A posteriori quality control for the curation and reuse of public proteomics data

Proteomics

Volumn 11, Issue 11, 2011, Pages 2182-2194

  Foster, Joseph M ^a   Degroeve, Sven ^b,c   Gatto, Laurent ^d   Visser, Matthieu ^e   Wang, Rui ^a   Griss, Johannes ^f   Apweiler, Rolf ^a   Martens, Lennart ^b,c  

^a EUROPEAN BIOINFORMATICS INSTITUTE   (United Kingdom)

^b DEPARTMENT OF PLANT SYSTEMS BIOLOGY   (Belgium)

^c GHENT UNIVERSITY   (Belgium)

^d UNIVERSITY OF CAMBRIDGE   (United Kingdom)

^e PHILIPS RESEARCH LABORATORIES   (Netherlands)

^f UNIVERSITY OF VIENNA   (Austria)

Author keywords

Bioinformatics; PRIDE; Quality assurance; Quality control

Indexed keywords

ARTICLE; AUTOMATION; DATA BASE; INFORMATION PROCESSING; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEOMICS; QUALITY CONTROL;

DATA MINING; DATABASE MANAGEMENT SYSTEMS; DATABASES, PROTEIN; HUMANS; PROTEOMICS;

EID: 79956281509     PISSN: 16159853     EISSN: 16159861     Source Type: Journal    
DOI: 10.1002/pmic.201000602     Document Type: Article

References (30)

