Multiple Skyline report templates combined into single Excel Workbook?

Multiple Skyline report templates combined into single Excel Workbook? josiah.hutton  2024-04-17 11:28

Hello Skyline Team,

First of all, thanks for such a great tool, I've used Skyline for almost a decade now to design and analyze targeted proteomics dataset.

I have recently been exporting my reports for my datasets as multiple individual .csv documents, as I found it cumbersome to export all the information I wanted (fragment ion peak area, MS1 IM, MS1 peak area, total area, fragment ion dotp score, etc.) in a single report and then going through and separating the information into separate tabs. Currently, I take all the multiple individual .csv reports and combine them into multiple tabs into a single Excel Workbook, as this is sometimes easier to manipulate for downstream analysis and is a somewhat more logical document when provided to collaborators. Would it be possible to modify the Report Export procedure so that I can tell Skyline to output into a single Excel Workbook a document with multiple tabs that contain information from different report templates? For example, a new Merged Report Output option that combines the report template from Report Template 1, Report Template 2, and Report Template 5 as three separate excel tabs in a single document? Or, did I just not adequately search the forum for this topic? I currently have a tool to combine the separate single reports into a single merged document, but I still have to tell Skyline to export 5 different reports, and it would be convenient to have a method within Skyline to export a single merged document.

Thanks in advance!

Nick Shulman responded:  2024-04-17 14:39

If you are exporting that many reports it might make sense to use Skyline's command line interface to automate the process.

You might find useful information on the Skyline Batch page:

There is also a menu item in Skyline "Help > Documentation > Command Line" which will give you more information.

The way command line to export the "Transition Results" from a Skyline document called "" would be something like:
skylinerunner.exe "--report-name=Transition Results" --report-file=outputfile.csv

Hope this helps,
-- Nick

josiah.hutton responded:  2024-04-18 14:55

Thanks for the response Nick! I will give it a try this next week, seems like there are some interesting things in there that could help me in multiple different ways.