Spectrast.usermods

From SPCTools

Revision as of 06:16, 19 January 2010 Henrylam (Talk | contribs) ← Previous diff		Current revision Henrylam (Talk | contribs)
Line 1:		Line 1:
	<pre><nowiki>		<pre><nowiki>
	# spectrast.usermods		# spectrast.usermods
-	# This file should contain specifications of amino acid modifications of peptides. Specifications are of the form <amino acid>[<tag>]|<mass change>|<mod type>, e.g.	+	# This file should contain specifications of amino acid modifications of peptides.
		+	# Specifications are of the form <amino acid>[<tag>]|<mass change>|<mod type>. For example,
	M[foo]|+12.34567|MyMod		M[foo]|+12.34567|MyMod
Line 7:		Line 8:
	# Note that tag and mod type must not start with a number, and should not contain space or special characters		# Note that tag and mod type must not start with a number, and should not contain space or special characters
-	# Leave blank the [<tag>] unless you have a strong reason to do so. SpectraST will construct one that conforms to TPP convention. Note that some components of TPP may fail if you specify your own tag. e.g.	+	# Leave blank the [<tag>] unless you have a strong reason to do so. SpectraST will construct one that conforms to TPP convention.
		+	# (Note that some components of TPP may fail if you specify your own tag.) For example,
	C|+57.021464|Carbamidomethyl		C|+57.021464|Carbamidomethyl
-	# Leave blank the mod type if you don’t know a good name for it, or don’t know if the mod is already encoded in SpectraST.	+	# Leave blank the mod type if you don’t know a good name for it, or don’t know if the mod is already encoded in SpectraST. For example,
	M|+16|		M|+16|
-	# SpectraST should recognize this is oxidation and use the accurate mass (+15.99491) accordingly.</nowiki></pre>	+	# SpectraST should recognize this is oxidation and use the accurate mass (+15.99491) accordingly.
		+	</nowiki></pre>

---

Current revision

# spectrast.usermods
# This file should contain specifications of amino acid modifications of peptides. 
# Specifications are of the form <amino acid>[<tag>]|<mass change>|<mod type>. For example,

M[foo]|+12.34567|MyMod

# Note that tag and mod type must not start with a number, and should not contain space or special characters

# Leave blank the [<tag>] unless you have a strong reason to do so. SpectraST will construct one that conforms to TPP convention. 
# (Note that some components of TPP may fail if you specify your own tag.) For example,

C|+57.021464|Carbamidomethyl

# Leave blank the mod type if you don’t know a good name for it, or don’t know if the mod is already encoded in SpectraST. For example,

M|+16|

# SpectraST should recognize this is oxidation and use the accurate mass (+15.99491) accordingly.