IPeak: An open source tool to combine results from multiple MS/MS search engines |
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| Authors: | Guilin Li Fawaz Ghali Andrew R Jones Lukas Käll Shaohang Xu Ruo Zhou Zhe Ren Qiang Feng Xun Xu Jun Wang |
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| Institution: | 1. BGI‐Shenzhen, Shenzhen, P. R. China;2. Institute of Integrative Biology, University of Liverpool, Liverpool, UK;3. Science for Life Laboratory, School of Biotechnology, Royal Institute of Technology ‐ KTH, Solna, Sweden;4. Swedish e‐Science Research Center, Royal Institute of Technology ‐ KTH, Solna, Sweden;5. Department of Biology, University of Copenhagen, Copenhagen, Denmark;6. Princess Al Jawhara Center of Excellence in the Research of Hereditary Disorders, King Abdulaziz University, Jeddah, Saudi Arabia;7. Macau University of Science and Technology, Taipa, P. R. China;8. Department of Medicine, University of Hong Kong, Hong Kong, P. R. China |
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| 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/ . |
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| Keywords: | Bioinformatics Mass spectrometry Peptide identification Shotgun proteomics |
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