Hi,
I've added an enzyme section for a mixed enzyme (CNBr+Trypsin) to the
Mascot_MSMS_example.axml file in the examples directory.
At the moment, for a mixed enzyme there is no place for the name chosen
from the search form drop down list for the enzyme. Likewise, if in any
search engine someone chose to call Trypsin, say "Bovine Trypsin",
there's no place for this name as we should just give the accession for
Trypsin?
In the schema, we could restrict CTermGain and NTermGain to what we
would expect in hemical formulae? [A-Z][a-z][0..9][ ] to stop someone
entering a decimal number?
I've put the regex plus the CV, don't know if that is what is intended.
David
-------- Original Message --------
Subject: [psi-pi commit] r167 - trunk/examples
Date: Thu, 02 Oct 2008 03:50:47 -0700
From: cod...@go...
To: dc...@ma...
Author: dcreasy
Date: Thu Oct 2 03:50:39 2008
New Revision: 167
Modified:
trunk/examples/Mascot_MSMS_example.axml
Log:
Added enzyme section
Modified: trunk/examples/Mascot_MSMS_example.axml
==============================================================================
--- trunk/examples/Mascot_MSMS_example.axml (original)
+++ trunk/examples/Mascot_MSMS_example.axml Thu Oct 2 03:50:39 2008
@@ -501,6 +501,20 @@
<SpecificityRule accession="" cvRef="" name=""
unitAccession=""
unitName="" />
</SearchModification>
</ModificationParams>
+ <Enzymes independent="0">
+ <Enzyme id="ENZ_0" CTermGain="OH" NTermGain="H"
missedCleavages="1" semiSpecific="0">
+ <SiteRegexp><![CDATA[(?<=[M])|(?=[])]]></SiteRegexp>
+ <EnzymeName>
+ <pf:cvParam accession="PI:TODO" name="CNBr" cvRef="PSI-PI" />
+ </EnzymeName>
+ </Enzyme>
+ <Enzyme id="ENZ_1" CTermGain="OH" NTermGain="H"
missedCleavages="1" semiSpecific="0">
+ <SiteRegexp><![CDATA[(?<=[KR])|(?=[P])]]></SiteRegexp>
+ <EnzymeName>
+ <pf:cvParam accession="PI:TODO" name="Trypsin" cvRef="PSI-PI"
/>
+ </EnzymeName>
+ </Enzyme>
+ </Enzymes>
<MassTable id="0">
<Residue Code="A" Mass="71.037114"/>
<Residue Code="B" Mass="114.53494"/>
--
David Creasy
Matrix Science
64 Baker Street
London W1U 7GB, UK
Tel: +44 (0)20 7486 1050
Fax: +44 (0)20 7224 1344
dc...@ma...
http://www.matrixscience.com
Matrix Science Ltd. is registered in England and Wales
Company number 3533898
|
