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Error: test library not found in settings allikrest  2016-09-30
 
Hello,

I am getting this error whenever AutoQC Loader tries to import my skyline document to Panorama. I am using Skyline version 3.5.0.9319, 64-bit. Any idea what is going on?

Thanks,
Allison

30 Sep 2016 07:14:18,818 INFO : Starting to import Skyline document from Weekly_Yeast_QEx_2016-09-30_10-13-58.sky.zip
30 Sep 2016 07:14:18,818 INFO : Expanding Weekly_Yeast_QEx.skyd
30 Sep 2016 07:14:18,859 INFO : Expanding Weekly_Yeast_QEx.sky.view
30 Sep 2016 07:14:18,860 INFO : Expanding Weekly_Yeast_QEx.sky
30 Sep 2016 07:14:18,861 WARN : The version of this Skyline document is 3.5. This is newer than the highest supported version 2.62
30 Sep 2016 07:14:19,525 INFO : Inserting peptides1
30 Sep 2016 07:14:19,570 ERROR: Skyline document import failed
java.lang.IllegalStateException: 'test' library not found in settings.
    at org.labkey.targetedms.SkylineDocImporter.insertPrecursor(SkylineDocImporter.java:1244)
    at org.labkey.targetedms.SkylineDocImporter.insertPeptideOrSmallMolecule(SkylineDocImporter.java:1040)
    at org.labkey.targetedms.SkylineDocImporter.insertPeptideGroup(SkylineDocImporter.java:923)
    at org.labkey.targetedms.SkylineDocImporter.importSkylineDoc(SkylineDocImporter.java:533)
    at org.labkey.targetedms.SkylineDocImporter.importRun(SkylineDocImporter.java:149)
    at org.labkey.targetedms.pipeline.TargetedMSImportPipelineJob.run(TargetedMSImportPipelineJob.java:85)
    at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:511)
    at java.util.concurrent.FutureTask.run(FutureTask.java:266)
    at java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.access$201(ScheduledThreadPoolExecutor.java:180)
    at java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:293)
    at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
    at java.lang.Thread.run(Thread.java:745)
 
 
vsharma responded:  2016-09-30
Hi Allison,

Do you have a spectrum library associated with your Skyline document? You can check under Settings > Peptide Settings > Library. When I open the attached Weekly_yeast_QEx2.sky I don't see any spectrum libraries selected in settings. But two of the peptides (IATYQER, TASGNIIPSSTGAAK) should have associated spectrum library information, as per the .sky file. I wonder how that happened. Would you please send me a shared zip file from Skyline - from the "File" menu select "Share..". If you are asked to choose between "complete" and "minimal" please choose "complete".

Thanks,
Vagisha
 
allikrest responded:  2016-10-03
Hi Vagisha,

I ended up deleting the document and making a new one, and that seemed to solve the problem! However, now I am having a different problem! Three of the peptides in a different skyline document aren't showing up (see screen shot below and attachment). There is no error message this time. Is this due to the same type problem? I have since created three other AutoQC subfolders with their own skyline files for our different instruments and have not run into this problem, so I am not sure what is going on with this particular file.

Thanks,
Allison
 
vsharma responded:  2016-10-03
Hi Allison,

The screenshots didn't make it through. But, based on the attached Skyline file name, I am guessing that you are referring to data uploaded in your "AutoQC_BSA_QEx" folder (https://panoramaweb.org/labkey/project/Wayne%20State%20U%20-%20IEHS%20Proteomics%20Core/AutoQC_BSA_QEx/begin.view?)? I see all 11 precursors from your Skyline document in this folder. Are you referring to another PanoramaWeb folder?

Thanks,
Vagisha
 
allikrest responded:  2016-10-03
Hi Vagisha,

Here is the screen shot again, sorry I must have not attached it previously. All 11 precursors show up in the skyline file but 3 of them don't show up in Panorama for most of the runs (for some reason there are three files/runs that do show them on Panorama).

Allison
 
vsharma responded:  2016-10-03
Hi Allison,

Thanks for the screenshot. I had a look at the Skyline documents uploaded to this folder, and only the last three or so have chromatograms for the three peptides (YICDNQDTISSK, LVTDLTK, LVNELTEFAK) in all the replicates. The older Skyline doucments don't have any chromatograms for these peptides.

For example, Weekly_BSA_QEx_2016-09-29_14-47-51, uploaded on 9/29 did not have any data for these peptides from the raw file BSA_40fmol_02_09-12-16_QEx. But there is data for same raw file in the document uploaded on 9/30.

Do you know how that happened? Did you add these peptides to your Skyline documents after you had done the initial raw data import? And then did you re-import the raw files sometime on 9/30 after the document had already been uploaded to Panorama?

Panorama imports data from a replicate (raw file) only once. So, for example, data from BSA_40fmol_02_09-12-16_QEx, with no chromatograms for the three peptides, was imported on 9/29. Data from this replicate was ignored from all Skyline documents uploaded after that.

You could, at this point, delete all the older uploads (see under the "Runs" tab in your folder) and re-upload the latest version of your Skyline document to Panorama. This will import data from all the replicates that are getting ignored right now.

I hope this helps.

-Vagisha
 
allikrest responded:  2016-10-03
Vagisha,

Thank you so much. Your guess at the scenario that caused this is exactly correct! I did alter the peptides in my skyline document after the initial import. I was seeing a message in the AutoQC Loader log about certain relocates being ignored and couldn't figure out why but this all makes perfect sense now. When you refer to re-uploading my latest skyline document, do you mean that I should do it manually? Should I also manually the delete the old document or will it be ignored if a newer version is uploaded? Once again, thank you so much for your help!

Allison
 
vsharma responded:  2016-10-03
Hi Allison,

You don't need to manually upload your Skyline document if you are using AutoQC Loader. It will get uploaded next time a new raw file is added. You will, however, have to manually delete the old documents (from the "Runs" tab in your folder in PanoramaWeb"). This is required so that all the data associated with replicates in those documents is removed from the Panorama database, and when AutoQC uploads the document again data for all the replicates that were just deleted will get re-imported and this time it will include your three peptides. Sorry for the inconvenience.

Let me know if you run into any issues.

Thanks!
-Vagisha