Table 2.

Search Parameters Used in Byonic Software. Options 1, 2, and 3 Were Used to Compare the Modification of D, E, and/or Protein C-Terminal

Setting	Item	Parameter	Remark
Digestion and instrument	Missed cleavage	1
	Precursor mass tolerance	5 ppm
	Fragmentation	QToF & HCD
	Fragment mass tolerance	0.3 Da
Spectrum input	Maximum precursor mass	10 kDa
	Maximum # of precursors per MS2	1
Peptide output	Manual score cut	10
	Show all N-glycopeptides	Yes
Protein output	Protein FDR	2%
Amino acid modification	Carbamidomethyl	57.021454	C, fixed
	Oxidation	15.994915	M, rare
	Gln → pyro-Glu	− 17.026549	Nterm Q, rare
	Gln → pyro-Glu	− 18.010565	Nterm E, rare
	Ammonia loss	− 17.026549	Nterm C, rare
Option 1	Ethyl esterification	28.031301	D, E, Cterm, rare
Option 2	Ethyl esterification	28.031301	D, E, Cterm, rare
	Amidation	42.058183	D, E, Cterm, rare
Option 3	Amidation	42.058183	D, E, Cterm, rare
Sialic acid modification	a2,-Linked	28.031301
	a2,3-Linked	42.058183