Couple minor issues with the most recent skyline update hs334  2021-11-04

First, synchronized integration is awesome! However, is it possible to update the software to allow us to click/drag to or use shift/click to select multiple samples under the synchronize integration tab? Currently when you go to synchronize integration if you want to select/deselect multiple sample items you have to individually check or uncheck each item. Often times I want to select/deselect upwards of 75 samples out of 100+ to synchronize together and its very tedious to select all of them individually by clicking.

Next, for some reason this update of skyline has made it so that I can’t double click on a skyline file and open with Skyline daily (i.e. if I go to a skyline file in my file explorer and double click it does not open it with Skyline daily.) The only way I can open these files currently is through using the open file function in skyline – which has prevented me from opening more than one skyline file at a time. It is really useful to have more than one skyline file open simultaneously for comparison purposes.

Brendan MacLean responded:  2021-11-04

Thanks for taking the time to post this feedback. I agree with your first suggestion. We do have the ability to Select / deselect all, and I guess we were hoping that less than 50% of your samples would not be such a large number, but we will also look into a better way to check ranges of runs at a time.

The second issue is known and will be fixed in the next Skyline-daily. Sorry for that bug. We will try to get a Skyline-daily out very soon with that and a number of fixes to synchronized integration.

Thanks again for your feedback.


Juan C. Rojas E. responded:  2021-11-05

Hi all,

First, this "Synchronize Integration" function is great!

Brendan, I think you have actually implemented a solution for his problem with Skyline. But you need to create new "Annotations" in the "Document Settings..." tab. I have multiple annotations for replicates for downstream analysis, but it was quite nice to see that the "Synchronized Integration" recognized them and allows me to just correct for the replicates under a certain annotation.

So here for example hs334 could create a replicate annotation for only those that he is interested in integrating and leaving the others outside?

One thing I noticed was that when "Synchronize Integration" is active when you correct one of the precursor ions below a peptide/molecule (containing multiple) the boundaries are not always corrected for all the precursors of the peptide/molecule as it usually does which might end up with different boundaries for the same precursor ions associated to the same peptide/molecule. Was this intended like this or is it a bug?

Thanks for the great work!

Kaipo responded:  2021-11-05

Hi JC,
Are all the precursors unmodified in this case? If there are modifications, the peak boundaries might not be adjusted for others.


Juan C. Rojas E. responded:  2021-11-10

Hi Kaipo,

Sorry for the late reply. Attached is an example of the peak boundaries issue I described for peptide F.NWYVDGVEVHNAK.T [155, 167] with two precursor ions supporting it. I corrected the peak boundaries with "Synchronized integration" for the dark red precursor (which are all alligned), but the correction was not applied to the other red precursor. When "Synchronized integration" is deactivated, if I change the peak boundaries for one precursor the other is adapted as well.

I treat peptides with PTMs as different "parent" peptides if that is what you meant by "modifications.

Juan C.

Kaipo responded:  2021-11-16

Hi Juan C.,
Does this behavior still occur with the latest release of Skyline-daily? If so, would you mind sharing an example document with which I can reproduce the issue?


Juan C. Rojas E. responded:  2021-11-18

Hi Kaipo,

I am using Skyline-daily (64-bit) and the issue is still there (example attached).

I have uploaded the Skyline file I have been working on the private Panorama server "U of Leipzig - AG Bioanalytics/Skyline Support" with only some exemplary HDMSE files in the "Raw Data" section.

Let me know if you need anything else.


roman sakson responded:  2021-11-20

Hi Kaipo and Juan,

I am also using the same daily-version and I can confirm the effect Juan reported. I have a heavy and a light precursor for my peptides (common proteomics isotope modifications for C-term K and R). Both synchronized integration and "Apply Peak to All" seem to adjust only across light or heavy precursors, respectively. One could now debate whether this kind of flexibility, which I believe was not offered before, is desirable or rather error-prone. I am happy to provide example data but I guess that Juan has already got you covered.

Thank you for the new feature anyway, I am sure it will prove very useful!

Kaipo responded:  2021-11-23

Hi JC and Roman,
Thank you for reporting this bug and providing example data. The issue has been fixed for the next release.