Importing result from TimsTOF (TDF forrmat)

Importing result from TimsTOF (TDF forrmat) m anna monika  2019-05-24

I was wondering if you could help me with a result importing issue. For some reason when I try to import results from a run performed on a TimsTOF instrument Skyline doesn't seem to recognise the TDF file. I'm using Skyline 4.2.

Brendan MacLean responded:  2019-05-24

We don't expect you to go directly to a .tdf file. You should be trying to import the containing .d folder. But the Import Results UI should be recognizing the .d folder as mass spec data and not even allowing you to see inside it.

Is your TDF file inside a .d folder? Maybe a screenshot or two of what you are doing and seeing would help.

Let me also ask what kind of timsTOF acquisition method you are performing. ddaPASEF? If so, do you have search results? What search engine and have you successfully built a spectral library from them? We also support PRM and other PASEF methods are in the works.

Thanks for posting to the Skyline support board.


m anna monika responded:  2019-05-27

Thank you very much. The folder was the issue. I thought I only needed the .tdf file and relocated it from the original folder. My bad.

However, once I could open the file I couldn't see any chromatograms. I ran a mixture of heavy peptides using diaPASEF method, without any specific adjustment. I wonder if it is an issue with the ms data itself or my settings on Skyline are not right.

Nick Shulman responded:  2019-05-27

If you send us your Skyline document, we might be able to figure out what is going wrong.

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

If that .zip file is less than 50MB you can attach it to this support request.
Otherwise, you can upload it here:

It sounds like we will also need to take a look at your ms data file. Can you zip up that entire .d directory and upload it?
-- Nick
m anna monika responded:  2019-05-29
Thank you for the help. I have uploaded both the skyline and the .d files under the name: Importing results (TDF format)
Brian Pratt responded:  2019-05-29
Hi Anna,

I see the file, but I don't see the .d files. You'll need to zip that directory up seperately.


m anna monika responded:  2019-05-29
Hi Brian,

I think my file is too big (even in zipped format). Is there an other way I could share it?
Brian Pratt responded:  2019-05-29
They are monsters! Can you share it on a google drive, or some other service?
Brendan MacLean responded:  2019-05-29
Even posting to

That shouldn’t have a file size limit. What kind of error are you getting? How big is the ZIP file?
m anna monika responded:  2019-05-30
It's 13GB. I don't get any error message, it just doesn't appear on the list once I hit the upload button. I will try to use google drive instead.
m anna monika responded:  2019-05-31
Sharing it on google drive. Please let me know if it worked.
This is the link:
Brian Pratt responded:  2019-05-31
It worked! This will be very helpful, thanks.

I'll keep you updated. BTW most of the Skyline team is at ASMS next week, so I won't have anything to report right away.


Brian Pratt responded:  2019-06-17
Hi Anna,

I note a couple of things:
From inspection of the .tdf file (it's an SQLite database) this doesn't appear to be diaPASEF data. It is PASEF data though.
I'm not seeing any ion mobility information in your Skyline document, so we won't be able to make use of the IMS values anyway.

Best Regards,

Brian Pratt