Export of Scan Indexes

Export of Scan Indexes jfoe  2019-04-16

Dear Skyline Team,

I have been exporting skyline chromatograms to perform some diagnostics with scan header information.
For export of the chromatograms I use the Report Objects:
Proteins/Peptides/Precursors/Transitions/Transition Results/Chromatogram/Raw Data/...
.../Raw Times
.../Raw Intensities

When automating this with a lot of files etc, it turns out that matching diagnostic data via scan retention times can get quite messy due to loss of precision on export.
You also store a Vector of ScanIndexes with Chromatograms. Could you maybe add an option to export those?

Best regards,

Nick Shulman responded:  2019-04-16
This is now available in the latest update of Skyline-Daily (
There are new columns on the Chromatogram things under Transition Results:
Chromatogram / Raw Data / Raw Spectrum Ids
Chromatogram / Interpolated Data / Interpolated Spectrum Ids

These are the vendor-specific spectrum identifiers, which look like a series of integers separated by dots (e.g. "0.1.16598"). Some vendors do not have a well-defined ordering to the spectra in their raw files, so we can't always describe a scan index as a single number.
-- Nick
jfoe responded:  2019-04-16
Just a few days ago I see.
My bad then, thanks a lot for that feature!