Hello,

Currently CPAS only supports loading XPRESS and Q3 quantitation data. It should successfully parse and load pepXML and protXML files that have been processed by Libra, but will ignore the Libra data.

It wouldn't be especially difficult to add support for this, especially for the data that overlaps with XPRESS or Q3, but it hasn't been prioritized for inclusion in an upcoming release. I'd be happy to provide some pointers into the Java code for where this would need to be supported.

Thanks,
Josh

Hey Josh,

we would be happy about some pointers into the Java code. I am not sure at the moment we have the expertise to actually program this but we give it a try.
I attach part of a proteinprophet results file as an example:

protein_group group_number="1" probability="1.0000">
<protein protein_name="AT1G04480.1" n_indistinguishable_proteins="3" probability="1.0000" percent_coverage="18.6" unique_stripped_peptides="GSAITGPIGK+NLYIISVK+VLPAVIVR" group_sibling_id="a" total_number_peptides="7" pct_spectrum_ids="0.32" confidence="0.97">
<analysis_result analysis="libra">
<libra_result number="7">
<intensity mz="114.0" ratio="1.00" error="0.01"/>
<intensity mz="115.0" ratio="2.26" error="0.01"/>
<intensity mz="116.0" ratio="2.99" error="0.01"/>
<intensity mz="117.0" ratio="0.66" error="0.01"/>

Thanks,

Maik

Hi Maik,

Unfortunately, it looks like Libra does quantitation based on individual mz values. XPRESS and Q3, which CPAS can handle right now, only give one quantitation result for the entire protein group. It would require a somewhat significant database schema change to support storing all of the different values.

If there is a roll-up value for the whole protein group, that would be much simpler to get loaded. It would be possible to calculate one in the Java code as well, even if Libra doesn't produce one.

For ProteinProphet, the relevant source code is in <LABKEY_SRC_ROOT>/server/modules/ms2/src/org/labkey/ms2/reader/ProtXmlReader.java. On or around line 195, inside the loadChildren() method, you'd need to add a check for an element named "libra_result". You would then need to set _quantRatio to a new QuantitationRatio object, and set the appropriate quantitation values on it.

Loading peptide quantitation would involve making a new Libra class that's patterned on <LABKEY_SRC_ROOT>server/modules/ms2/src/org/labkey/ms2/reader/XPressAnalysisSummary.java

That should get the right values into the database, and then you should be able to view the data just as you can for XPRESS or Q3 results.

Some links that might be useful include:

https://www.labkey.org/wiki/home/Documentation/page.view?name=build

https://www.labkey.org/wiki/home/Documentation/page.view?name=quantitation

Thanks,
Josh