title: IPeak: An open source tool to combine results from multiple MS/MS search engines.
abstract: 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/.
authors.affiliation: BGI-Shenzhen, Shenzhen, P. R. China.|BGI Cognitive Genomics Lab, Shenzhen, P. R. China.
authors.forename: Bo
authors.initials: B
authors.lastname: Wen
authors.affiliation: BGI-Shenzhen, Shenzhen, P. R. China.
authors.forename: Chaoqin
authors.initials: C
authors.lastname: Du
authors.affiliation: BGI-Shenzhen, Shenzhen, P. R. China.
authors.forename: Guilin
authors.initials: G
authors.lastname: Li
authors.affiliation: Institute of Integrative Biology, University of Liverpool, Liverpool, UK.
authors.forename: Fawaz
authors.initials: F
authors.lastname: Ghali
authors.affiliation: Institute of Integrative Biology, University of Liverpool, Liverpool, UK.
authors.forename: Andrew R
authors.initials: AR
authors.lastname: Jones
authors.affiliation: Science for Life Laboratory, School of Biotechnology, Royal Institute of Technology - KTH, Solna, Sweden.|Swedish e-Science Research Center, Royal Institute of Technology - KTH, Solna, Sweden.
authors.forename: Lukas
authors.initials: L
authors.lastname: Käll
authors.affiliation: BGI-Shenzhen, Shenzhen, P. R. China.
authors.forename: Shaohang
authors.initials: S
authors.lastname: Xu
authors.affiliation: BGI-Shenzhen, Shenzhen, P. R. China.
authors.forename: Ruo
authors.initials: R
authors.lastname: Zhou
authors.affiliation: BGI-Shenzhen, Shenzhen, P. R. China.
authors.forename: Zhe
authors.initials: Z
authors.lastname: Ren
authors.affiliation: BGI-Shenzhen, Shenzhen, P. R. China.|Department of Biology, University of Copenhagen, Copenhagen, Denmark.
authors.forename: Qiang
authors.initials: Q
authors.lastname: Feng
authors.affiliation: BGI-Shenzhen, Shenzhen, P. R. China.
authors.forename: Xun
authors.initials: X
authors.lastname: Xu
authors.affiliation: BGI-Shenzhen, Shenzhen, P. R. China.|Department of Biology, University of Copenhagen, Copenhagen, Denmark.|Princess Al Jawhara Center of Excellence in the Research of Hereditary Disorders, King Abdulaziz University, Jeddah, Saudi Arabia.|Macau University of Science and Technology, Taipa, P. R. China.|Department of Medicine, University of Hong Kong, Hong Kong, P. R. China.
authors.forename: Jun
authors.initials: J
authors.lastname: Wang
mesh_terms: D000465:Algorithms; D030562:Databases, Protein; D006801:Humans; D010455:Peptides / Q000032:analysis; D011381:Programming Languages; D040901:Proteomics / Q000379:methods*; D057386:Search Engine; D012984:Software; D053719:Tandem Mass Spectrometry / Q000379:methods*
chemical_list: D010455:Peptides
keywords: Bioinformatics; Mass spectrometry; Peptide identification; Shotgun proteomics