Proteins identified by SEQUEST and X!Tandem were categorized into priority groups based upon the quality of the protein identification. Proteins with a best peptide confidence level of 99% or higher were assigned to priority 1 (two or more unique peptide sequences) or 2 (a single unique peptide sequence). Proteins with a best peptide confidence level of 75-89% were assigned to the ‘moderate’ category. Peptides with a confidence level less than 75% were filtered out from further analysis. SEQUEST and X!Tandem database search algorithms were used for peptide sequence identification. Each algorithm compares the observed peptide MS/MS spectrum and theoretically derived spectra from the database to assign quality scores. These quality scores and other important predictors were combined in the algorithm that assigns an overall % ID confidence level for each peptide; the assignment was based on a random forest recursive partition supervised learning algorithm (Higgs et al., 2005; 2007). The priority system was based upon the quality of the amino acid sequence identification and whether one or more sequences were identified. Only proteins with priority 1 (confidence level > 99% with 2 independent peptides) were included for further analysis in the present study.
