Informed-Proteomics: Open-source Software Package for Top-down Proteomics
Title | Informed-Proteomics: Open-source Software Package for Top-down Proteomics |
Publication Type | Journal Article |
Year of Publication | 2017 |
Authors | Park 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. |
Journal | Nat. Methods |
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. |