.G., Cociorva, D. & Yates, J.R. III. Large-scale database searching using tandem mass spectra: looking up the answer in the back of the book. Nat. Methods 1, 195-202 (2004).
7. Ong, S.E. & Mann, M. Mass spectrometry-based proteomics turns quantitative. Nat. Chem. Biol. 1, 252-262 (2005).
8. Bantscheff, M., Schirle, M., Sweetman, G., Rick, J. & Kuster, B. Quantitative mass spectrometry in proteomics: a critical review. Anal. Bioanal. Chem. 389, 1017-1031 (2007).
9. Listgarten, J. & Emili, A. Statistical and computational methods for comparative proteomic profiling using liquid chromatography-tandem mass spectrometry. Mol. Cell. Proteomics 4, 419-434 (2005).
10. Colinge, J. & Bennett, K.L. Introduction to computational proteomics. PLOS Comput. Biol. 3, e114 (2007).
11. Matthiesen, R. Methods, algorithms and tools in computational proteomics: a practical point of view. Proteomics 7, 2815-2832 (2007).
12. Mead, J.A., Shadforth, I.P. & Bessant, C. Public proteomic MS repositories and pipelines: available tools and biological applications. Proteomics 7, 2769-2786 (2007).
13. Perkins, D.N., Pappin, D.J., Creasy, D.M. & Cottrell, J.S. Probability-based protein identification by searching sequence databases using mass spectrometry data. Electrophoresis 20, 3551-3567 (1999).
14. Cox, J. & Mann, M. Is proteomics the new genomics? Cell 130, 395-398 (2007).
15. Senko, M.W., Beu, S.C. & McLafferty, F.W. Determination of monoisotopic masses and ion populations for large biomolecules from resolved isotopic distributions. J. Am. Soc. Mass Spectrom. 6, 229-233 (1995).
16. Ong, S.E. et al. Stable isotope labeling by amino acids in cell culture, SILAC, as a simple and accurate approach to expression proteomics. Mol. Cell. Proteomics 1, 376-386 (2002).
17. Blagoev, B., Ong, S.E., Kratchmarova, I. & Mann, M. Temporal analysis of phosphotyrosine-dependent signaling networks by quantitative proteomics. Nat. Biotechnol. 22, 1139-1145 (2004).
18. Sokal, A.D. Monte Carlo Methods in Statistical Physics: Foundations and New Algorithms (Lausanne, Switzerland, 1996).
19. Zubarev, R. & Mann, M. On the proper use of mass accuracy in proteomics. Mol. Cell. Proteomics 6, 377-381 (2007).
20. Olsen, J.V. et al. Parts per million mass accuracy on an Orbitrap mass spectrometer via lock mass injection into a C-trap. Mol. Cell. Proteomics 4, 2010-2021 (2005).
21. Olsen, J.V. & Mann, M. Improved peptide identification in proteomics by two consecutive stages of mass spectrometric fragmentation. Proc. Natl. Acad. Sci. USA 101, 13417-13422 (2004).
22. Elias, J.E. & Gygi, S.P. Target-decoy search strategy for increased confidence in large-scale protein identifications by mass spectrometry. Nat. Methods 4, 207-214 (2007).
23. Käll, L., Storey, J.D., MacCoss, M.J. & Nobel, W.S. Assigning significance to peptides identified by tandem mass spectrometry using decoy databases. J. Proteome Res. 7, 29-34 (2008).
24. Nesvizhskii, A.I. & Aebersold, R. Interpretation of shotgun proteomic data: the protein inference problem. Mol. Cell. Proteomics 4, 1419-1440 (2005).
25. Selbach, M. et al. Widespread changes in protein synthesis induced by microRNAs. Nature 455, 58-63 (2008).
26. Bonaldi, T. et al. Combined use of RNAi and quantitative proteomics to study gene function in Drosophila. Mol. Cell 31, 762-772 (2008).
27. Benjamini, Y. & Hochberg, Y. Controlling the false discovery rate: a practical and powerful approach to multiple testing. J. R. Statist. Soc. B 57, 289-300 (1995).
28. Laporte, J. et al. MTM1 mutations in X-linked myotubular myopathy. Hum. Mutat. 15, 393-409 (2000).
29. Wishart, M.J. & Dixon, J.E. PTEN and myotubularin phosphatases: from 3-phosphoinositide dephosphorylation to disease. Trends Cell Biol. 12, 579-585 (2002).
30. Matys, V. et al. TRANSFAC: transcriptional regulation, from patterns to profiles. Nucleic Acids Res. 31, 374-378 (2003).
31. Swinnen, J.V. et al. Stimulation of tumor-associated fatty acid synthase expression by growth factor activation of the sterol regulatory element-binding protein pathway. Oncogene 19, 5173-5181 (2000).
32. Liu, T., Belov, M.E., Jaitly, N., Qian, W.J. & Smith, R.D. Accurate mass measurements in proteomics. Chem. Rev. 107, 3621-3653 (2007).
33. Kuster, B., Schirle, M., Mallick, P. & Aebersold, R. Scoring proteomes with proteotypic peptide probes. Nat. Rev. Mol. Cell Biol. 6, 577-583 (2005).
34. de Godoy, L.M. et al. Comprehensive mass-spectrometry-based proteome quantification of haploid versus diploid yeast. Nature 455, 1251-1254 (2008).
35. Huh, W.K. et al. Global analysis of protein localization in budding yeast. Nature 425, 686-691 (2003).
36. Ghaemmaghami, S. et al. Global analysis of protein expression in yeast. Nature 425, 737-741 (2003).
37. King, N.L. et al. Analysis of the Saccharomyces cerevisiae proteome with Peptide Atlas. Genome Biol. 7, R106 (2006).
38. Graumann, J. et al. SILAC-labeling and proteome quantitation of mouse embryonic stem cells to a depth of 5111 proteins. Mol. Cell Proteomics 7, 672-683 (2008).
39. Eriksson, J. & Fenyo, D. Improving the success rate of proteome analysis by modeling protein-abundance distributions and experimental designs. Nat. Biotechnol. 25, 651-655 (2007).
40. Mann, M. & Kelleher, N.L. Special feature: precision proteomics: The case for high resolution and high mass accuracy. Proc. Natl. Acad. Sci. USA. published online, doi: 10.1073/pnas.0800788105 (25 September 2008).
41. Cox, J., Hubner, N.C. & Mann, M. How much peptide sequence information is contained in ion trap tandem mass spectra? J. Am. Soc. Mass. Spectrom. published online, doi:10.1016/j.jasms.2008.07.024 (7 August 2008).
42. Ong, S.E. & Mann, M. A practical recipe for stable isotope labeling by amino acids in cell culture (SILAC). Nat. Protocols 1, 2650-2660 (2006).
43. Rappsilber, J., Mann, M. & Ishihama, Y. Protocol for micro-purification, enrichment, pre-fractionation and storage of peptides for proteomics using StageTips. Nat. Protocols 2, 1896-1906 (2007).