[Psidev-pi-dev] [Fwd: [psi-pi commit] r167 - trunk/examples]

[David C. <dc...@ma...>]

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