Fig. 1

Above: comparison of 6frame and proteome databases for peptide identification using the comet search algorithm. Three barplots are shown for 1, 6, and 10 PSMs required to call a protein. Each bar represents the size of protein sets. Blue shows the cut-off number of proteins which are annotated but not called by the use of any database. Green shows the number of proteins, which are called using the NCBI E. coli genome annotation as a database. Grey shows the number of proteins indenpendently detected by both databases. Red shows the number of proteins called by the 6frame data base. The dotted line shows the size of the complete NCBI annotation. Below: The score distributions of the PSMs for different sets of called proteins are shown. The score is given as a common logarithm. Red shows the set of proteins which are only detected by the 6frame database. The green set are the proteins which are only detected by using the NCBI annotation as the search database. Grey is the intersection of proteins that are identified by both databases