Informed-Proteomics: open-source software package for top-down proteomics.

Informed-Proteomics: open-source software package for top-down proteomics. Related Articles

Informed-Proteomics: open-source software package for top-down proteomics.

Nat Methods. 2017 Aug 07;:

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Authors: Park J, Piehowski PD, Wilkins C, Zhou M, Mendoza J, Fujimoto GM, Gibbons BC, Shaw JB, Shen Y, Shukla AK, Moore RJ, Liu T, Petyuk VA, Tolić N, Paša-Tolić L, Smith RD, Payne SH, Kim S

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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