Old skyline release

Old skyline release Zac  2023-04-26

Unusual request but is there a way we could get access to an old release of skyline? -Release or a release close to this.

Nick Shulman responded:  2023-04-26
The place to download old versions of Skyline is the "Unplugged" installer page:

After you click "I agree" you will see a "archive" link which will take you to a page where you can download old installers.
-- Nick
Zac responded:  2023-04-26
Great thanks, i never noticed the archive there before
Brian Pratt responded:  2023-04-26
May I ask why you're interested in an older version? Just wondering if there are any issues we should be aware of.


Brian Pratt
Zac responded:  2023-04-26
We have maintained the older version on our data analysis machines as our QA system requires us to validate every time we update. So we try to limit the number of updates. We plan to update now and i wanted to confirm that we will have a roll back option... Being able to download the old installer will also allow me to do some testing on another offline workstation. I have just started testing, the one thing we did notice is that it seems like we are getting different R2 values for our calibration curves between the two versions, i am still looking at this more closely but possibly there was a fix/patch between the old and current version?
Nick Shulman responded:  2023-04-26
If you send us your Skyline document I would be able to give you an explanation of any differences that you might be seeing between any two versions of Skyline.
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. You can upload larger files here:

I know that we have fixed some bugs which would happen if your normalization method was "Equalize Medians" or "Total Ion Current", but other than that I can't think of anything that might cause Skyline to get different R-squared values in the calibration curve if the underlying peak areas were the same.
-- Nick
Zac responded:  2023-05-02
Thanks. The file is 'WU-1035 YYNP 2+ QUANT.sky'. The target peptide is YYNPSLQSR - 564.277 . We seem to be getting different R2 values between the old version 21.1 and the latest skyline version. All settings seem to be the same but it is possible that some default change has been missed.
Nick Shulman responded:  2023-05-02
I see that the "Regression Fit" setting at "Settings > Peptide Settings > Quantification" is "Linear in log space".

There used to be a bug in the way that R-squared was calculated for Linear in Log Space:

I do not remember exactly what Skyline was doing wrong, but the R-squared values that you were getting from Skyline 21.1 were completely incorrect.

The code change that fixed the bug is here:
-- Nick