Mercurial > repos > iracooke > msgfplus

annotate tool-data/msgfplus_mods_var.loc.sample @ 18:f46cca39ea64 draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Add Q Exactive option
author iracooke
date Wed, 10 Feb 2016 01:53:56 -0500
parents 66a149ef79f7
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
16
66a149ef79f7 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/msgfplus/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
parents:
diff changeset
1 #This file lists the names of inbuilt chemical modifications accepted by msgfplus
66a149ef79f7 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/msgfplus/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
parents:
diff changeset
2 #Each entry consists of 4 tab separated fields like this
66a149ef79f7 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/msgfplus/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
parents:
diff changeset
3 #<Displayed Name> <DBKey> <Modification String> <DBKey>
66a149ef79f7 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/msgfplus/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
parents:
diff changeset
4 #
66a149ef79f7 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/msgfplus/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
parents:
diff changeset
5 #Modification strings should conform to the standard MSGFPlus syntax with the following exception
66a149ef79f7 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/msgfplus/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
parents:
diff changeset
6 #The ModType field is overridden by the msgfplus_search.rb tool. In other words any of these mods
66a149ef79f7 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/msgfplus/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
parents:
diff changeset
7 #May be passed to the tool as a variable or fixed mod and the tool will substitute the appropriate ModType
66a149ef79f7 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/msgfplus/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
parents:
diff changeset
8 #value
66a149ef79f7 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/msgfplus/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
parents:
diff changeset
9 #
66a149ef79f7 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/msgfplus/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
parents:
diff changeset
10 #Standard MSGFPlus syntax is
66a149ef79f7 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/msgfplus/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
parents:
diff changeset
11 #
66a149ef79f7 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/msgfplus/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
parents:
diff changeset
12 # To input a modification, use the following command:
66a149ef79f7 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/msgfplus/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
parents:
diff changeset
13 # Mass or CompositionStr, Residues, ModType, Position, Name (all the five fields are required).
66a149ef79f7 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/msgfplus/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
parents:
diff changeset
14 # CompositionStr (C[Num]H[Num]N[Num]O[Num]S[Num]P[Num])
66a149ef79f7 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/msgfplus/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
parents:
diff changeset
15 # - C (Carbon), H (Hydrogen), N (Nitrogen), O (Oxygen), S (Sulfer) and P (Phosphorus) are allowed.
66a149ef79f7 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/msgfplus/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
parents:
diff changeset
16 # - Atom can be omitted. The sequence of atoms must be followed.
66a149ef79f7 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/msgfplus/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
parents:
diff changeset
17 # - Negative numbers are allowed.
66a149ef79f7 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/msgfplus/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
parents:
diff changeset
18 # - E.g. C2H2O1 (valid), H2C1O1 (invalid)
66a149ef79f7 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/msgfplus/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
parents:
diff changeset
19 # Mass can be used instead of CompositionStr. It is important to specify accurate masses (integer masses are insufficient).
66a149ef79f7 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/msgfplus/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
parents:
diff changeset
20 # - E.g. 15.994915
66a149ef79f7 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/msgfplus/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
parents:
diff changeset
21 # Residues: affected amino acids (must be upper letters)
66a149ef79f7 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/msgfplus/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
parents:
diff changeset
22 # - Must be uppor letters or *
66a149ef79f7 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/msgfplus/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
parents:
diff changeset
23 # - Use * if this modification is applicable to any residue.
66a149ef79f7 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/msgfplus/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
parents:
diff changeset
24 # - * should not be "anywhere" modification (e.g. "15.994915, *, opt, any, Oxidation" is not allowed.)
66a149ef79f7 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/msgfplus/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
parents:
diff changeset
25 # - E.g. NQ, *
66a149ef79f7 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/msgfplus/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
parents:
diff changeset
26 # ModType: "fix" for fixed modifications, "opt" for variable modifications (case insensitive)
66a149ef79f7 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/msgfplus/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
parents:
diff changeset
27 # Position: position in the peptide where the modification can be attached.
