Chapter 3: Peptide Spectrum Matching via Database Search and Spectral Library Search

Brian Netzel, Surendra Dasari

Research output: Chapter in Book/Report/Conference proceedingChapter


High-throughput shotgun proteomics is the mainstay of protein identification in biological samples. Efficient proteomic analysis requires streamlined and accurate workflows for protein identification. Database searching has been the most basic and reliable workflow for identifying the peptides and proteins that are present in the sample. This method derives peptides from a list of protein sequences and matches them against the experimental MS2 spectra. The resulting peptide spectrum matches are scored to quantify their goodness of fit. Spectral library searching has been recently developed as a fast, and viable, alternative to sequence database searching. This method attempts to identify the peptides by matching their corresponding experimental MS2 spectra to a library of curated MS2 peptide spectra. Each method has its own merit and application in the proteomics field. This chapter aims to highlight the foundations of peptide spectrum matching via protein sequence database and spectral library searching.

Original languageEnglish (US)
Title of host publicationProteome Informatics
EditorsSimon J. Gaskell, Conrad Bessant
PublisherRoyal Society of Chemistry
Number of pages30
ISBN (Electronic)9781782624288
StatePublished - 2017

Publication series

NameNew Developments in Mass Spectrometry
ISSN (Electronic)2045-7553

ASJC Scopus subject areas

  • Analytical Chemistry
  • Spectroscopy


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