Table I

Conservative filter parameters for SEQUEST results

The spectra for proteins with three or fewer unique peptide hits that met these criteria were manually inspected before inclusion to the protein list. Each protein with three or fewer passing peptide identifications had an average of 33 identifications that did not pass the above criteria but scored better than a 1.5 Xcorr and had a DelCN of at least 0.05.

ChargeXcorrPeptide type
+1≥1.9Fully tryptic
+1≥2.1Chymotryptic and/or elastic
+1≥2.2Partially tryptic, chymotryptic, and/or elastic
+2≥2.2Fully tryptic
+2≥2.4Partially tryptic, chymotryptic, and/or elastic
+2≥3.0No protease rules
+3≥3.75Tryptic, chymotryptic, and/or elastic only