X! Tandem search error with trypsin/chymotrypsin

General Server Forum (Inactive)
X! Tandem search error with trypsin/chymotrypsin t s loo  2018-05-21 03:51
Status: Closed

Good evening,

It seems the pipeline looks for [FKLMRWY]|{P} for trypsin/chymotrypsin digest but the GUI inputs as strict chymotrypsin in the XML:

<note label="protein, cleavage site" type="input">[RKWYF]|{P}</note>

I tried to correct the XML script to match and the GUI came up with an error: The enzyme '[RKWYFML]|{P}' was not found.

Is there a quick fix for this?

Best regards,


Windows 7 Enterprise SP1 (64 bit)

Firefox Quantum 60.0.1 (64 bit)

Labkey v18.1-57017.17

Sorry there isn't an error code other than the following (trimmed out the list of accepted enzymes except the one in question).

21 May 2018 22:20:10,500 INFO : ERROR: Unsupported search enzyme.

21 May 2018 22:20:10,501 INFO : Use one of the following cleavage site specifications:

21 May 2018 22:20:10,508 INFO : trypsin/chymotrypsin - [FKLMRWY]|{P}

21 May 2018 22:20:10,504 INFO : Failed to complete task 'org.labkey.ms2.pipeline.tandem.XTandemSearchTask'

21 May 2018 22:20:10,510 ERROR: Failed running C:\Program Files (x86)\LabKey Server\bin\Tandem2XML, exit code 1

Jon (LabKey DevOps) responded:  2018-06-01 22:40

Unfortunately, what you're observing is a limitation with the Tandem2XML utility from the Trans Proteomic Pipeline.

It only supports certain predefined enzymes.

It's possible that newer version of the TPP may have added support for this, but that is outside of the LabKey platform and would be an update of the TPP software.