MS-Tag UnKnome Instructions

A de-novo sequencing tool from the that can be used to fit the fragment-ion tag data contained in a user's tandem mass spectrum to a peptide sequence of < 1300 Da. All fragment-ions in the tag need not be of the same ion series, and amino-acid composition from immonium ions MUST BE added. Note: This form uses exactly the same MS-Tag program as the other HTML forms, it's just that some of the input parameters are different.
MS-Fit MS-Pattern MS-Seq
MS-Digest MS-Product MS-Comp DB-Stat MS-Isotope
MS-Tag Simple
MS-Tag
Database:
Digest:
      Max. # missed cleavages:
Cys modified by:
N terminus:
C terminus:
Maximum Reported Hits:
Max. % unmatched ions:
Fragment-ion Tag
Masses are:
Parent mass (m/z):
 Charge (z):
Mass (m/z) Charge (z)
Allowed Fragment-Ion types (some ion types require presence of specific AA's in the ion)
Instrument: Use instrument specific defaults to override ion types below
N-term ions C-term ions Neutral-loss ions
(from ions also selected)		 Internal
ions		 Ladder
ions
a b
b+H2O R,H,K,N 		c y NH3
(a,b,y) R,K,Q,N 		H2O
(b,y) S,T,D,E 		H3PO4
(a,b,y) s,t,y 		SOCH4
(b,y) Mso
 internal N-term
C-term
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) 		-80
PO4 - S,T,Y
(homology) 		-98
PO4 - S,T
(homology) 		-64
Mso
(homology) 		-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.
Sample ID (comment):

Absent Amino Acids (Check to Prevent Possible Inclusion in Unknome Searches)

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 in Unknome Searches)

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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