Q-TOF .raw data search stops after certain retention time

Q-TOF .raw data search stops after certain retention time Yao Chen  2019-08-13

Dear Skyline Team,

I am importing Waters .raw data generated by Q-TOF instruments into Skyline. The whole file collects data for 120 min (pic 1), however, the searches in Skyline seems stopped at around 60-70 min for almost all the transitions I was monitoring (pic 2 shows four examples).
I could see a very clear signal of a spiked-in standard peptide in the raw file, which eluted at 77 min (pic 3), however, its retention time was not reached in the search of Skyline (pic 2, upper left). How should I change my settings so I can do a full chromatographic search, please?

I have my partial skyline processing file attached.



Nick Shulman responded:  2019-08-13
I cannot think of a reason that things would look the way they do.

Can you send us your Skyline document?

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.

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

It would also be very helpful if you could send us at least one of your raw files.
-- Nick
Yao Chen responded:  2019-08-13
Thanks Nick!

I uploaded the file and one raw data to the link. They are named: sample data.raw.rar and simplified.sky.zip.
Please let me know if anything else is needed.


matt.chambers42 responded:  2019-08-14
Hi Yao,

When you open that raw file in the Waters software, do the spectra after 63 minutes retention time appear blank? If not I'll have to forward this to a Waters contact because the spectra we are getting past that point are empty, though their TIC metadata says they have a lot of signal.
Yao Chen responded:  2019-08-14
Hello Nick

Yes, the spectrums are still there after 63 min when I opened with Waters Software.

Is there an import data size limit? As every injection file is very big. Each file contains two (MS and MS/MS) channels, which were collected on a 32 bit computer. Both channels collected maximum allowed data of 4GB. So the total data file size of one inject was 8GB.

Please let me know if you need anything else from me and I am looking forward to hear from your contact in Waters.

Thank you,

Yao Chen responded:  2019-08-19
Hello Nick

Have you gain any insight to this problem from your contact from Waters?


matt.chambers42 responded:  2019-08-22
Hi Yao,

The Waters contact linked us to an updated SDK but it turned out that it was actually the version we were already using. So I've notified him and we'll probably need to wait for another SDK update. I'll post on this issue when we get it.
Yao Chen responded:  2019-08-22
Thank you very much Matt!
Yao Chen responded:  2019-09-30
Hello Matt

Is there any updates from the Waters SDK yet?

Thank you,

matt.chambers42 responded:  2019-10-07
Not yet, I'll update this thread when we do get it fixed though.
matt.chambers42 responded:  2021-02-17
Hi Yao Chen,

Sorry for letting this issue lapse so long. It still happens with the latest SDK. I actually thought I sent your data to my Waters contact but it turns out I sent the wrong one, so I don't think he ever saw the real issue. Now I've sent him your actual data and he asked me about how it was acquired. Do you remember whether this was acquired with MassLynx, or whether it's exported from UNIFI? Which version of the acquisition software (in either case)?