Export Report Extremely Slow graham delafield  2022-03-29

Hi there,

My current Skyline project includes signal extraction from a large proteomics spectral library in order to do MS1 and MS2 LFQ. The projects complete successfully, even if it takes time to chug through the library.

However, when I wish to export a report (~10-15 columns),it takes an extremely long time - sometimes 12 hours for only 50,000 rows. I have applied filters to reduce the number of rows, but there is always a significant stall when the report is 75-90% complete, regardless of the number of rows.

My questions are 1) any tips on why this may be happening? and 2) is the skyline data accessible any other way? For example, can I write some custom SQL to access file where the data is stored?

Skyline Version:

System: Windows 10 x64, i9-10940x, 64 GB RAM

Thank you!

Nick Shulman responded:  2022-03-29
Can you send me your Skyline document and report definition?
You can include the report definition in your Skyline document by going to:
Settings > Document Settings > Reports
and checking the checkbox next to your slow report.

Then, when you do:
File > Share
to create a .zip file containing your Skyline document and supporting files including extracted chromatograms, the document will include that report definition.

If that .zip is less than 50MB you can attach it to this support request. You can upload larger files here:

Sometimes reports are slow because they include a column which takes a long time to calculate. For instance, I remember a support request where the report definition included both the "Protein Abundance" column as well as columns from Transition Results. This meant that there was one row per transition and replicate, and the protein abundance was having to be recalculated on each row. In this case, it would have been better to have two reports: one which only had one row per Protein Result and included the Protein Abundance column, and a separate report which had one row per Transition Result and which included only columns which were not slow.

If for some reason you cannot send me your Skyline document, you should send me your report definition.
You can export the report definition by going to:
File > Export Report
and then push the "Edit List" button
and then, in the "Manage Reports" dialog, select the report and push the "Share" button. This will allow you to create a .skyr file which contains you report definition.

-- Nick
Nick Shulman responded:  2022-03-29
I see that you have uploaded a Skyline document with 18 million transitions and one replicate.
I do not see any report definition.
Which report were you looking at which was slow? Was it one of the standard reports which come with Skyline ("Transition Results", etc), or was it a custom report that you designed yourself.

If it was a custom report, please go to:
File > Export > Report
and press "Edit List" and "Share" to create a .skyr file containing that report definition.

Whenever we investigate issues like this where a very large Skyline document is slow in some way, we usually find several things that can be improved about Skyline.
-- Nick
graham delafield responded:  2022-03-29
Hi Nick,

Sorry, I was replying to the email messages instead of this webpage - it's my first post to the forum.

Yes, that is my project. The report I was looking at was titled 'Comprehensive_MS1,' which is a custom report. I have attached the .skyr file below, which should be more helpful in isolating the problem.

 - Graham
Nick Shulman responded:  2022-03-29
Thanks for sending that report.
You should remove the "Protein Abundance" column from your report.

Skyline ends up calculating the protein abundance value for each row in the report. Things really slow to a crawl when it gets to the Decoys protein, because that protein has nine million transitions in it.
When Skyline calculates the protein abundance, Skyline looks at all of the transition peak areas under the protein. This does not really make sense to do in the case of the Decoys peptide list, but Skyline blindly does it anyway.

Also, Skyline does not remember the value of the protein abundance from one row of the report to the next, so Skyline ends up having to redo that calculation for every row of the report.

You are the second person to run into issues with the protein abundance column being slow. Here is the first such support request:

For now, the simplest thing to do is to remove the Protein Abundance column from your report. If it is important for you to see those numbers you can create a separate report which only has protein columns in it, and would therefore have only one row per protein.
-- Nick
graham delafield responded:  2022-03-30

Perfect, everything works smoothly now. I will be sure to start new threads in the future if any new issues arise!