Figure 2. Diagram showing intercomponent data flow and communication scheme for HTAPP. HPLC: high performance liquid chromatography system; MS: mass spectrometer; PC-1: Data acquisition component; PC-2: transfer raw data files and perform SEQUEST or Mascot database search; Cluster: perform clustered SEQUEST or Mascot search; PC-3: autonomous post-acquisition analysis such as spectral validation, peptide quantitation, and upload proteomics data into PeptideDepot database; PC-4: database server (PeptideDepot) for visualization of proteomic data.  Once data is deposited into PeptideDepot, it is incrementally backed-up offsite daily.