Identification and Characterization of Disulfide Bonds in Proteins and Peptides from Tandem MS Data by Use of the MassMatrix MS/MS Search Engine

• DOI: 10.1021/pr070363z
• Publication Date: 2007-12-12T06:01:33Z
• Authors: Hua Xu; Liwen Zhang; Michael A. Freitas
• Keywords: Bovine pancreatic ribonuclease; Disulfide Linkage; Database search engine

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