期刊
JOURNAL OF PROTEOME RESEARCH
卷 7, 期 1, 页码 170-181出版社
AMER CHEMICAL SOC
DOI: 10.1021/pr070444v
关键词
mass spectrometry; post-translational modifications; crystallin; human lens; Dictyostelium; lens proteins
资金
- NATIONAL CENTER FOR RESEARCH RESOURCES [R01RR016522, C06RR017588, P41RR008605] Funding Source: NIH RePORTER
- NATIONAL EYE INSTITUTE [R29EY007755, R01EY007755] Funding Source: NIH RePORTER
Proteins are extensively modified after translation due to cellular regulation, signal transduction, or chemical damage. Peptide tandem mass spectrometry can discover post-translational modifications, as well as sequence polymorphisms. Recent efforts have studied modifications at the proteomic scale. In this context, it becomes crucial to assess the accuracy of modification discovery. We discuss methods to quantify the false discovery rate from a search and demonstrate how several features can be used to distinguish valid modifications from search artifacts. We present a tool, PTMFinder, which implements these methods. We summarize the corpus of post-translational modifications identified on large data sets. Thousands of known and novel modification sites are identified, including site-specific modifications conserved over vast evolutionary distances.
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