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Informed-Proteomics: open-source software package for top-down proteomics
 Authors and Affiliations  Authors and Affiliations
Jungkap Park1, Paul D Piehowski1 , Christopher Wilkins1, Mowei Zhou2 , Joshua Mendoza1, Grant M Fujimoto1, Bryson C Gibbons1, Jared B Shaw2, Yufeng Shen1, Anil K Shukla1, Ronald J Moore1, Tao Liu1, Vladislav A Petyuk1, Nikola Tolić2, Ljiljana Paša-Tolić2, Richard D Smith1 , Samuel H Payne1 & Sangtae Kim1,3
1Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington, USA. 2Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington, USA. 3Present address: Illumina Inc., San Diego, California, USA. Correspondence should be addressed to S.H.P. or S.K..
Abstract
Top-down proteomics, the analysis of intact proteins in their endogenous form, preserves valuable information about post-translation modifications, isoforms and proteolytic processing. The quality of top-down liquid chromatography–tandem MS (LC-MS/MS) data sets is rapidly increasing on account of advances in instrumentation and sample-processing protocols. However, top-down mass spectra are substantially more complex than conventional bottom-up data. New algorithms and software tools for confident proteoform identification and quantification are needed. Here we present Informed-Proteomics, an open-source software suite for top-down proteomics analysis that consists of an LC-MS feature-finding algorithm, a database search algorithm, and an interactive results viewer. We compare our tool with several other popular tools using human-in-mouse xenograft luminal and basal breast tumor samples that are known to have significant differences in protein abundance based on bottom-up analysis.
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박정갑 (Agilent Technologies Inc.)
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