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.

Conflict	Peptide sequence	SLoMo score	Charge	Manual analysis
1	TVpTPASSAKTpSPAKQQAPPVR	24.3 CID	3	Both correct: co-eluting isoforms
	TVTPApSSAKTpSPAKQQAPPVR	21.5 ECD	3	Both correct: co-eluting isoforms
2	TVpTPASSAKTpSPAKQQAPPVR	41.2 CID	3	Both correct: co-eluting isoforms
	TVTPASpSAKTpSPAKQQAPPVR	22.3 ECD	3	Both correct: co-eluting isoforms
3	AKPAAQSEEETATpSPAASPTPQSAER	22.3 CID	3	CID correct
	AKPAAQSEEETApTSPAASPTPQSAER	27.0 ECD	3	ECD incorrect
4	RNpSLTGEEGELVK	36.4 CID	2	ID conflict
	gLSRWWWRpSR	89.2 ECD	2	ID conflict