Crescendo: A protein sequence database search engine for tandem mass spectra

Jianqi Wang, Yajie Zhang, Yonghao Yu

Research output: Contribution to journalArticlepeer-review

Abstract

A search engine that discovers more peptides reliably is essential to the progress of the computational proteomics. We propose two new scoring functions (L-and P-scores), which aim to capture similar characteristics of a peptide-spectrum match (PSM) as Sequest and Comet do. Crescendo, introduced here, is a software program that implements these two scores for peptide identification. We applied Crescendo to test datasets and compared its performance with widely used search engines, including Mascot, Sequest, and Comet. The results indicate that Crescendo identifies a similar or larger number of peptides at various predefined false discovery rates (FDR). Importantly, it also provides a better separation between the true and decoy PSMs, warranting the future development of a companion post-processing filtering algorithm. [Figure not available: see fulltext.]

Original languageEnglish (US)
Pages (from-to)1077-1084
Number of pages8
JournalJournal of the American Society for Mass Spectrometry
Volume26
Issue number7
DOIs
StatePublished - Jul 22 2015

Keywords

  • Peptide-spectrum match
  • Search engine
  • Tandem mass spectrometry

ASJC Scopus subject areas

  • Structural Biology
  • Spectroscopy

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