Comparison with MS-GFDB

Since the published MS-GFDB did not support variable PTMs at the time that this research was carried out, both MS-GFDB and PEAKS DB were run without specifying any variable PTMs. The other parameters, including the fixed PTMs, remained the same as described in the results section. The results are shown in Figure S2 for CID and Figure S3 for ETD datasets, respectively. Note that the removal of the variable PTMs reduced PEAKS DB’s performance on ETD dataset but not on CID dataset. This difference is likely because the different organisms, different sample preparations, and different fragmentation methods used for the two datasets. As a result, the CID dataset contains a significantly fewer number of modified peptides than the ETD dataset.