期刊
NATURE METHODS
卷 14, 期 9, 页码 909-+出版社
NATURE PUBLISHING GROUP
DOI: 10.1038/NMETH.4388
关键词
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资金
- NIH National Institute of General Medical Sciences [GM103493]
- National Cancer Institute Clinical Proteomic Tumor Analysis Consortium (CPTAC) [U24CA160019]
- National Institute of Allergy and Infectious Diseases NIH/DHHS [Y1-A1-8401-01]
- U.S. Department of Energy (DOE) Office of Science and Office of Biological and Environmental Research, under the Pan-omics program
- High Resolution and Mass Accuracy Capability development project at the Environmental Molecular Science Laboratory (EMSL), a U.S. DOE national scientific user facility at Pacific Northwest National Laboratory (PNNL) in Richland, Washington
- DOE [DE-AC05-76RLO01830]
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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