Filter 2: using two or more overlapping peptides to improve modification confidence. A peptide can have no missed cleavage or one missed cleavage (MC) at either the N-terminus or C-terminus of the peptide. The modification site has to be found in two or more overlapping peptides for it to be accepted for subsequent analyses. There are a few scenarios where these modification sites can be found. a) There can be one peptide with no missed cleavage overlapping with another peptide with one missed cleavage. b) The modification site can be found in two overlapping peptides each with one missed cleavage. c) In the third scenario, the modification site may be found in three peptides, one peptide with no missed cleavage, and two peptides with one missed cleavage each. In all of the above cases, at least one peptide in the overlapping peptides has to be an unambiguous peptide match. Cases where this was not seen were excluded from all subsequent analyses.
Pang et al. BMC Genomics 2010 11:92 doi:10.1186/1471-2164-11-92