Criteria for Protein Identification

Scaffold (version Scaffold\_4.8.4, Proteome Software Inc., Portland, OR, USA) was used to validate MS/MS-based peptide and protein identifications. A false discovery rate of 1% was used for peptide and protein. Proteins that contained similar peptides and could not be differentiated based on MS/MS analysis alone were grouped to satisfy the principles of parsimony. The total spectrum count value, which corresponds to the total number of spectra identified for a protein, was used to identify selected protein spots from the 2D gels, as this parameter was reported to be a semi-quantitative measure for a given protein abundance in proteomic studies [31,32].
