Issues running analysis : error IMP.apQuant.Quantifier.aQFeature isn't available

[Daniel Chang]

Hello,

I'm fairly new with this software, but we are running into issues when trying to run the analysis after installing the nodes.  We installed MS Amanda and apquant, but it errors out 

6/5 03:51 PM (15) IMP-apQuant Peptide and Protein Quantifier Error Quantification failed (The entity object of type 'aQFeature' isn't available!)

at Thermo.Magellan.EntityDataFramework.EntityDataService.GetEntity(Type entityType)

at Thermo.Magellan.EntityDataFramework.EntityDataService.GetProperty[TEntity,TPropertyType](Expression`1 propertyExpression)

at IMP.apQuant.Quantifier.AqQuantifierNode.AddQValue[T,D](ScoreConfig config)

at IMP.apQuant.Quantifier.AqQuantifierNode.DoProcessing[T](Int32 workflowId, Boolean xlink)

at IMP.apQuant.Quantifier.AqQuantifierNode.ProcessScoring()

at IMP.apQuant.Quantifier.AqQuantifierNode.Start()

6/5 04:38 PM (15) IMP-apQuant Peptide and Protein Quantifier Warning Unable to calculate Scores. Error was: The entity type IMP.apQuant.Quantifier.aQFeature isn't available

If I could assistance with this, it would be much appreciated.

Thank you.

[Daniel Chang]

Hi Gerhard,

This is Gretchen, working with Daniel to resolve this issue. Thanks for your help with this and apologies for the delayed response. I have included a link that includes our analysis workflow, the raw file, and the fasta file for you to reproduce the error. Let me know if you have any issues viewing the files. Any help in resolving this issue would be greatly appreciated!

Best, Gretchen

On Jun 6, 2023, at 11:58 PM, Gerhard Dürnberger <gerhard.due...@gmail.com> wrote:

Dear Daniel, 

this error occurs in IMP-apQuant which we at IMP/VBC are taking care of. Could you share your analysis workflow (.pdStudy file), the fasta database and the raw file you used with me so that I can reproduce the error. Can you please send a link with these data to gerhard.duernberger [AT] gmi.oeaw.ac.at and I will have a look.

Kind regards, Gerhard

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[Gerhard Dürnberger]

Dear Gretchen and Daniel,

sorry also for the late reply, I was out of office in the last weeks. I found a way how to fix the issue:

The problem originates because the wrong score is specified in the apQuant Processing node. Probably you already got an error in the Processing workflow already (attached screenshot). To fix the issue please change the Parameter “Score Name” to “MS Amanda 2.0: Amanda Score”. If that option is not available you have to define that score manually. This can be done by going to Configuration > MSF Files > PSM scores and duplicating the MS Amanda score into a new line and editing the name to “MS Amanda 2.0: Amanda Score”. Please don’t forget to press Apply to save the score changes. A graphical description of this can also be found in the slide linked below. After reopening the study you should have the option for MS Amanda 2.0 available. Please change the apQuant processing Node setting accordingly and perform a complete reprocessing of the data.

Unfortunately defining the score cannot be done automatically. If there are still issues in analysing the data do not hesitate to contact me.

Kind regards from Vienna, Gerhard