Results found 2 samples instead of 34 samples from the msms file

Results found 2 samples instead of 34 samples from the msms file yael hirschberg  2022-12-02 00:25

Hello Skyline Team,

I ran 34 samples on Maxquant and tried to import the msms file on Skyline. However, Skyline only continued with 2 samples and 17 replicates of each. I attach a screenshort of the import and the msms file. What did I do wrong?

Thank you,

Nick Shulman responded:  2022-12-02 00:34

It sounds like you meant to attach some files to this support request, but no files were actually attached.
Sometimes that happens because the files you were trying to attach were too large.
The maximum size of a file which can be attached to a support request is 50MB.
You can upload larger files here:

-- Nick
yael hirschberg responded:  2022-12-02 01:12
Hello Nick, I uploaded the and "Importing" - screenshot.
Nick Shulman responded:  2022-12-02 01:24
Thank you for uploading that screenshot:

I see that the same filename has been repeated 17 times in the "Extract Chromatograms" part of the Import Peptide Search wizard. I am not sure why Skyline would do that.

We will actually need a few more files from you in order to reproduce this.
In addition to that "msms.txt" file, we will also need your "mqpar.xml" file, and, if you have them "modifications.xml" and/or "evidence.txt".
It would also be helpful if you could zip up "1.AD1-2_S1-A2_1_9348.d" and "2.AD17-7_S1-C4_1_9384.d" and upload those too.

Also, if you could send us your Skyline document (even if that Skyline document is blank), that would be helpful too.
In Skyline you can use the menu item:
File > Share to create a .zip file containing your Skyline document and supporting files including extracted chromatograms and spectral libraries.

You can put all of those things into one big zip file and upload them here:
-- Nick
yael hirschberg responded:  2022-12-02 02:33
Thank you for your quick reactions, Nick. Everything is uploaded in the file.

Nick Shulman responded:  2022-12-02 09:04
Thank you for sending those files.
It looks like Skyline is getting really confused by the fact that your filenames have a dot so close to the beginning of the filename.
When Skyline is trying to figure out which raw file matches which file in the peptide search results, Skyline often has to ignore everything after the first dot. For instance, your peptide search results might have searched a file called "MyFile.mgf", but you actually want to extract chromatograms from something called "MyFile.raw" or "MyFile.d".

In your case, you have a raw file folder named "1.AD1-2_S1-A2_1_9348.d", and Skyline thinks that that is the file that goes with everything that starts with "1." in the msms.txt including things like "1.AD15-10_S1-A11_1_9363".

It might be tricky for us to fix this bug. In the meantime I would recommend that you work around this by renaming all of your .d folders so that they do not have any dots before the ".d" at the end. You will then need to run your MaxQuant search again, but I think everything will work after that.
-- Nick