Export hundreds of MS1 chromatrograms

Export hundreds of MS1 chromatrograms nesgio  2024-06-11 05:50

Hi guys,

I am trying to export all the chromatograms of the species detected with a contaminants template published by Rardin (https://link.springer.com/article/10.1007/s13361-018-1940-z) in a RAW sample acquired in full scan.
However, when I "Right Click --> Copy Data" on the chromatogram and I have only 100 intensities while the documenport the group name (i.e., protein.name) TIC for each contaminants - would it be possible? I ts contains more than 700 of "MS1 filtering". I would like to click on "Export --> Chromatogram --> Precursor" but I do not see "Retention Time" and "Intensity" column.

Many thanks and best regards,


Nick Shulman responded:  2024-06-11 08:55
When you use the "File > Export > Chromatograms" menu item, you get one row per chromatogram.
All of the retention times are in a single column called "Times" which contains a comma separated list of numbers.
The corresponding intensities are are in a column called "Intensities".

It sounds like you might have been hoping for a big long list with one retention time and intensity per row, but Skyline cannot give you chromatogram data in that form.

A different way to export chromatogram data is to create a custom report.
The columns with the retention times and intensities are called "Raw Times" and "Raw Intensities". In the "Customize Report" window there is a binoculars button which will let you search for columns by name.

If you have not created a custom report or used the Document Grid before, you should read the Custom Reports tutorial:

The data that you get using "File > Export > Chromatograms" will be similar to what you would get if you export a custom report, but the custom report method gives you more control over exactly what other columns you get and filters can control what rows you get.
-- Nick
nesgio responded:  2024-06-21 08:20
Hi Nick,

Many thanks for your reply - very useful.

I tried to export from "File > Export > Chromatograms" and all the signals were present.

The custom report is also interesting, but I would like to pivot the "List Name" or "Name" instead of "Replicate Name" (see attached screenshot). I would like to have the Molecule Name as columns with the corresponding Raw Times and Raw Intensities as rows. Do you know if this is possible?

Is it also possible to export smoothed chromatograms?

Thanks and best regards,

Nick Shulman responded:  2024-06-21 09:15
No, it is not possible to pivot in the way you are asking.
It is possible to pivot on more than just the "Replicate Name" and "Isotope Label" options that you get in the Customize Report dialog.
There is a more complicated "Pivot Editor" that you can read about here:
However, I don't think even the Pivot Editor would be able to accomplish what you have described.

It is not possible to export Savitzky-Golay smoothed chromatograms.
The only thing that you can export other other than the "Raw" chromatogram is the "Interpolated" chromatogram ("Interpolated Times" and "Interpolated Intensities") which is what Skyline got after interpolating in the retention time dimension in order to evenly space the points.
-- Nick
nesgio responded:  2024-06-24 01:04
Hello Nick,

Thanks for your help and clarification. In the end I used the "File > Export > Chromatograms", perform the "Text-to-column" and pivoting in Excel. It's an extra step, but it answered my question ;)

Best regards,