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IPeak: An open source tool to combine results from multiple MS/MS search engines
Author(s) -
Wen Bo,
Du Chaoqin,
Li Guilin,
Ghali Fawaz,
Jones Andrew R.,
Käll Lukas,
Xu Shaohang,
Zhou Ruo,
Ren Zhe,
Feng Qiang,
Xu Xun,
Wang Jun
Publication year - 2015
Publication title -
proteomics
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.26
H-Index - 167
eISSN - 1615-9861
pISSN - 1615-9853
DOI - 10.1002/pmic.201400208
Subject(s) - computer science , unix , pipeline (software) , java , interface (matter) , mascot , software , operating system , microsoft windows , source code , identification (biology) , open source , graphical user interface , os x , database , botany , bubble , maximum bubble pressure method , political science , law , biology
Liquid chromatography coupled tandem mass spectrometry (LC‐MS/MS) is an important technique for detecting peptides in proteomics studies. Here, we present an open source software tool, termed IPeak, a peptide identification pipeline that is designed to combine the Percolator post‐processing algorithm and multi‐search strategy to enhance the sensitivity of peptide identifications without compromising accuracy. IPeak provides a graphical user interface (GUI) as well as a command‐line interface, which is implemented in JAVA and can work on all three major operating system platforms: Windows, Linux/Unix and OS X. IPeak has been designed to work with the mzIdentML standard from the Proteomics Standards Initiative (PSI) as an input and output, and also been fully integrated into the associated mzidLibrary project, providing access to the overall pipeline, as well as modules for calling Percolator on individual search engine result files. The integration thus enables IPeak (and Percolator) to be used in conjunction with any software packages implementing the mzIdentML data standard. IPeak is freely available and can be downloaded under an Apache 2.0 license at https://code.google.com/p/mzidentml‐lib/ .