Comparative Evaluation of Tandem MS Search Algorithms Using a Target-Decoy Search Strategy*S

Peptide identification of tandem mass spectra by a variety of available search algorithms forms the foundation for much of modern day mass spectrometry-based proteomics. Despite the critical importance of proper evaluation and interpretation of the results generated by these algorithms there is still little consistency in their application or understanding of their similarities and differences. A survey was conducted of four tandem mass spectrometry peptide identification search algorithms, including Mascot, Open Mass Spectrometry Search Algorithm, Sequest, and X! Tandem. The same input data, search parameters, and sequence library were used for the searches. Comparisons were based on commonly used scoring methodologies for each algorithm and on the results of a target-decoy approach to sequence library searching. The results indicated that there is little difference in the output of the algorithms so long as consistent scoring procedures are applied. The results showed that some commonly used scoring procedures may lead to excessive false discovery rates. Finally an alternative method for the determination of an optimal cutoff threshold is proposed.

• Publication year

  2007

• Venue

  Molecular & Cellular Proteomics

• Publication date

  2007-09-01

• Fields of study

  Biology, Medicine, Chemistry

• Identifiers
  DOI 10.1074/mcp.M600469-MCP200PMID 17533222
• External record

  Open on Semantic Scholar

• Source metadata

  Semantic Scholar, PubMed

• No claims are published for this paper.

• No concepts are published for this paper.

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