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missing Detection Q values joli  2018-09-04 16:15
 

Hi Skyline Team,

I'm trying to use the MSstats "design sample size" function on my DIA proteomics dataset to do a power analysis and I keep getting this following error:

"Some DetectionQValue have no value. Please check "Result Grid" in View.
Error in runDSS() :

Can't finish analysis."

I checked the Document Settings Grid and exported the csv file and found that more than half of the peptides have #N/A Detection Q values. I am not sure how to troubleshoot this problem. I am running Skyline (64-bit) version 4.1.0.18169 and I've uploaded my Skyline document.

Thanks in advance for your help!

John
 
 
Nick Shulman responded:  2018-09-04 16:43
Thanks for uploading that file.

For some reason, that .zip file is missing the file "LSmerged-Gilltemp.skyd" file that I would expect to be in there, so I cannot look your results in Skyline.

I am not sure why some of your peptides would be have a detection q-value, and some would not. You might want to try doing:
Edit > Refine > Reintegrate
in order to get Skyline to calculate a Q-value for all of your peptides.

MSstats insists that if any of your peptides has a Detection QValue, then all of your peptides have to have one. You can edit the "MSstats Input" report and remove the "Detection Q Value" column, and then MSstats will think that none of your peptides have a q-value.
To edit the "MSstats Input" report you do:
View > Document Grid
Choose "External Tools > MSstats Input" from the Views dropdown on the Document Grid
Edit View
remove the column, etc.

If you have any questions about what MSstats does with the "Detection Q Value" column, they might be able to answer that on the MSstats support board:
https://groups.google.com/forum/#!forum/msstats
 
joli responded:  2018-09-04 18:15
Thanks so much Nick!