--- a/tool-data/msgfplus_mods.loc.sample	Mon Jan 05 17:17:45 2015 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,50 +0,0 @@
-#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_
\ No newline at end of file