Data extraction from proteomics raw data: An evaluation of nine tandem MS tools using a large Orbitrap data set

Journal of Proteomics

Volumn 75, Issue 17, 2012, Pages 5293-5303

  Mancuso, Francesco ^a   Bunkenborg, Jakob ^b   Wierer, Michael ^a   Molina, Henrik ^a,c  

^a CENTRE FOR GENOMIC REGULATION CRG   (Spain)

^b UNIVERSITY OF SOUTHERN DENMARK   (Denmark)

^c ROCKEFELLER UNIVERSITY   (United States)

Author keywords

CID; Extraction tools; HCD; Orbitrap; Tandem mass spectrometry

Indexed keywords

PEPTIDE;

ACCURACY; AMINO ACID SEQUENCE; ARTICLE; DATA EXTRACTION; PRIORITY JOURNAL; PROTEIN DENATURATION; PROTEIN PHOSPHORYLATION; PROTEOMICS; TANDEM MASS SPECTROMETRY;

AUTOMATIC DATA PROCESSING; DATA INTERPRETATION, STATISTICAL; DATABASES, PROTEIN; MODELS, BIOLOGICAL; PEPTIDES; PHOSPHORYLATION; PROTEIN KINASES; PROTEOMICS; REPRODUCIBILITY OF RESULTS; SEARCH ENGINE; SOFTWARE; TANDEM MASS SPECTROMETRY; VALIDATION STUDIES AS TOPIC;

EID: 84865553658     PISSN: 18743919     EISSN: 18767737     Source Type: Journal    
DOI: 10.1016/j.jprot.2012.06.012     Document Type: Article

References (32)

