U.S. Department of Energy

Pacific Northwest National Laboratory

Informed-Proteomics: Open-source Software Package for Top-down Proteomics

TitleInformed-Proteomics: Open-source Software Package for Top-down Proteomics
Publication TypeJournal Article
Year of Publication2017
AuthorsPark J., Piehowski P.D, Wilkins C., Zhou M., Mendoza J., Fujimoto G.M, Gibbons B.C, Shaw J.B, Shen Y., Shukla A.K, Moore R.J, Liu T., Petyuk V.A, Toli? N., Pa?a-Toli? L., Smith R.D, Payne S.H, Kim S.
JournalNat. Methods

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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