Skyline is slow on my computer cmwats2  2021-05-03
 

Below are my computer specifications. I am only doing targeted peptide methods. I noticed a few months ago that my imports were taking a long time and telling me that the import is taking longer than it should. I figured I was pushing my computer too hard and the data files uploaded so I didn't address it. Now I am trying to save a skyline file with 950 data files and 750 transitions. Skyline saves the file and then says it is "optimizing data file..." This always take a long time so I let is optimize overnight and it had not finished by this morning. I end up canceling the process so I can use skyline. There is quite a response delay when I select a different replicate. The data files and skyline files are saved on the C: drive in My Documents. I am uploading Thermo Raw files that are about 20MB each (scheduled MRM 15min method). I am using Skyline (64-bit) 20.2.0.343. The long imports and optimizing data file happens in multiple saved skyline files that are created from one another. I have removed all the data and re-imported but that did not resolve any issues. I am sure I forgot to include something important.

Can someone tell me how to improve skyline performance on my computer? I've searched the supports pages but all related issues involve users doing things that seem more complicated than my situation.

Device name LAPTOP-P29U4S18
Processor Intel(R) Core(TM) i7-8565U CPU @ 1.80GHz 1.99 GHz
Installed RAM 16.0 GB (15.8 GB usable)
System type 64-bit operating system, x64-based processor

Thanks in advance,
Caroline

 
 
Nick Shulman responded:  2021-05-03
Caroline,

You should try this with Skyline-Daily.

Back in February of this year, I fixed a problem where "Optimizing Data File" was very slow.
The "Optimizing Data File" is not supposed to take very long. Skyline is making sure that the .skyd file contains data for the replicates that are still in your document. Unfortunately, in 2017 I accidentally made it much slower than it was supposed to be.

It sounds like you are also experiencing slowness while importing results. Skyline will become incredibly slow if Skyline tries to use more RAM than there is in your computer. At the bottom of the "Import Results" dialog there is a dropdown "Files to import simultaneously". If your computer has a lot of RAM, it is faster to choose "Many", however, if your computer has less RAM, then it would be faster to choose either "Several" or "One at a time" so that Skyline does not use up all of the RAM in the computer and cause the operating system to have to start using the swap file.
Also, ever since October 2020, the amount of RAM that Skyline-Daily uses during chromatogram extraction is a lot less than it was in Skyline 20.2.

If things are still slow for you when you try this in Skyline-Daily, then you should send us your files and we can take a look.

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:
https://skyline.ms/files.url

You should probably also send us at least one of the raw files that you were trying to import.

-- Nick
 
cmwats2 responded:  2021-05-05
Skyline daily seems to have resolved all the issues I was having. Thanks for the quick response!

Caroline