Finding high confidence modified peptides using 5 filtering strategies. By removing peptides that matched to both methylated peptides and unmodified peptides (filter 1) and peptides which contains D or E residues (filter 2), 2,641 peptides were left. By filtering for overlapping peptides (filter 3), and where at least one of the overlapping peptide is an unambiguous peptide match (filter 4), 163 peptides remained. These included 108 unambiguous peptide matches, 43 ambiguous peptide matches, and 12 peptides in both categories. Found in these peptides are 45 lysine methylation sites and 38 arginine methylation sites, all of which are of high confidence (filter 5).
Pang et al. BMC Genomics 2010 11:92 doi:10.1186/1471-2164-11-92