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oxi_tmt_mods.txt
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# This file is used to specify modifications
# # for comments
#
# Max Number of Dynamic/Variable Modifications per peptide
# If this value is large, the search takes long.
NumMods=1
# To input a modification, use the following command:
# Mass or CompositionStr, Residues, ModType, Position, Name (all the five fields are required).
# CompositionStr (C[Num]H[Num]N[Num]O[Num]S[Num]P[Num]Br[Num]Cl[Num]Fe[Num])
# - C (Carbon), H (Hydrogen), N (Nitrogen), O (Oxygen), S (Sulfur), P (Phosphorus), Br (Bromine), Cl (Chlorine), Fe (Iron), and Se (Selenium) are allowed.
# - Negative numbers are allowed.
# - E.g. C2H2O1 (valid), H2C1O1 (invalid)
# Mass can be used instead of CompositionStr. It is important to specify accurate masses (integer masses are insufficient).
# - E.g. 15.994915
# Residues: affected amino acids (must be upper letters)
# - Must be upper letters or *
# - Use * if this modification is applicable to any residue.
# - * should not be "anywhere" modification (e.g. "15.994915, *, opt, any, Oxidation" is not allowed.)
# - E.g. NQ, *
# ModType: "fix" for fixed modifications, "opt" for variable modifications, "custom" for custom amino acids (case insensitive)
# Position: position in the peptide where the modification can be attached.
# - One of the following five values should be used:
# - any (anywhere), N-term (peptide N-term), C-term (peptide C-term), Prot-N-term (protein N-term), Prot-C-term (protein C-term)
# - Case insensitive
# - "-" can be omitted
# - E.g. any, Any, Prot-n-Term, ProtNTerm => all valid
# Name: name of the modification (Unimod PSI-MS name)
# - For proper mzIdentML output, this name should be the same as the Unimod PSI-MS name
# - E.g. Phospho, Acetyl
# - Visit http://www.unimod.org to get PSI-MS names.
C2H3N1O1,C,fix,any,Carbamidomethyl # Fixed Carbamidomethyl C
# Variable Modifications (default: none)
O1,M,opt,any,Oxidation # Oxidation M
#15.994915,M,opt,any,Oxidation # Oxidation M (mass is used instead of CompositionStr)
#H-1N-1O1,NQ,opt,any,Deamidated # Negative numbers are allowed.
#C2H3NO,*,opt,N-term,Carbamidomethyl # Variable Carbamidomethyl N-term
#H-2O-1,E,opt,N-term,Glu->pyro-Glu # Pyro-glu from E
#H-3N-1,Q,opt,N-term,Gln->pyro-Glu # Pyro-glu from Q
#C2H2O,*,opt,Prot-N-term,Acetyl # Acetylation Protein N-term
#C2H2O1,K,opt,any,Acetyl # Acetylation K
#CH2,K,opt,any,Methyl # Methylation K
#HO3P,STY,opt,any,Phospho # Phosphorylation STY
# Custom amino acids (default: none)
# Formula, letter symbol, custom, unused, name
# Formula:
# - Only supports empirical formulas of elements C H N O S.
# - If other elements are needed, or a specific mass is needed, they can be added as fixed modifications to the custom amino acid on following lines.
# - Warning: maximum 255 C, 255 H, 63 N, 63 O, 15 S
# Letter symbol:
# - Can be B, J, O, U, X, Z
# custom:
# - Special ModType "custom" to denote custom amino acids
# unused:
# - Field is currently not used internally, but the parser requires a value here
# name:
# - Name of custom amino acid
# - Not used internally or output to results, but the parser requires a value here
#
# NOTE: All modifications that affect the custom amino acid(s) must be specified below the custom amino acid(s).
#
# Example 1:
#C5H7N1O2S0,J,custom,P,Hydroxylation # Hydroxyproline
#
# Example 2:
#C3H5NO, U, custom, U, Selenocysteine # Custom amino acids can only have C, H, N, O, and S
#79.9166, U, fix, any, Se80 # Use a static mod to add Se
229.16293,K,fix,any,labeling # TMT-labeling
229.16293,*,fix,N-term,labeling # TMT-labeling