Fig. 2.

Annotation of contigs and meta-contigs with MS-GFDB spectrum identifications. The annotation of a SPS contig is shown here but the same procedure applies for meta-contigs. Above the contig PRM spectrum are all sequence calls that align to the reference. Below the contig PRM spectrum are all spectra from overlapping peptides that were assembled to yield the contig PRM spectrum. Only assembled peaks are shown in each assembled PRM spectrum. For a sequence call to be labeled correct, it must be flanked by at least one pair of annotated PRM or SRM peaks in the same ion series that map to the same protein. If a sequence call that is not labeled correct is flanked by at least one pair of peaks from an identified spectrum then it is labeled incorrect. If a sequence call is not flanked by at least one pair of peaks from an identified spectrum then it is labeled un-annotated.