--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/msgfplus_mods.loc.sample	Mon Mar 04 20:48:04 2013 -0500
@@ -0,0 +1,50 @@
+#This file lists the names of inbuilt chemical modifications accepted by msgfplus
+#Each entry consists of 4 tab separated fields like this
+#<Displayed Name>	<DBKey>	<Modification String>	<DBKey>
+#
+#Modification strings should conform to the standard MSGFPlus syntax with the following exception
+#The ModType field is overridden by the msgfplus_search.rb tool. In other words any of these mods
+#May be passed to the tool as a variable or fixed mod and the tool will substitute the appropriate ModType
+#value
+#
+#Standard MSGFPlus syntax is
+#
+# 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])
+# 	- C (Carbon), H (Hydrogen), N (Nitrogen), O (Oxygen), S (Sulfer) and P (Phosphorus) are allowed.
+# 	- Atom can be omitted. The sequence of atoms must be followed. 
+# 	- 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 uppor 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 (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
+#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,Pyro_glu			# Pyro-glu from E
+#H-3N-1,Q,opt,N-term,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,Methy				# Methylation K
+#HO3P,STY,opt,any,Phospho			# Phosphorylation STY
+
+Carbamidomethyl C	carbamidomethyl_c_	C2H3N1O1,C,opt,any,Carbamidomethyl	carbamidomethyl_c_
+Oxidation M	oxidation_m_	O1,M,opt,any,Oxidation	oxidation_m_
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