Informed-Proteomics: open-source software package for top-down proteomics
Jungkap Park,Paul D. Piehowski,Christopher S. Wilkins,Mowei Zhou,Joshua Mendoza,Grant M. Fujimoto,Bryson C. Gibbons,Jared B. Shaw,Yufeng Shen,Anil K. Shukla,Ronald J. Moore,Tao Liu,Vladislav A. Petyuk,Nikola Tolić,Ljiljana Paša-Tolić,Richard D. Smith,Samuel H. Payne,Sangtae Kim +17 more
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TL;DR: Informed-Proteomics is presented, 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 that is compared with several other popular tools using human-in-mouse xenograft luminal and basal breast tumor samples.
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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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