Table II. Validation of the specificity and suitability of the top five product ion peptide quality control using immunopeptidomes from JY cells and spiked isotope labeled synthetic peptides.

(A) MS: natural peptides, precursor masses
Replicates	1	2	3
Unique	1181	1260	1362
Duplicate	7	12	12

(B) MSMS: natural peptides, five top-fragment masses
Replicates	1	2	3
Unique	70	116	120
Duplicate	0	2	0

(C) MS: synthetic peptides
Replicates	1	2	3
Unique	61	62	61
Duplicate	0	0	0

(A) Overlap of the detected peptide precursor masses in MS mode of the natural peptides at four decimals. (B) Overlap of the measured top five product ion masses of the manifold peptide precursor masses from (A) in MS/MS mode of the natural peptides at four decimals. (C) Overlap of the measured 62 synthetic peptide precursor masses in MS mode at four decimals.