MS-Product Instructions

A tool from the that calculates the possible fragment ions resulting from fragmentation of a peptide in a mass spectrometer. Fragmentation possibilities for post-source decay (PSD), high-energy collision-induced dissociation (CID), and low-energy CID processes may be calculated. The fragment ion types seen in PSD are the default selections. The program generally uses the standard Biemann-style nomenclature: Biemann, K. Method Enzymol. 1990, 193, 886-888.
MS-Fit MS-Seq MS-Pattern
MS-Digest MS-Comp DB-Stat MS-Isotope
Calculate masses as: Max. Reported Charge: Cysteines Modified by:
----Peptide----
Enter Sequence in Capital letters except:
| m - Met-ox | q - Pyroglutamic acid | h - Homoserine lactone | s,t,y - Phosphorylated S,T,Y | u - user specified amino acid |
N-terminus Sequence (50 residues max.) C-terminus

----- Fragment Ion Types to be Listed -----
(some types require presence of specific AA's in ion)

Instrument: Use instrument specific defaults to override ion types below

AA Composition ions N-term sequence ions C-term sequence ions Internal
Fragment-ions		 Ladder
sequencing ions
i m a b c x y Y z internal N-term C-term
Satellite Sequence Ions
( side-chain loss )		 Neutral-loss Sequence Ions Peeling Sequence Ions
d v w -H2O
S, T, E, D 		-NH3
R, K, Q, N 		-H3PO4
s, t, y
( S, T, Y + PO4) 		-SOCH4
m
( M + Ox) 		b+H2O
R, H, K, N

User Specified AA elemental composition (u): C: H: N: O: S: P: ( default is Glycine )

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