Table II

CID/ECD localization conflicts

In total, 340 pairs gave confident localization (SLoMo > 19) from both CID and ECD data. A SLoMo score of 19 corresponds to a 1.26% error rate, which would predict nine errors from the 680 identifications. In fact we saw three localization conflicts and one identification (ID) conflict. Of the localization conflicts, 1 and 2 are cases where both isoforms are present, i.e. both are correct. pT and pS indicate phosphothreonine and phosphoserine, respectively. g indicates N-acetylation.

ConflictPeptide sequenceSLoMo scoreChargeManual analysis
1TVpTPASSAKTpSPAKQQAPPVR24.3 CID3Both correct: co-eluting isoforms
TVTPApSSAKTpSPAKQQAPPVR21.5 ECD3Both correct: co-eluting isoforms
2TVpTPASSAKTpSPAKQQAPPVR41.2 CID3Both correct: co-eluting isoforms
TVTPASpSAKTpSPAKQQAPPVR22.3 ECD3Both correct: co-eluting isoforms
3AKPAAQSEEETATpSPAASPTPQSAER22.3 CID3CID correct
AKPAAQSEEETApTSPAASPTPQSAER27.0 ECD3ECD incorrect
4RNpSLTGEEGELVK36.4 CID2ID conflict
gLSRWWWRpSR89.2 ECD2ID conflict