1. Balgley B.M., Laudeman T., Yang L., Song T., Lee C.S. Comparative evaluation of tandem MS search algorithms using a target-decoy search strategy. Mol Cell Proteomics 2007, 6:1599-1608.
2. Kandasamy K., Pandey A., Molina H. Evaluation of several MS/MS search algorithms for analysis of spectra derived from electron transfer dissociation experiments. Anal Chem 2009, 81:7170-7180.
3. Kapp E.A., Schutz F., Connolly L.M., Chakel J.A., Meza J.E., Miller C.A., et al. An evaluation, comparison, and accurate benchmarking of several publicly available MS/MS search algorithms: sensitivity and specificity analysis. Proteomics 2005, 5:3475-3490.
4. Gentzel M., Kocher T., Ponnusamy S., Wilm M. Preprocessing of tandem mass spectrometric data to support automatic protein identification. Proteomics 2003, 3:1597-1610.
5. Kocher T., Pichler P., Mazanek M., Swart R., Mechtler K. Altered Mascot search results by changing the m/z range of MS/MS spectra: analysis and potential applications. Anal Bioanal Chem 2011, 400:2339-2347.
6. Hu Q., Noll R.J., Li H., Makarov A., Hardman M., Graham Cooks R. The Orbitrap: a new mass spectrometer. J Mass Spectrom 2005, 40:430-443.
7. Mayampurath A.M., Jaitly N., Purvine S.O., Monroe M.E., Auberry K.J., Adkins J.N., et al. DeconMSn: a software tool for accurate parent ion monoisotopic mass determination for tandem mass spectra. Bioinformatics 2008, 24:1021-1023.
8. Mortensen P., Gouw J.W., Olsen J.V., Ong S.E., Rigbolt K.T., Bunkenborg J., et al. MSQuant, an open source platform for mass spectrometry-based quantitative proteomics. J Proteome Res 2010, 9:393-403.
9. 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.
10. Cox J., Matic I., Hilger M., Nagaraj N., Selbach M., Olsen J.V., et al. A practical guide to the MaxQuant computational platform for SILAC-based quantitative proteomics. Nat Protoc 2009, 4:698-705.
11. Cox J., Neuhauser N., Michalski A., Scheltema R.A., Olsen J.V., Mann M. Andromeda: a peptide search engine integrated into the MaxQuant environment. J Proteome Res 2011, 10:1794-1805.
12. Olsen J.V., de Godoy L.M., Li G., Macek B., Mortensen P., Pesch R., et al. Parts per million mass accuracy on an Orbitrap mass spectrometer via lock mass injection into a C-trap. Mol Cell Proteomics 2005, 4:2010-2021.
13. Matthiesen R. Virtual Expert Mass Spectrometrist v3.0: an integrated tool for proteome analysis. Methods Mol Biol 2007, 367:121-138.
14. Matthiesen R., Trelle M.B., Hojrup P., Bunkenborg J., Jensen O.N. VEMS 3.0: algorithms and computational tools for tandem mass spectrometry based identification of post-translational modifications in proteins. J Proteome Res 2005, 4:2338-2347.
15. 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 1999, 20:3551-3567.
16. Vizcaino J.A., Cote R., Reisinger F., Barsnes H., Foster J.M., Rameseder J., et al. The Proteomics Identifications database: 2010 update. Nucleic Acids Res 2010, 38:D736-D742.
17. Xu M., Geer L.Y., Bryant S.H., Roth J.S., Kowalak J.A., Maynard D.M., et al. Assessing data quality of peptide mass spectra obtained by quadrupole ion trap mass spectrometry. J Proteome Res 2005, 4:300-305.
18. Bern M., Goldberg D., McDonald W.H., Yates J.R. Automatic quality assessment of peptide tandem mass spectra. Bioinformatics 2004, 20(Suppl. 1):i49-i54.
19. Salmi J., Moulder R., Filen J.J., Nevalainen O.S., Nyman T.A., Lahesmaa R., et al. Quality classification of tandem mass spectrometry data. Bioinformatics 2006, 22:400-406.
20. Flikka K., Martens L., Vandekerckhove J., Gevaert K., Eidhammer I. Improving the reliability and throughput of mass spectrometry-based proteomics by spectrum quality filtering. Proteomics 2006, 6:2086-2094.
21. Renard B.Y., Kirchner M., Monigatti F., Ivanov A.R., Rappsilber J., Winter D., et al. When less can yield more-computational preprocessing of MS/MS spectra for peptide identification. Proteomics 2009, 9:4978-4984.
22. Brosch M., Swamy S., Hubbard T., Choudhary J. Comparison of Mascot and X!Tandem performance for low and high accuracy mass spectrometry and the development of an adjusted Mascot threshold. Mol Cell Proteomics 2008, 7:962-970.
23. Frese C.K., Altelaar A.F., Hennrich M.L., Nolting D., Zeller M., Griep-Raming J., et al. Improved peptide identification by targeted fragmentation using CID, HCD and ETD on an LTQ-Orbitrap Velos. J Proteome Res 2011, 10:2377-2388.
24. Elias J.E., Gygi S.P. Target-decoy search strategy for increased confidence in large-scale protein identifications by mass spectrometry. Nat Methods 2007, 4:207-214.
25. Kall L., Canterbury J.D., Weston J., Noble W.S., MacCoss M.J. Semi-supervised learning for peptide identification from shotgun proteomics datasets. Nat Methods 2007, 4:923-925.
26. Renard B.Y., Timm W., Kirchner M., Steen J.A., Hamprecht F.A., Steen H. Estimating the confidence of peptide identifications without decoy databases. Anal Chem 2010, 82:4314-4318.
27. Gupta N., Pevzner P.A. False discovery rates of protein identifications: a strike against the two-peptide rule. J Proteome Res 2009, 8:4173-4181.
28. Kim S., Gupta N., Pevzner P.A. Spectral probabilities and generating functions of tandem mass spectra: a strike against decoy databases. J Proteome Res 2008, 7:3354-3363.
29. Vaudel M., Burkhart J.M., Sickmann A., Martens L., Zahedi R.P. Peptide identification quality control. Proteomics 2011, 11:2105-2114.
30. Lam H., Deutsch E.W., Aebersold R. Artificial decoy spectral libraries for false discovery rate estimation in spectral library searching in proteomics. J Proteome Res 2010, 9:605-610.
31. Hartler J., Thallinger G.G., Stocker G., Sturn A., Burkard T.R., Korner E., et al. MASPECTRAS: a platform for management and analysis of proteomics LC-MS/MS data. BMC Bioinformatics 2007, 8:197.
32. Price T.S., Lucitt M.B., Wu W., Austin D.J., Pizarro A., Yocum A.K., et al. EBP, a program for protein identification using multiple tandem mass spectrometry datasets. Mol Cell Proteomics 2007, 6:527-536.