Mercurial > repos > iracooke > msgfplus
comparison tool-data/msgfplus_mods.loc.sample @ 0:1049de3f4aed
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| author | iracooke |
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| date | Sun, 06 Jan 2013 20:06:08 -0500 |
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| -1:000000000000 | 0:1049de3f4aed |
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| 1 #This file lists the names of inbuilt chemical modifications accepted by msgfplus | |
| 2 #Each entry consists of 4 tab separated fields like this | |
| 3 #<Displayed Name> <DBKey> <Modification String> <DBKey> | |
| 4 # | |
| 5 #Modification strings should conform to the standard MSGFPlus syntax with the following exception | |
| 6 #The ModType field is overridden by the msgfplus_search.rb tool. In other words any of these mods | |
| 7 #May be passed to the tool as a variable or fixed mod and the tool will substitute the appropriate ModType | |
| 8 #value | |
| 9 # | |
| 10 #Standard MSGFPlus syntax is | |
| 11 # | |
| 12 # To input a modification, use the following command: | |
| 13 # Mass or CompositionStr, Residues, ModType, Position, Name (all the five fields are required). | |
| 14 # CompositionStr (C[Num]H[Num]N[Num]O[Num]S[Num]P[Num]) | |
| 15 # - C (Carbon), H (Hydrogen), N (Nitrogen), O (Oxygen), S (Sulfer) and P (Phosphorus) are allowed. | |
| 16 # - Atom can be omitted. The sequence of atoms must be followed. | |
| 17 # - Negative numbers are allowed. | |
| 18 # - E.g. C2H2O1 (valid), H2C1O1 (invalid) | |
| 19 # Mass can be used instead of CompositionStr. It is important to specify accurate masses (integer masses are insufficient). | |
| 20 # - E.g. 15.994915 | |
| 21 # Residues: affected amino acids (must be upper letters) | |
| 22 # - Must be uppor letters or * | |
| 23 # - Use * if this modification is applicable to any residue. | |
| 24 # - * should not be "anywhere" modification (e.g. "15.994915, *, opt, any, Oxidation" is not allowed.) | |
| 25 # - E.g. NQ, * | |
| 26 # ModType: "fix" for fixed modifications, "opt" for variable modifications (case insensitive) | |
| 27 # Position: position in the peptide where the modification can be attached. | |
| 28 # - One of the following five values should be used: | |
| 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) | |
| 30 # - Case insensitive | |
| 31 # - "-" can be omitted | |
| 32 # - E.g. any, Any, Prot-n-Term, ProtNTerm => all valid | |
| 33 # Name: name of the modification (Unimod PSI-MS name) | |
| 34 # - For proper mzIdentML output, this name should be the same as the Unimod PSI-MS name | |
| 35 # - E.g. Phospho, Acetyl | |
| 36 #C2H3N1O1,C,fix,any,Carbamidomethyl # Fixed Carbamidomethyl C | |
| 37 # Variable Modifications (default: none) | |
| 38 #O1,M,opt,any,Oxidation # Oxidation M | |
| 39 #15.994915,M,opt,any,Oxidation # Oxidation M (mass is used instead of CompositionStr) | |
| 40 #H-1N-1O1,NQ,opt,any,Deamidated # Negative numbers are allowed. | |
| 41 #C2H3NO,*,opt,N-term,Carbamidomethyl # Variable Carbamidomethyl N-term | |
| 42 #H-2O-1,E,opt,N-term,Pyro_glu # Pyro-glu from E | |
| 43 #H-3N-1,Q,opt,N-term,Pyro-glu # Pyro-glu from Q | |
| 44 #C2H2O,*,opt,Prot-N-term,Acetyl # Acetylation Protein N-term | |
| 45 #C2H2O1,K,opt,any,Acetyl # Acetylation K | |
| 46 #CH2,K,opt,any,Methy # Methylation K | |
| 47 #HO3P,STY,opt,any,Phospho # Phosphorylation STY | |
| 48 | |
| 49 Carbamidomethyl C carbamidomethyl_c_ C2H3N1O1,C,opt,any,Carbamidomethyl carbamidomethyl_c_ | |
| 50 Oxidation M oxidation_m_ O1,M,opt,any,Oxidation oxidation_m_ |