期刊
ANALYTICAL CHEMISTRY
卷 80, 期 6, 页码 2018-2025出版社
AMER CHEMICAL SOC
DOI: 10.1021/ac701697w
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资金
- NCRR NIH HHS [P41 RR11823-01, P41 RR011823] Funding Source: Medline
- NHLBI NIH HHS [R01 HL079442] Funding Source: Medline
- NIGMS NIH HHS [P41 GM103533] Funding Source: Medline
- NIMH NIH HHS [R01 MH067880, 5R01MH067880-02] Funding Source: Medline
We investigated and compared three approaches for shotgun protein identification. by combining MS and MS/ MS information using LTQ-Orbitrap high mass accuracy data. In the first approach, we employed a unique mass identifier method where MS peaks matched to peptides predicted from proteins identified from an MS/MS database. search are first subtracted before using the MS peaks as unique mass identifiers for protein identification. In the second method, we used an accurate mass and time tag method by building a potential mass and retention time database from previous MudPIT analyses. For the third method, we used a peptide mass fingerprinting-like approach in combination with a randomized database for protein identification. We show that we can improve protein identification sensitivity for low-abundance proteins by combining MS and MS/MS information. Furthermore, one-hit wonders from MS/MS database searching can be further substantiated by MS information and the approach improves the identification of low-abundance proteins. The advantages and disadvantages for the three approaches are then discussed.
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