期刊
JOURNAL OF PROTEOME RESEARCH
卷 18, 期 4, 页码 1902-1906出版社
AMER CHEMICAL SOC
DOI: 10.1021/acs.jproteome.8b00954
关键词
proteomics; mass spectrometry; tandem mass tags; isobaric labeling; phosphorylation; database search
资金
- National Defense Science and Engineering Graduate Fellowship (NDSEG) Program
- National Institutes of Health [R01 GM121818]
- National Science Foundation [1633939]
- Division Of Ocean Sciences
- Directorate For Geosciences [1633939] Funding Source: National Science Foundation
Searching tandem mass spectra against a peptide database requires accurate knowledge of various experimental parameters, including machine settings and details of the sample preparation protocol. In some cases, such as in reanalysis of public data sets, this experimental metadata may be missing or inaccurate. We describe a method for automatically inferring the presence of various types of modifications, including stable-isotope and isobaric labeling and tandem mass tags as well as the enrichment of phosphorylated peptides, directly from a given set of mass spectra. We demonstrate the sensitivity and specificity of the proposed approach, and we provide open-source Python and C++ implementations in a new version of the software tool Param-Medic.
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