Figure 2.

Many PSMs typically assigned to peptides from canonical proteins can be assigned to peptides from altProts and novel isoforms with better statistical confidence measures. (A) The left and right panels show the Percolator score distributions for the same set of 6493 spectra from two analyses of the same dataset. On the left, only canonical proteins were present in the database at the peptide-spectrum matching step. On the right, altProts and novel isoforms were included. The dashed line represents the q-value at which PSMs on the right are excluded when enforcing an FDR below 1%. (B) Percolator-derived peptide posterior error probability (log10) for the same 6493 spectra from A associated either to peptide from canonical proteins (custom database with canonical proteins only; grey) or to peptides from altProts and novel isoforms (custom database with canonical proteins, altProts and novel isoforms; green), as indicated.