computer resource configuration

computer resource configuration bobxiong  2022-07-12

Hi Skyline Team,

I have an odd question about computer configuration in support of Skyline usage. I tested a manually prepared transition list of 4000 transitions on a 3G mzML DDA data file using the Molecule interface. While importing the transition list and the result mzML data seemed slow, it was not responding to any kind of clicking to view the data afterwards. The computer hung up. Please see the attached for my current computer properties.

Assume that I have generous funding, what kind of computer resource configuration should I go for? I do not want to be bottlenecked by a computer to perform Skyline work. For a disulfide linked tri-peptide molecule, the transition list can easily reach 50K transitions to consider a combination of multiply charged precursor and product ions. I expect it to become even more demonding if multiple replicates of mzML data are loaded in Skyline.

I would greatly appreciate any suggestion/recommendation.

Thanks a lot,

Bob Xiong, Ph.D.
Joinn Laboratories
Beijing, China
Email address:

Nick Shulman responded:  2022-07-12
Here is the web page where we talk about what Skyline's system requirements are:

I see that you have 32GB of RAM. With that much memory, Skyline should be perfectly happy working with documents which are a hundred times larger than what you describe. It might be that there is something else going on which is making things slow.

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.
The file will also contain the .sky.view file which will tell us the layout of the graphs that you have displayed.
Sometimes when Skyline is slow, it is because one of the graphs that you have displayed is doing a lot of work to display itself. If that is the case, we will be able to tell you which graphs you should hide so that Skyline will be more responsive.

If you feel like it, you could also send us your .mzML files.

If your files are less than 50MB you can attach them to this support request. You can upload larger files here:

-- Nick
bobxiong responded:  2022-07-12
Hi Nick,

Thanks for your reply. Please see attached the .zip file. I tried to upload the mzML file, but got an error message (screenshot attached).

Come to think of my problem, it might have something to do with my employer's network speed. I'll try it on a hard-drive installed Skyline to see what happens. Just curious.

Thank you so much for looking into my problem.


Nick Shulman responded:  2022-07-12
Thank you for sending your Skyline document.
I see that you have one molecule in your document, and there are two precursors and each precursor has 2000 transitions.

Yes, Skyline is very slow in this scenario. It looks like Skyline is spending all of its time drawing the chromatogram graph. Things will go faster for you if you right-click on the chromatogram graph and choose either "Transitions > Single" or "Transitions > Total".

We did not anticipate that anyone would have that many transitions under a single precursor, so we have not really tried to optimize the performance of that scenario.
It is always very interesting to see Skyline documents like this which expose weaknesses in Skyline's performance. We will certainly think about whether there is anything we can do in the future to make a scenario like this faster.
-- Nick
bobxiong responded:  2022-07-12
Hi Nick,

Thanks for your quick investigation. Much appreciated.

As one user, I see tremendous value of using Skyline as an independent tool for confirming/rejecting DDA analysis results produced by instrument vendors' software. In my experience, it is not uncommon to see erroneously identified PTM (e.g. disulfide bond) that had no corresponding chroma peaks displayed in Skyline. "Show me the chroma" has practically boosted confidence in data analysis results in our lab. To that end, I would lobby in spirit for Skyline to enhance its support for sizable transition list per precursor.

I tested the "unplugged" installation of Skyline on the same transition list and DDA mzML. It fared much better than the web version Skyline. The computer did not hang and responded to clicks :)