Skip to main page content
Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2007 Aug;Chapter 25:Unit25.2.
doi: 10.1002/0471140864.ps2502s49.

Overview of Tandem Mass Spectrometry (MS/MS) Database Search Algorithms


Overview of Tandem Mass Spectrometry (MS/MS) Database Search Algorithms

Eugene Kapp et al. Curr Protoc Protein Sci. .


Mass spectrometry-based methods for the identification of proteins are fundamental platform technologies for proteomics. One comprehensive approach is to subject trypsinized peptides to tandem mass spectrometry (MS/MS) to obtain detailed structural information. Different strategies are available for interpreting MS/MS data and hence deducing the amino acid sequence of the peptides. The most common method is to use a search algorithm to identify peptides by correlating experimental and theoretical MS/MS data (the latter being generated from possible peptides in the protein sequence database). Identified peptides are collated and protein entries from the sequence database inferred. This unit focuses on the most widely used tandem MS peptide identification search algorithms (commercial and open source), their availability, ease of use, strengths, speed and scoring, as well as their relative sensitivity and specificity.

Similar articles

See all similar articles

Cited by 12 articles

See all "Cited by" articles

LinkOut - more resources