Internal controls were added to each sample to provide a QC check of the sample preparation and LC-MS data collection process. These “Process Controls” consisted of the addition of yeast enolase protein after lysis and prior to digestion and the Pierce Retention Time Calibration (PRTC; 15 synthetic stable isotope labeled peptides) peptide mixture following digestion. The “Protein Internal Control” was used to assess the protein digest and peptide recovery and the “Peptide Internal Control” was used to distinguish between sample preparation and measurement issues post-digestion.