Spectral library searching in proteomics

Proteomics

Volumn 16, Issue 5, 2016, Pages 729-740

  Griss, Johannes ^a,b  

^a Universitatsklinik fur Dermatologie   (Austria)

^b WELLCOME TRUST SANGER INSTITUTE   (United Kingdom)

Author keywords

Bioinformatics; Spectral libraries; Spectral library searching; Spectrum clustering

Indexed keywords

ALGORITHM; AMINO ACID SEQUENCE; BIOINFORMATICS; CLOUD COMPUTING; DATA ANALYSIS; PRIORITY JOURNAL; PROTEOMICS; QUALITY CONTROL; REVIEW; SCORING SYSTEM; SEARCH ENGINE; SPECTRAL LIBRARY SEARCH; SUPPORT VECTOR MACHINE; TANDEM MASS SPECTROMETRY; PEPTIDE LIBRARY; PROCEDURES; PROTEIN DATABASE;

PEPTIDE LIBRARY;

ALGORITHMS; DATABASES, PROTEIN; PEPTIDE LIBRARY; PROTEOMICS; SEARCH ENGINE; TANDEM MASS SPECTROMETRY;

EID: 84959562694     PISSN: 16159853     EISSN: 16159861     Source Type: Journal    
DOI: 10.1002/pmic.201500296     Document Type: Review

References (61)

