MS-Comp Instructions

A tool from the that can be used to complete the possible amino acid composition of a peptide given a parent or fragment m/z and partial composition from the immonium ion or other data contained in a user's tandem mass spectrum. If you are trying to work out the composition of a fragment ion then it is possible to specify several possible alternative ion types.
MS-Fit MS-Seq MS-Edman
MS-Digest MS-Product DB-Stat MS-Isotope
m/z: Da
Charge (z): m/z is: 		Instrument:
Ion types:
Cys modified by:
N terminus:
C terminus:
Maximum Reported Compositions:
Combination Type: 		Note: If the mass tolerance is large and few ions below are checked then the program will take a long time to run.


AA Composition (based on immonium and related ions)
60
S 		70
R,P 		72
V 		74
T 		86
L,I 		87
N,R 		88
D 		84,101,129
K,Q 		102
E
104
M 		110
H 		120
F 		126
P 		136
Y 		117,130,159,170
W 		70,73,87,100,112,185
R
AA Composition (based on loss from parent ion)
-SRH,-R
C (select modified Cys above) 		-80,-98
PO4 - S,T (check s and t below) 		-64
Mso (check m below) 		-17
R
Note: For ions with multiple residues (i.e. 86: means I or L).
Note: Requires presence of at least one AA for each composition ion selected.

Absent Amino Acids (Check to Prevent Possible Inclusion)

A
C
D
E
F
G
H
I
K
L
M
N
P
Q
R
S
T
V
W
Y

Modified Amino Acids Possibly Present (Check to Allow Inclusion)

m
q
h
s
t
y
u
Met-ox Pyroglutamic
acid 		Homoserine
lactone 		Phosphorylated
S,T,Y 		User Specified AA
(Provide Elemental Composition Below)

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