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Nat Methods. 2017 Sep;14(9):909-914. doi: 10.1038/nmeth.4388. Epub 2017 Aug 7.

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

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Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington, USA.
Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington, USA.


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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