Define the characteristics of peptides to search for:

• How the experimental peptides have been generated, the enzyme used, the kind of protonation, etc.
• The treatment and chemical modifications you have made on your sample
• The chemical reactions that you think could have appeared on your sample (oxidation...)

Enzyme and cleavage rules

Enzyme or Reagent	Cleaves where?	Exceptions
Trypsin	C-terminal side of K or R	if P is C-term to K or R
Trypsin (C-term to K/R, even before P)	C-terminal side of K or R
Trypsin (higher specificity)	C-terminal side of K or R	if P is C-term to K or R; after K in CKY, DKD, CKH, CKD, KKR; after R in RRH, RRR, CRK, DRD, RRF, KRR
Lys C	C-terminal side of K
CNBr	C-terminal side of M
Arg C	C-terminal side of R	if P is C-term to R
Asp N	N-terminal side of D
Asp N + N-terminal Glu	N-terminal side of D or E
Glu C (bicarbonate)	C-terminal side of E	if P is C-term to E, or if E is C-term to E
Glu C (phosphate)	C-terminal side of D or E	if P is C-term to D or E, or if E is C-term to D or E
Chymotrypsin (C-term to F/Y/W/M/L, not before P, not after Y if P is C-term to Y)	C-terminal side of F, L, M, W, Y	if P is C-term to F, L, M, W, Y, if P is N-term to Y
Chymotrypsin (C-term to F/Y/W/, not before P, not after Y if P is C-term to Y)	C-terminal side of F, Y, W	if P is C-term to F, Y, W, if P is N-term to Y
Trypsin/Chymotrypsin (C-term to K/R/F/Y/W, not before P, not after Y if P is C-term to Y)	C-terminal side of K, R, F, Y, W	if P is C-term to K, R, F, Y, W, if P is N-term to Y
Pepsin (pH 1.3)	C-terminal side of F, L
Pepsin (pH > 2)	C-terminal side of F, L, W, Y, A, E, Q
Proteinase K	C-terminal side of A, C, G, M, F, S, Y, W