1. MacCoss, M. J., Computational analysis of shotgun proteomics data. Curr. Opin. Chem. Biol. 2005, 9, 88-94.
2. Zhang, X., Li, Y., Shao, W., Lam, H., Understanding the improved sensitivity of spectral library searching over sequence database searching in proteomics data analysis. Proteomics 2011, 11, 1075-1085.
3. Ahrne, E., Masselot, A., Binz, P. A., Muller, M., Lisacek, F., A simple workflow to increase MS2 identification rate by subsequent spectral library search. Proteomics 2009, 9, 1731-1736.
4. Ning, K., Fermin, D., Nesvizhskii, A. I., Computational analysis of unassigned high-quality MS/MS spectra in proteomic data sets. Proteomics 2010, 10, 2712-2718.
5. Lam, H., Deutsch, E. W., Eddes, J. S., Eng, J. K. et al., Development and validation of a spectral library searching method for peptide identification from MS/MS. Proteomics 2007, 7, 655-667.
6. Craig, R., Cortens, J. C., Fenyo, D., Beavis, R. C., Using annotated peptide mass spectrum libraries for protein identification. J. Proteome Res. 2006, 5, 1843-1849.
7. Frewen, B. E., Merrihew, G. E., Wu, C. C., Noble, W. S., MacCoss, M. J., Analysis of peptide MS/MS spectra from large-scale proteomics experiments using spectrum libraries. Anal. Chem. 2006, 78, 5678-5684.
8. Liu, J., Bell, A. W., Bergeron, J. J., Yanofsky, C. M. et al., Methods for peptide identification by spectral comparison. Proteome Sci. 2007, 5, 3.
9. Lee, S., Kwon, M. S., Lee, H. J., Paik, Y. K. et al., Enhanced peptide quantification using spectral count clustering and cluster abundance. BMC Bioinformatics 2011, 12, 423.
10. 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.
11. Baumgardner, L. A., Shanmugam, A. K., Lam, H., Eng, J. K., Martin, D. B., Fast parallel tandem mass spectral library searching using GPU hardware acceleration. J. Proteome Res. 2011, 10, 2882-2888.
12. Mohammed, Y., Mostovenko, E., Henneman, A. A., Marissen, R. J. et al., Cloud parallel processing of tandem mass spectrometry based proteomics data. J. Proteome Res. 2012, 11, 5101-5108.
13. Shao, W., Zhu, K., Lam, H., Refining similarity scoring to enable decoy-free validation in spectral library searching. Proteomics 2013, 13, 3273-3283.
14. Ma, C. W., Lam, H., Hunting for unexpected post-translational modifications by spectral library searching with tier-wise scoring. J. Proteome Res. 2014, 13, 2262-2271.
15. Onder, O., Shao, W., Lam, H., Brisson, D., Tracking the sources of blood meals of parasitic arthropods using shotgun proteomics and unidentified tandem mass spectral libraries. Nature Protocols 2014, 9, 842-850.
16. Wang, J., Perez-Santiago, J., Katz, J. E., Mallick, P., Bandeira, N., Peptide identification from mixture tandem mass spectra. Mol. Cell. Proteomics 2010, 9, 1476-1485.
17. Ahrne, E., Nikitin, F., Lisacek, F., Muller, M., QuickMod: a tool for open modification spectrum library searches. J. Proteome Res. 2011, 10, 2913-2921.
18. Dasari, S., Chambers, M. C., Martinez, M. A., Carpenter, K. L. et al., Pepitome: evaluating improved spectral library search for identification complementarity and quality assessment. J. Proteome Res. 2012, 11, 1686-1695.
19. Ma, Z. Q., Dasari, S., Chambers, M. C., Litton, M. D., et al., IDPicker 2.0: improved protein assembly with high discrimination peptide identification filtering. J. Proteome Res. 2009, 8, 3872-3881.
20. Jones, A. R., Eisenacher, M., Mayer, G., Kohlbacher, O. et al., The mzIdentML data standard for mass spectrometry-based proteomics results. Mol. Cell. Proteomics 2012, 11, M111 014381.
21. Stein, S. E., Scott, D. R., Optimization and testing of mass spectral library search algorithms for compound identification. J. Am. Soc. Mass Spectrom. 1994, 5, 859-866.
22. Craig, R., Beavis, R. C., TANDEM: matching proteins with tandem mass spectra. Bioinformatics 2004, 20, 1466-1467.
23. Wu, X., Tseng, C. W., Edwards, N., HMMatch: peptide identification by spectral matching of tandem mass spectra using hidden Markov models. J. Comput. Biol. 2007, 14, 1025-1043.
24. Ye, D., Fu, Y., Sun, R. X., Wang, H. P. et al., Open MS/MS spectral library search to identify unanticipated post-translational modifications and increase spectral identification rate. Bioinformatics 2010, 26, i399-406.
25. Yen, C. Y., Houel, S., Ahn, N. G., Old, W. M., Spectrum-to-spectrum searching using a proteome-wide spectral library. Mol. Cell. Proteomics 2011, 10, M111 007666.
26. Yen, C. Y., Meyer-Arendt, K., Eichelberger, B., Sun, S. et al., A simulated MS/MS library for spectrum-to-spectrum searching in large scale identification of proteins. Mol. Cell. Proteomics 2009, 8, 857-869.
27. Tabb, D. L., Fernando, C. G., Chambers, M. C., MyriMatch: highly accurate tandem mass spectral peptide identification by multivariate hypergeometric analysis. J. Proteome Res. 2007, 6, 654-661.
28. Cannon, W. R., Rawlins, M. M., Baxter, D. J., Callister, S. J. et al., Large improvements in MS/MS-based peptide identification rates using a hybrid analysis. J. Proteome Res. 2011, 10, 2306-2317.
29. Kalyanaraman, A., Cannon, W. R., Latt, B., Baxter, D. J., MapReduce implementation of a hybrid spectral library-database search method for large-scale peptide identification. Bioinformatics 2011, 27, 3072-3073.
30. Li, H., Zong, N. C., Liang, X., Kim, A. K. et al., A novel spectral library workflow to enhance protein identifications. J. Proteomics 2013, 81, 173-184.