66a149ef79f7 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/msgfplus/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
parents:
diff changeset
28 # - One of the following five values should be used:
66a149ef79f7 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/msgfplus/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
parents:
diff changeset
29 # - any (anywhere), N-term (peptide N-term), C-term (peptide C-term), Prot-N-term (protein N-term), Prot-C-term (protein C-term)
66a149ef79f7 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/msgfplus/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
parents:
diff changeset
30 # - Case insensitive
66a149ef79f7 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/msgfplus/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
parents:
diff changeset
31 # - "-" can be omitted
66a149ef79f7 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/msgfplus/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
parents:
diff changeset
32 # - E.g. any, Any, Prot-n-Term, ProtNTerm => all valid
66a149ef79f7 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/msgfplus/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
parents:
diff changeset
33 # Name: name of the modification (Unimod PSI-MS name)
66a149ef79f7 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/msgfplus/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
parents:
diff changeset
34 # - For proper mzIdentML output, this name should be the same as the Unimod PSI-MS name
66a149ef79f7 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/msgfplus/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
parents:
diff changeset
35 # - E.g. Phospho, Acetyl
66a149ef79f7 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/msgfplus/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
parents:
diff changeset
36 #C2H3N1O1,C,fix,any,Carbamidomethyl # Fixed Carbamidomethyl C
66a149ef79f7 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/msgfplus/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
parents:
diff changeset
37 # Variable Modifications (default: none)
66a149ef79f7 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/msgfplus/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
parents:
diff changeset
38 #O1,M,opt,any,Oxidation # Oxidation M
66a149ef79f7 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/msgfplus/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
parents:
diff changeset
39 #15.994915,M,opt,any,Oxidation # Oxidation M (mass is used instead of CompositionStr)
66a149ef79f7 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/msgfplus/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
parents:
diff changeset
40 #H-1N-1O1,NQ,opt,any,Deamidated # Negative numbers are allowed.
66a149ef79f7 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/msgfplus/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
parents:
diff changeset
41 #C2H3NO,*,opt,N-term,Carbamidomethyl # Variable Carbamidomethyl N-term
66a149ef79f7 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/msgfplus/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
parents:
diff changeset
42 #H-2O-1,E,opt,N-term,Pyro_glu # Pyro-glu from E
66a149ef79f7 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/msgfplus/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
parents:
diff changeset
43 #H-3N-1,Q,opt,N-term,Pyro-glu # Pyro-glu from Q
66a149ef79f7 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/msgfplus/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
parents:
diff changeset
44 #C2H2O,*,opt,Prot-N-term,Acetyl # Acetylation Protein N-term
66a149ef79f7 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/msgfplus/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
parents:
diff changeset
45 #C2H2O1,K,opt,any,Acetyl # Acetylation K
66a149ef79f7 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/msgfplus/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
parents:
diff changeset
46 #CH2,K,opt,any,Methy # Methylation K
66a149ef79f7 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/msgfplus/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
parents:
diff changeset
47 #HO3P,STY,opt,any,Phospho # Phosphorylation STY
66a149ef79f7 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/msgfplus/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
parents:
diff changeset
48
66a149ef79f7 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/msgfplus/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
parents:
diff changeset
49 Oxidation M oxidation_m_ O1,M,opt,any,Oxidation oxidation_m_
66a149ef79f7 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/msgfplus/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
parents:
diff changeset
50 Acetylation Protein N-term acetyl_nterm_ C2H2O,*,opt,Prot-N-term,Acetyl acetyl_nterm_
66a149ef79f7 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/msgfplus/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
parents:
diff changeset
51 Deamidation NQ deamidation_nq_ H-1N-1O1,NQ,opt,any,Deamidated deamidation_nq_
66a149ef79f7 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/msgfplus/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
parents:
diff changeset
52 Acetylation K acetyl_k_ C2H2O1,K,opt,any,Acetyl acetyl_k_
66a149ef79f7 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/msgfplus/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
parents:
diff changeset
53 Methylation K methyl_k_ CH2,K,opt,any,Methy methyl_k_
66a149ef79f7 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/msgfplus/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
parents:
diff changeset
54 Phosphorylation STY phospho_sty_ HO3P,STY,opt,any,Phospho phospho_sty_
66a149ef79f7 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/msgfplus/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
parents:
diff changeset
55 Carbamidomethyl N-term carbamidomethyl_nterm_ C2H3NO,*,opt,N-term,Carbamidomethyl carbamidomethyl_nterm_