• Sign In
  1. Requests

Request for Assistance with Chromatogram Export Functionalities

support

View Request

view list print
Request for Assistance with Chromatogram Export Functionalities 1150767964  2025-04-09 01:27
 
Dear Skyline Technical Support Team:
      First and foremost, I would like to express my sincere gratitude for developing such an indispensable tool for PRM proteomics data analysis. As a long-time user, Skyline has been instrumental in advancing my targeted proteomics research.
      I am writing to seek your expertise regarding two technical challenges I recently encountered:
     1. High-Resolution Chromatogram Export
     When exporting chromatogram images via the current interface (right click single sample's chromatogram > Save Image As), the resolution (approximately 300 dpi) falls short of the quality required for publication figures. While manual screenshot capture can improve clarity, this approach becomes impractical when processing multiple samples. Could you kindly advise if there is an undocumented high-resolution export option or whether such a feature might be considered in future updates?
     2. Bulk Export of Raw Chromatogram Data
     For experiments involving numerous peptides/samples, the current workflow of exporting raw chromatogram data (via Copy Chromatogram Data for individual entries) remains time-intensive. I attempted to extract raw retention times and intensities through customized reports (File > Export > Report), but the exported data failed to reconstruct chromatograms matching the quality displayed in Skyline. Is there an existing workaround for bulk export of raw chromatogram data, or could this functionality potentially be automated via the scripting interface?
     Given your team’s deep understanding of user workflows, any guidance on these matters—or insights into potential solutions under development—would greatly enhance my research efficiency. I am happy to provide additional context or testing datasets if needed.
     Thank you for your time and continued support. Looking forward to your guidance.

Best regards,
Meifeng
Wuhan spec-ally company
2025.04.09
 
 
Nick Shulman responded:  2025-04-09 06:54
When you right-click on a chromatogram graph in Skyline, there is a menu item "Copy Metafile" which will copy a higher-quality scalable image to the clipboard.
Not all programs can handle these metafiles, but you can paste it into Microsoft PowerPoint.

If you want to export the chromatogram times and intensities as a text file you can use the menu item "File > Export > Chromatograms".
Alternatively, you can create a Custom Report which includes the "Raw Times" and "Raw Intensities" columns.
You can learn about Custom Reports and the Document Grid here:
https://skyline.ms/wiki/home/software/Skyline/page.view?name=tutorial_custom_reports

-- Nick
 
1150767964 responded:  2025-04-09 17:50
Hi Nick! Thank you so much for your prompt and effective solutions! Your support perfectly solved my trouble! ! ! Thanks so much sincerely!

Best wishes
Meifeng
 
SebastianM responded:  2025-05-06 04:44
Hi Nick and Meifeng, since Im doing something similar I will piggyback on Meifengs initial question...
@Nick: As you suggested Im using the "Raw Times" and "Raw Intensities" columns to create a document which contains all chromatograms. I use R and knitter to generate a *.docx file with all the chromatograms, its just some lines of code and works really nice. We need these reports since we are obliged to archive chromatograms as "raw" data.
With a newer version of Skyline the chromatograms looked somehow funny so I compared the reports.
Initially I used Skyline 22.2.0.527 to generate the export.

Today I used Skyline 24.1.0.414

As you can see the precision of the Raw Times and Raw Intensisites changed. In the newer report / export I now have two intensities for the same time since the precision is to low to discriminate between the two times.
Is it possible to have a higher precision again somehow?
I hope this request makes sense. Many thanks in advance!
 
Nick Shulman responded:  2025-05-06 07:14
I am surprised that the behavior was different back in version 22.2.

In current versions of Skyline you can tell Skyline to use a different format on those columns.
That is, you can right-click on the "Raw Times" and "Raw Intensities" columns in the Document Grid and choose "Number Format" and then in the "Choose Format" window you can select "Full Precision" in the dropdown.
After you do this, the values in the comma-separated lists in the "Raw Times" and "Raw Intensities" columns will change to be displayed with more digits of precision.
Next, you need to tell Skyline to remember these formatting choices, and apply them every time the report is shown to you. To do that, click the dropdown next to the pivot button near the top-left corner of the Document Grid and choose "Remember Current Layout". Give the layout any name that you want, but be sure to check the checkbox "Make this the default layout for this report".

After you do this, those two columns will have more digits of precision when you export the report using "File > Export > Report" or any other way that you might export the report.

For most numeric columns, if you choose "Invariant" as the language at the bottom of the "Export Report" dialog, all numbers will be written out with full digits of precision. However, the Raw Times and Raw Intensities columns are not treated that way, which is why you have to do this extra step of explicitly specifying the format.

If you want to learn more about the "Remember current layout" menu item, there is a bit of information about it in the documentation for the Pivot Editor:
https://skyline.ms/wiki/home/software/Skyline/page.view?name=PivotEditor
-- Nick
 
SebastianM responded:  2025-05-06 09:10
Hey Nick,

thanks for the quick answer, that helps a lot an solved it!

Im using Skyline since 10+ years and still learning tricks.
Never used the pivot feature before, but this help me and my colleagues as well!

Best regards
Sebastian