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PMID: 18072732 Published · ppublish English Journal Article Research Support, N.I.H., Extramural Research Support, Non-U.S. Gov't

Identification and characterization of disulfide bonds in proteins and peptides from tandem MS data by use of the MassMatrix MS/MS search engine.

Journal of proteome research ·Vol. 7 ·No. 1 ·2008-01-00 ·Pages 138-44

Xu H, Zhang L, Freitas MA

Abstract

A new database search algorithm has been developed to identify disulfide-linked peptides in tandem MS data sets. The algorithm is included in the newly developed tandem MS database search program, MassMatrix. The algorithm exploits the probabilistic scoring model in MassMatrix to achieve identification of disulfide bonds in proteins and peptides. Proteins and peptides with disulfide bonds can be identified with high confidence without chemical reduction or other derivatization. The approach was tested on peptide and protein standards with known disulfide bonds. All disulfide bonds in the standard set were identified by MassMatrix. The algorithm was further tested on bovine pancreatic ribonuclease A (RNaseA). The 4 native disulfide bonds in RNaseA were detected by MassMatrix with multiple validated peptide matches for each disulfide bond with high statistical scores. Fifteen nonnative disulfide bonds were also observed in the protein digest under basic conditions (pH = 8.0) due to disulfide bond interchange. After minimizing the disulfide bond interchange (pH = 6.0) during digestion, only one nonnative disulfide bond was observed. The MassMatrix algorithm offers an additional approach for the discovery of disulfide bond from tandem mass spectrometry data.

MeSH Terms
Algorithms Animals Cattle Databases, Factual Disulfides/analysis Information Storage and Retrieval Models, Statistical Peptides/analysis Proteins/analysis Ribonuclease, Pancreatic Tandem Mass Spectrometry/methods
Chemicals
Disulfides Peptides Proteins Ribonuclease, Pancreatic
Authors & Affiliations
3 authors, click to expand affiliations / ORCID
Xu Hua
Department of Chemistry, The Ohio State University, Columbus, Ohio 43210, USA.
Zhang Liwen
Freitas Michael A
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Article Info
Journal
Journal of proteome research
Abbr.
J Proteome Res
ISSN
1535-3893
DOI
10.1021/pr070363z
Published
2008-01-00
Epub
2007-00-12
Pages
138-44
Language
English
Region
United States
NLM ID
101128775
PMCID
PMC2749473
Subset
IM
Grants
NCI NIH HHS · R01 CA107106-01 · United States
NCRR NIH HHS · S10 RR023647 · United States
NCI NIH HHS · R01 CA107106-04 · United States
NCRR NIH HHS · S10 RR023647-01 · United States
NCI NIH HHS · R01 CA107106-03 · United States
NCI NIH HHS · R01 CA107106-02 · United States
NCI NIH HHS · R56 CA107106 · United States
NCI NIH HHS · R01 CA107106 · United States
NCI NIH HHS · CA107106 · United States
External Links
PubMed source DOI: 10.1021/pr070363z PMC Full Text View journal details
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