Using Spectral Libraries for Peptide Identification from Tandem Mass Spectrometry (MS/MS) Data
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Abstract
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. Curr. Protoc. Protein Sci. 60:25.5.1?25.5.9. © 2010 by John Wiley & Sons, Inc.
Keywords: spectral library; spectral searching; X!Hunter; Bibliospec; SpectraST; NIST MS search
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PDF or HTML at Wiley Online LibraryTable of Contents
- Background
- Advantages and Limitations of Spectral Searching
- Spectral Search Engines
- Libraries
- Conclusions
- Acknowledgment
- Literature Cited
- Figures
- Tables
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Figure 25.5.1 Spectral searching identifies more spectra than sequence searching at the same confidence level. A large dataset from Human Proteome Organization (HUPO) Plasma Proteome Project (PPP) is searched with the spectral search engine SpectraST against the NIST human library (v2.0). The same dataset is searched with the sequence search engine X!Tandem with K‐score plugin against two different databases: the full International Protein Index (IPI) database, dated 2005‐09‐20, and a reduced database containing only peptides in the NIST human library (v2.0). This illustrates that the advantage in sensitivity enjoyed by spectral searching is only partially explained by the reduction of search space; the use of real reference spectra must also play a role. View Image -
Figure 25.5.2 Peptide identification by spectral searching. The top spectrum is the library spectrum of the peptide ion VGVHLGLFNC[339]IK (+2). The bottom spectrum (upside down) is a relatively noisy spectrum that cannot be identified by SEQUEST, a sequence search engine, but identified by SpectraST, a spectral search engine. In spectral searching, a correct match is indicated by the global similarity between the library and query spectra, and not merely the presence of canonical fragment peaks. Shown here is a screenshot of the accompanying spectrum visualization tool of SpectraST. View Image
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Literature Cited
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