31. Toghi Eshghi, S., Shah, P., Yang, W., Li, X., Zhang, H., GPQuest: a spectral library matching algorithm for site-specific assignment of tandem mass spectra to intact N-glycopeptides. Anal. Chem. 2015, 87, 5181-5188.
32. Wang, M., Bandeira, N., Spectral library generating function for assessing spectrum-spectrum match significance. J. Proteome Res. 2013, 12, 3944-3951.
33. Desiere, F., Deutsch, E. W., King, N. L., Nesvizhskii, A. I. et al., The PeptideAtlas project. Nucleic Acids Res. 2006, 34, D655-658.
34. 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.
35. Taus, T., Kocher, T., Pichler, P., Paschke, C. et al., Universal and confident phosphorylation site localization using phosphoRS. J. Proteome Res. 2011, 10, 5354-5362.
36. Griss, J., Foster, J. M., Hermjakob, H., Vizcaino, J. A., PRIDE Cluster: building a consensus of proteomics data. Nat. Methods 2013, 10, 95-96.
37. 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.
38. Srikumar, T., Jeram, S. M., Lam, H., Raught, B., A ubiquitin and ubiquitin-like protein spectral library. Proteomics 2010, 10, 337-342.
39. Simicevic, J., Moniatte, M., Hamelin, R., Ahrne, E., Deplancke, B., A mammalian transcription factor-specific peptide repository for targeted proteomics. Proteomics 2015, 15, 752-756.
40. Dong, Q., Yan, X., Kilpatrick, L. E., Liang, Y. et al., Tandem mass spectral libraries of peptides in digests of individual proteins: Human Serum Albumin (HSA). Mol. Cell. Proteomics 2014, 13, 2435-2449.
41. Hu, Y., Lam, H., Expanding tandem mass spectral libraries of phosphorylated peptides: advances and applications. J. Proteome Res. 2013, 12, 5971-5977.
42. van der Plas-Duivesteijn, S. J., Mohammed, Y., Dalebout, H., Meijer, A. et al., Identifying proteins in zebrafish embryos using spectral libraries generated from dissected adult organs and tissues. J. Proteome Res. 2014, 13, 1537-1544.
43. Yang, X., Neta, P., Stein, S. E., Quality control for building libraries from electrospray ionization tandem mass spectra. Anal. Chem. 2014, 86, 6393-6400.
44. Zhang, Z., Prediction of low-energy collision-induced dissociation spectra of peptides with three or more charges. Anal. Chem. 2005, 77, 6364-6373.
45. Li, S., Arnold, R. J., Tang, H., Radivojac, P., On the accuracy and limits of peptide fragmentation spectrum prediction. Anal. Chem. 2011, 83, 790-796.
46. Ji, C., Arnold, R. J., Sokoloski, K. J., Hardy, R. W. et al., Extending the coverage of spectral libraries: a neighbor-based approach to predicting intensities of peptide fragmentation spectra. Proteomics 2013, 13, 756-765.
47. Suni, V., Imanishi, S. Y., Maiolica, A., Aebersold, R., Corthals, G. L., Confident site localization using a simulated phosphopeptide spectral library. J. Proteome Res. 2015, 14, 2348-2359.
48. Nesvizhskii, A. I., Vitek, O., Aebersold, R., Analysis and validation of proteomic data generated by tandem mass spectrometry. Nat. Methods 2007, 4, 787-797.
49. Ahrne, E., Ohta, Y., Nikitin, F., Scherl, A. et al., An improved method for the construction of decoy peptide MS/MS spectra suitable for the accurate estimation of false discovery rates. Proteomics 2011, 11, 4085-4095.
50. Cheng, C. Y., Tsai, C. F., Chen, Y. J., Sung, T. Y., Hsu, W. L., Spectrum-based method to generate good decoy libraries for spectral library searching in peptide identifications. J. Proteome Res. 2013, 12, 2305-2310.
51. Kocher, T., Pichler, P., De Pra, M., Rieux, L. et al., Development and performance evaluation of an ultralow flow nanoliquid chromatography-tandem mass spectrometry set-up. Proteomics 2014, 14, 1999-2007.
52. Chambers, M. C., Maclean, B., Burke, R., Amodei, D. et al., A cross-platform toolkit for mass spectrometry and proteomics. Nat. Biotechnol. 2012, 30, 918-920.
53. Tabb, D. L., Thompson, M. R., Khalsa-Moyers, G., VerBerkmoes, N. C., McDonald, W. H., MS2Grouper: group assessment and synthetic replacement of duplicate proteomic tandem mass spectra. J. Am. Soc. Mass Spectrom. 2005, 16, 1250-1261.
54. Frank, A. M., Bandeira, N., Shen, Z., Tanner, S. et al., Clustering millions of tandem mass spectra. J. Proteome Res. 2008, 7, 113-122.
55. Frank, A. M., Monroe, M. E., Shah, A. R., Carver, J. J. et al., Spectral archives: extending spectral libraries to analyze both identified and unidentified spectra. Nat. Methods 2011, 8, 587-591.
56. Onder, O., Shao, W., Kemps, B. D., Lam, H., Brisson, D., Identifying sources of tick blood meals using unidentified tandem mass spectral libraries. Nat. Commun. 2013, 4, 1746.
57. Bandeira, N., Tsur, D., Frank, A., Pevzner, P. A., Protein identification by spectral networks analysis. Proc. Natl. Acad. Sci. U S A 2007, 104, 6140-6145.
58. Bandeira, N., Clauser, K. R., Pevzner, P. A., Shotgun protein sequencing: assembly of peptide tandem mass spectra from mixtures of modified proteins. Mol. Cell. Proteomics 2007, 6, 1123-1134.
59. Bandeira, N., Pham, V., Pevzner, P., Arnott, D., Lill, J. R., Automated de novo protein sequencing of monoclonal antibodies. Nat. Biotechnol. 2008, 26, 1336-1338.
60. Falkner, J. A., Falkner, J. W., Yocum, A. K., Andrews, P. C., A spectral clustering approach to MS/MS identification of post-translational modifications. J. Proteome Res. 2008, 7, 4614-4622.
61. Hoopmann, M. R., Moritz, R. L., Current algorithmic solutions for peptide-based proteomics data generation and identification. Curr. Opi. Biotechnol. 2013, 24, 31-38.