Using spectral libraries for peptide identification from tandem mass spectrometry (MS/MS) data.
Spectral library searching is an emerging approach in proteomic data analysis for the inference of peptide identifications from tandem mass spectra. It offers a promising alternative to sequence database searching, currently the dominant method for this purpose. In spectral searching, a spectral library is first meticulously compiled from a large collection of previously observed and identified peptide MS/MS spectra. The spectrum of the unknown peptide can then by identified by comparing it to all the candidates in the spectral library for the best match. This unit covers the basic principles of spectral searching, describes its advantages and limitations, and reviews the available software tools developed for spectral library searching and building, in terms of their algorithms and their surrounding informatics support.
Lam
Henry
H
Hong Kong University of Science and Technology, Kowloon, Hong Kong.
Aebersold
Ruedi
R
Institute for Systems Biology, Seattle, Washington.
D003628:Database Management Systems; D030562:Databases, Protein; D020407:Internet; D010446:Peptide Fragments / Q000737:chemistry*; D019151:Peptide Library; D011506:Proteins / Q000737:chemistry*; D012984:Software; D053719:Tandem Mass Spectrometry / Q000379:methods*; D014584:User-Computer Interface
D010446:Peptide Fragments; D019151:Peptide Library; D011506:Proteins
Aebersold, R. and Mann, M. 2003. Mass spectrometry-based proteomics. Nature 422:198-207.
Craig, R. and Beavis, R.C. 2004. TANDEM: Matching proteins with tandem mass spectra. Bioinformatics 20:1466-1467.
Craig, R., Cortens, J.C., Fenyo, D., and Beavis, R.C. 2006. Using annotated peptide mass spectrum libraries for protein identification. J. Proteome Res. 5:1843-1849.
Domokos, L., Hennberg, D., and Weimann, B. 1984. Computer-aided identification of compounds by comparison of mass spectra. Anal. Chim. Acta 165:61-74.
Domon, B. and Aebersold, R. 2006. Challenges and opportunities in proteomics data analysis. Mol. Cell. Proteomics 5:1921-1926.
Eng, J.K., McCormack, A.L., and Yates, J.R., III. 1994. An approach to correlate tandem mass spectral data of peptides with amino acid sequences in a protein database. J. Am. Soc. Mass Spectrom. 5:976-989.
Frewen, B.E., Merrihew, G.E., Wu, C.C., Noble, W.S., and MacCoss, M.J. 2006. Analysis of peptide MS/MS spectra from large-scale proteomics experiments using spectrum libraries. Anal. Chem. 78:5678-5684.
Hunt, D.F. and Henderson, R.A. 1992. Characterization of peptides bound to the class I MHC molecule HLA-A2.1 by mass spectrometry. Science 255:1261-1263.
Keller, A., Eng, J., Zhang, N., Li, X.J., and Aebersold, R. 2005. A uniform proteomics MS/MS analysis platform utilizing open XML file formats. Mol. Sys. Biol. 1:17.
Kuster, B., Schirle, M., Mallick, P., and Aebersold, R. 2005. Scoring proteomes with proteotypic peptide probes. Nat. Rev. Mol. Cell Biol. 6:577-583.
Lam, H., Deutsch, E.W., Eddes, J.S., Eng, J.K., King, N., Stein, S.E., and Aebersold, R. 2007. Development and validation of a spectral library searching method for peptide identification from MS/MS. Proteomics 7:655-667.
Lam, H., Deutsch, E.W., Eddes, J.S., Eng, J.K., Stein, S.E., and Aebersold, R. 2008. Building consensus spectral libraries for peptide identification in proteomics. Nat. Methods 5:873-875.
Patterson, S.D. 2003. Data analysis-The Achilles heel of proteomics. Nat. Biotechnol. 21:221-222.
Picotti, P., Lam, H., Campbell, D., Deutsch, E., Mirzaei, H., Ranish, J., Domon, B., and Aebersold, R. 2008. A database of validated assays for the targeted mass spectrometric analysis of the S. cerevisiae proteome. Nat. Methods 5:913-914.
Prakash, A., Tomazela, D.M., Frewen, B., Maclean B., Merrihew, G., Peterman, S., and Maccoss, M.J. 2009. Expediting the development of targeted SRM assays: Using data from shotgun proteomics to automate method development. J. Proteome Res. 8:2733-2739.
Sherwood, C., Eastham, A., Peterson, A., Eng, J.K., Shteynberg, D., Mendoza, L., Deutsch, E., Risler, J., Lee, L.W., Tasman, N., Aebersold, R., Lam, H., and Martin, D.B. 2009. MaRiMba: A software application for spectral library-based MRM transition list assembly. J. Proteome Res. 8:4396-4405.
Steen, H. and Mann, M. 2004. The ABC's (and XYZ's) of peptide sequencing. Nature Rev. Mol. Cell Biol. 5:699-711.
Stein, S.E. and Scott, D.R. 1994. Optimization and testing of mass spectral library search algorithms for compound identification. J. Am. Soc. Mass Spectrom. 5:859-866.
Yates, J.R., 3rd, Morgan, S.F., Gatlin, C.L., Griffin, P.R., and Eng, J.K. 1998. Method to compare collision-induced dissociation spectra of peptides: Potential for library searching and subtractive analysis. Anal. Chem., 70:3557-3565.