From Wikipedia, the free encyclopedia
  (Redirected from PEAKS (software))
Jump to: navigation, search
Developer(s) Bioinformatics Solutions Inc
Stable release
PEAKS 8 / June 21, 2016
Operating system Windows
Type Mass Spec Protein Identification, De Novo Sequencing, Database Search & Quantification
License Proprietary commercial software

PEAKS is a proteomics software program for tandem mass spectrometry designed for peptide sequencing, protein identification and quantification.


PEAKS is commonly used for peptide identification (Protein ID) through de novo peptide sequencing assisted search engine database searching.[1] PEAKS has also integrated PTM and mutation characterization through automatic peptide sequence tag based searching (SPIDER)[2] and PTM Identification.[3]

PEAKS provides a complete sequence for each peptide, confidence scores on individual amino acid assignments, simple reporting for high-throughput analysis, amongst other information.

The software has the ability to compare results of multiple search engines. PEAKS inChorus will cross check test results automatically with other protein ID search engines, like Sequest, OMSSA, X!Tandem and Mascot. This approach guards against false positive peptide assignments.

PEAKS Q is an add-on tool for protein quantification, supporting label (ICAT, iTRAQ, SILAC, TMT, O18, etc.) and label free techniques.

A collection of algorithms used within the PEAKS software have been adapted and configured into a specialized project, PEAKS AB, which has proven to be the first method for automatic monoclonal antibody sequencing.[4]


  1. ^ Zhang, J.; Xin, L.; Shan, B.; Chen, W.; Xie, M.; Yuen, D.; Zhang, W.; Zhang, Z.; Lajoie, G.; Ma, B. (2011). "PEAKS DB: De Novo Sequencing Assisted Database Search for Sensitive and Accurate Peptide Identification". Molecular & Cellular Proteomics. 11: M111.010587. doi:10.1074/mcp.M111.010587. 
  2. ^ Ma B, Johnson. De Novo sequencing and homology searching Molecular & Cellular Proteomics. 10.1074/mcp.O111.014902 (2011).
  3. ^ Han, X.; He, L.; Xin, L.; Shan, B.; Ma, B. (2011). "PEAKS PTM: Mass Spectrometry Based Identification of Peptides with Unspecified Modifications". Journal of Proteomics Research. 10 (7): 2930–2936. doi:10.1021/pr200153k. 
  4. ^ Tran, Ngoc Hieu; Rahman, M. Ziaur; He, Lin; Xin, Lei; Shan, Baozhen; Li, Ming (2016-08-26). "Complete De Novo Assembly of Monoclonal Antibody Sequences". Scientific Reports. 6: 31730. ISSN 2045-2322. PMC 4999880Freely accessible. PMID 27562653. doi:10.1038/srep31730.