1. Service, R. F., Proteomics. Proteomics ponders prime time. Science 2008, 321, 1758-1761.
2. Omenn, G. S., States, D. J., Adamski, M., Blackwell, T. W. et al., Overview of the HUPO Plasma Proteome Project: results from the pilot phase with 35 collaborating laboratories and multiple analytical groups, generating a core dataset of 3020 proteins and a publicly-available database. Proteomics 2005, 5, 3226-3245.
3. Choudhary, C., Mann, M., Decoding signalling networks by mass spectrometry-based proteomics. Nat. Rev. Mol. Cell Biol. 2010 11, 427-439.
4. Przybylski, C., Jünger, M. A., Aubertin, J., Radvanyi, F. et al., Quantitative analysis of protein complex constituents and their phosphorylation states on a LTQ-orbitrap instrument. J. Proteome Res. 2010, 9, 5118-5132.
5. Rifai, N., Gillette, M. A., Carr, S. A., Protein biomarker discovery and validation: the long and uncertain path to clinical utility. Nat. Biotechnol. 2006, 24, 971-983.
6. Craig, R., Cortens, J. P., Beavis, R. C., Open source system for analyzing, validating, and storing protein identification data. J. Proteome Res. 2004, 3, 1234-1242.
7. Desiere, F., Deutsch, E. W., Nesvizhskii, A. I., Mallick, P. et al., Integration with the human genome of peptide sequences obtained by high-throughput mass spectrometry. Genome Biol. 2005, 6, R9.
8. Martens, L., Hermjakob, H., Jones, P., Adamski, M. et al., PRIDE: the proteomics identifications database. Proteomics 2005, 5, 3537-3545.
9. Slotta, D. J., Barrett, T., Edgar, R., NCBI Peptidome: a new public repository for mass spectrometry peptide identifications. Nat. Biotechnol. 2009, 27, 600-601.
10. Klie, S., Martens, L., Vizcaíno, J. A., Côté, R. et al., Analyzing large-scale proteomics projects with latent semantic indexing. J. Proteome Res. 2008, 7, 182-191.
11. Mueller, M., Vizcaíno, J. A., Jones, P., Côté, R. et al., Analysis of the experimental detection of central nervous system-related genes in human brain and cerebrospinal fluid datasets. Proteomics 2008, 8, 1138-1148.
12. Mallick, P., Schirle, M., Chen, S. S., Flory, M. R. et al., Computational prediction of proteotypic peptides for quantitative proteomics. Nat. Biotechnol. 2007, 25, 125-131.
13. Sherwood, C. A., Eastham, A., Lee, L. W., Peterson, A. et al., MaRiMba: a software application for spectral library-based MRM transition list assembly. J. Proteome Res. 2009, 8, 4396-4405.
14. Lam, H., Deutsch, E. W., Eddes, J. S., Eng, J. K. et al., Building consensus spectral libraries for peptide identification in proteomics. Nat. Methods 2008, 5, 873-875.
15. Tabb, D. L., Vega-Montoto, L., Rudnick, P. A., Variyath, A. M. et al., Repeatability and reproducibility in proteomic identifications by liquid chromatography-tandem mass spectrometry. J. Proteome Res. 2010, 9, 761-776.
16. Rudnick, P. A., Clauser, K. R., Kilpatrick, L. E., Tchekhovskoi, D. V. et al., Performance metrics for liquid chromatography-tandem mass spectrometry systems in proteomics analyses. Mol. Cell. Proteomics 2010, 9, 225-241.
17. Qian, W. J., Kaleta, D. T., Petritis, B. O., Jiang, H. et al., Enhanced detection of low abundance human plasma proteins using a tandem IgY12-SuperMix immunoaffinity separation strategy. Mol. Cell. Proteomics 2008, 7, 1963-1973.
18. Liu, T., Qian, W. J., Gritsenko, M. A., Xiao, W. et al., Inflammation and the host response to injury large scale collaborative research programm. High dynamic range characterization of the trauma patient plasma proteome. Mol. Cell. Proteomics 2006, 5, 1899-1913.
19. Bell, A. W., Deutsch, E. W., Au, C. E., Kearney, R. E. et al., HUPO Test Sample Working Group. A HUPO test sample study reveals common problems in mass spectrometry-based proteomics. Nat. Methods 2009, 6, 423-430.
20. Cox, J., Mann, M., MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification. Nat. Biotechnol. 2008, 26, 1367-1372.
21. Chelius, D., Bondarenko, P. V., Quantitative profiling of proteins in complex mixtures using liquid chromatography and mass spectrometry. J. Proteome Res. 2002, 1, 317-323.
22. Bondarenko, P. V., Chelius, D., Shaler, T. A., Identification and relative quantitation of protein mixtures by enzymatic digestion followed by capillary reversed-phase liquid chromatography-tandem mass spectrometry. Anal. Chem. 2002, 74, 4741-4749.
23. Schiess, R., Wollscheid, B., Aebersold, R., Targeted proteomic strategy for clinical biomarker discovery. Mol. Oncol. 2009, 3, 33-44.
24. Vizcaíno, J. A., Côté, R., Reisinger, F., Foster, J. M. et al., A guide to the Proteomics Identifications Database proteomics data repository. Proteomics 2009, 9, 4276-4283.
25. Yang, H. J., Hong, J., Lee, S., Shin, S. et al., Pressure-assisted tryptic digestion using a syringe. Rapid Commun. Mass Spectrom. 2010, 24, 901-908.
26. Keller, B. O., Sui, J., Young, A. B., Whittal, R. M., Interferences and contaminants encountered in modern mass spectrometry. Anal. Chim. Acta 2008, 627, 71-81.
27. Ross, P. L., Huang, Y. N., Marchese, J. N., Williamson, B. et al., Multiplexed protein quantitation in Saccharomyces cerevisiae using amine-reactive isobaric tagging reagents. Mol. Cell. Proteomics 2004, 3, 1154-1169.
28. Thompson, A., Schäfer, J., Kuhn, K., Kienle, S. et al., Tandem mass tags: a novel quantification strategy for comparative analysis of complex protein mixtures by MS/MS. Anal. Chem. 2003, 75, 1895-1904.
29. Houel, S., Abernathy, R., Renganathan, K., Meyer-Arendt, K. et al., Quantifying the impact of chimera MS/MS spectra on peptide identification in large-scale proteomics studies. J. Proteome Res. 2010, 9, 4152-4160.
30. Yi, J., Kim, C., Gelfand, C. A., Inhibition of intrinsic proteolytic activities moderates preanalytical variability and instability of human plasma. J. Proteome Res. 2007, 6, 1768-1781.