期刊
NATURE PROTOCOLS
卷 1, 期 5, 页码 2213-2222出版社
NATURE PUBLISHING GROUP
DOI: 10.1038/nprot.2006.330
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资金
- NATIONAL INSTITUTE OF ENVIRONMENTAL HEALTH SCIENCES [P30ES000267] Funding Source: NIH RePORTER
- NIEHS NIH HHS [P30 ES000267, P30 ES000267-40] Funding Source: Medline
Shotgun proteomics yields tandem mass spectra of peptides that can be identified by database search algorithms. When only a few observed peptides suggest the presence of a protein, establishing the accuracy of the peptide identifications is necessary for accepting or rejecting the protein identification. In this protocol, we describe the properties of peptide identifications that can differentiate legitimately identified peptides from spurious ones. The chemistry of fragmentation, as embodied in the 'mobile proton' and 'pathways in competition' models, informs the process of confirming or rejecting each spectral match. Examples of ion-trap and tandem time-of-flight (TOF/TOF) mass spectra illustrate these principles of fragmentation.
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