期刊
JOURNAL OF PROTEOME RESEARCH
卷 19, 期 12, 页码 4754-4765出版社
AMER CHEMICAL SOC
DOI: 10.1021/acs.jproteome.0c00648
关键词
phosphorylated peptides; phospho site localization; phosphopeptide enrichment; false identification rate; mass spectrometry; Human Proteome Organization (HUPO); Human Proteome Project (HPP); MS Resource Pillar; Phosphopeptide Challenge
资金
- National Institutes of Health, National Institute of General Medical Sciences [R01GM087221]
- Office of the Director [S10OD026936]
- National Institute of Allergy and Infectious Diseases [R21AI133335]
- National Institute on Aging [U19AG023122]
- NSF [1920268, ABI 1759980]
- NIH [NIH-NLM 1R01LM013115, P41GM103484, R24GM127667, P30ES017885, U24CA210967]
Mass spectrometry has greatly improved the analysis of phosphorylation events in complex biological systems and on a large scale. Despite considerable progress, the correct identification of phosphorylated sites, their quantification, and their interpretation regarding physiological relevance remain challenging. The MS Resource Pillar of the Human Proteome Organization (HUPO) Human Proteome Project (HPP) initiated the Phosphopeptide Challenge as a resource to help the community evaluate methods, learn procedures and data analysis routines, and establish their own workflows by comparing results obtained from a standard set of 94 phosphopeptides (serine, threonine, tyrosine) and their nonphosphorylated counterparts mixed at different ratios in a neat sample and a yeast background. Participants analyzed both samples with their method(s) of choice to report the identification and site localization of these peptides, determine their relative abundances, and enrich for the phosphorylated peptides in the yeast background. We discuss the results from 22 laboratories that used a range of different methods, instruments, and analysis software. We reanalyzed submitted data with a single software pipeline and highlight the successes and challenges in correct phosphosite localization. All of the data from this collaborative endeavor are shared as a resource to encourage the development of even better methods and tools for diverse phosphoproteomic applications. All submitted data and search results were uploaded to MassIVE (littps://massive.ucsd.edu/) as data set MSV000085932 with ProteomeXchange identifier PXD020801.
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