MS-Tag Instructions

A database searching 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 in an existing database. All fragment-ions in the tag need not be of the same ion series, and amino-acid composition from immonium ions can be added. Homology mode enables matching to database sequences which contain a single mutation, cross-species substitution, or modified amino acid.
MS-Fit MS-Pattern MS-Seq
MS-Digest MS-Product MS-Comp DB-Stat MS-Isotope
MS-Tag Simple
MS-Tag UnKnome
Database: DNA Frame translation:

Accession Numbers:
Digest:
      Max. # missed cleavages:
Cys modified by:
N term: C term: 		Search mode:

For HOMOLOGY MODE
Parent Mass Shift:
          Da
Mutation Matrix OFF:
Hide Star-ions:
Species:
Protein MW: (from to Da) All
Protein pI: (from to ) All
Names:
Maximum Reported Hits:
Maximum Hits:
  Max. % Unmatched Ions:
Max. Num Unmatched Ions:
  Min. Num Matched 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.
Exclude AA's Based on Missing Immonium Ions
Sample ID (comment):
Similar Programs (database searching):
Similar Programs (de novo interpretation):