Building and Searching Tandem Mass Spectral Libraries for Peptide Identification

Henry Lam

doi:10.1074/mcp.r111.008565

Abstract

Spectral library searching is an emerging approach in peptide identifications from tandem mass spectra, a critical step in proteomic data analysis. Conceptually, the premise of this approach is that the tandem MS fragmentation pattern of a peptide under some fixed conditions is a reproducible fingerprint of that peptide, such that unknown spectra acquired under the same conditions can be identified by spectral matching. In actual practice, a spectral library is first meticulously compiled from a large collection of previously observed and identified tandem MS spectra, usually obtained from shotgun proteomics experiments of complex mixtures. Then, a query spectrum is then identified by spectral matching using recently developed spectral search engines. This review discusses the basic principles of the two pillars of this approach: spectral library construction, and spectral library searching. An overview of the software tools available for these two tasks, as well as a high-level description of the underlying algorithms, will be given. Finally, several new methods that utilize spectral libraries for peptide identification in ways other than straightforward spectral matching will also be described.

Highlights

In the past decade and a half, mass spectrometry-based proteomics has witnessed breathtaking advances
The key steps of this approach are: [1] proteins are digested into shorter peptides that are more amenable to liquid chromatography (LC)-MS analysis, [2] peptides are further fragmented by tandem mass spectrometry (MS/MS)1 to yield characteristic fragmentation patterns, and [3] the MS/MS spectra are assigned to their originating peptides by various computational methods [1,2,3,4]
Concluding Remarks—This review offers a brief overview of the software tools and underlying algorithms in building and searching spectral libraries for proteomics applications

Summary

Henry Lam

Spectral library searching is an emerging approach in peptide identifications from tandem mass spectra, a critical step in proteomic data analysis. Received February 8, 2011, and in revised form, June 8, 2011 Published, MCP Papers in Press, September 6, 2011, DOI 10.1074/ mcp.R111.008565 1 The abbreviations used are: MS/MS, tandem MS; NIST, National Institute of Science of Technology This last step of assigning MS/MS spectra to their peptide identifications is often the rate-limiting step of the whole proteomics experiment, and has received well-deserved attention over the past decade. The widely used NIST/NIH/EPA mass spectral library (http://www.nist.gov/srd/nist1a.cfm), developed by the National Institute of Science of Technology (NIST), contains over 200,000 mass spectra of mostly small organic molecules (18 –20) It was only in 1999, that the concept of spectral library searching was introduced to proteomics, in the work of Yates et al [14], which demonstrated that peptide MS/MS spectra are reproducible enough for this

Building and Searching Peptide Spectral Libraries

Useful websites for spectral library building and searching tools