Hi Kolla,
What version of Labkey server are you using? The newest search form will have a pull down list with the mods available on the mascot server. Can you please post the mascot.xml file that was used for the search.
Thanks,
Bill

Hi Bill,
The modules are all 8.1 but the SQL server is 8.2.7. Looks like we should update to 8.2.

We were under the impression that LabKey would automatically update since we had selected ON (medium) for the "Automatically check for updates to LabKey Server, and report anonymous usage statistics to the LabKey team" selection in the Admin Console, Customize site. Is this not correct? Can you tell me how to update manually?

Kolla

Mascot.xml file used for search:
<?xml version="1.0" encoding="UTF-8"?>
<bioml>
  <note label="mascot, enzyme" type="input">Trypsin</note>
  <note label="spectrum, parent monoisotopic mass error plus" type="input">2.0</note>
  <note label="spectrum, parent monoisotopic mass error minus" type="input">1.0</note>
  <note label="spectrum, parent monoisotopic mass error units" type="input">Da</note>
  <note label="spectrum, fragment mass error" type="input">1.0</note>
  <note label="spectrum, fragment mass error units" type="input">Da</note>
  <note label="mascot, peptide_charge" type="input">2+ and 3+</note>
  <note label="scoring, maximum missed cleavage sites" type="input">2</note>
  <note label="mascot, variable modifications" type="input">Carbamidomethyl(C)</note>
</bioml>

I think it's just missing a space before the first paren. It has to be *exactly* like the Mascot form.
<note label="mascot, variable modifications" type="input">Carbamidomethyl (C)</note>

You might want to wait until 8.3. Should be very soon. I usually just download and install, I haven't tried setting for an auto update. Remember to update the labkeydbmgmt.pl script on your mascot server when you upgrade to 8.3.

Bill

Just noticed that you had an asymmetric parent mass error in your settings. These values should be the same for Mascot or Sequest searches.