MSstats from skyline return error jeonjh8817  2018-07-04 02:03
 

I have received the following error in the immediate result window running the external tool from Skyline. it is a DIA experiment and have been curated. The targets were corrected for the right peaks.

When the data were run in Data Processing and Group Comparison (Healthy vs Disease), setup as outlined in the pdf. Precursors have been removed.
If I tried to rescore or reimport the program tries to do all the runs.

** Reading the data for MSstats.....
** Peptides, that are used in more than one proteins, are removed.
** Truncated peaks are replaced with NA.
Error in SkylinetoMSstatsFormat(raw, filter_with_Qvalue = filter.qvalue) :
Please check precursors information. If your experiment is DIA, please remove the precursors. If your experiments is DDA, please check the precursor information.

Can't finish analysis.
 
 
Nick Shulman responded:  2018-07-04 05:47
You probably still have a few precursor transitions in your document.

If you want to find the precursor transitions in your document, you can use the Document Grid:
1. View > Document Grid
2. Choose "Transitions" from the Views dropdown at the top of the Document Grid
3. Right click on the "Fragment Ion" column and choose "Filter"
4. Set the filter type to "Starts With" and type "precursor" into the textbox.

If you are still getting this error after confirming that you have removed all of the precursors, then you should send us your Skyline document.

In Skyline you can use the menu item:
File > Share > (Complete)
to create a .zip file containing your Skyline document and supporting files.

You can upload that .zip file here:
https://skyline.ms/files.url
 
Nick Shulman responded:  2018-07-05 06:24
Thank you for uploading your Skyline documents.
I can see that you have both precursor (e.g. "precursor", "precursor [M+1]" etc) and product (e.g. "y9") transitions in your document. (see attached picture)

MSstats requires that you only have either precursors or products. If you have both types of transitions you need to delete either all of the precursors or all of the tr

I am not sure what you meant when you said "Precursors have been removed".

What do you mean "as outlined in the pdf"? Which pdf are you looking at?