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Reporting raw chromatograms for downstream processing

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Reporting raw chromatograms for downstream processing scurran  2018-01-29 10:54
 
Dear Skyline Support,

I like working with my traces in a downstream processing platform such as Python or Excel. I like the freedom to customize my graphs and etc. One *slow* way to do this is to manually copy the trace data for each transition (MRM) and paste into a .csv file. I would prefer an automated way to do this.

I would like to make a report that has my peptide name, the replicate, and the data for the trace (time and intensity). There is an option for this under Reports, but the output does not have the trace data (see attached image). Am I confused? Is there an easy way to do this?

Thank you,

Sam
 
 
Nick Shulman responded:  2018-01-29 11:14
That is certainly supposed to work.
One thing that would not work would be if this was a very old Skyline document (before Skyline 3.6) which did not have the raw data in it. In that case, you would have to look at the "Interpolated Data" columns instead of the "Raw Data" columns.

Can you send us your Skyline document?

In Skyline, you can use the menu item:
File > Share > (complete)
to create a .zip file containing your Skyline document and supporting files including extracted chromatograms.

If that .zip file is less than 50MB you can attach it to this support request. Otherwise, you can upload it here:
https://skyline.ms/files.url
 
scurran responded:  2018-01-29 11:35
I am using a very old Skyline file! The interpolated data column did do the job (image attached). What is the difference between interpolated and raw data?

I attached the Skyline document.

Thanks,

Sam
 
Nick Shulman responded:  2018-01-29 12:44
Before Skyline performs peak detection, Skyline interpolates in the time dimension so that all of the transitions for a given peptide use the same set of times, and the time interval is constant over the entire chromatogram. The main reason that we do this is that our algorithms for doing Savitzky Golay smoothing and also calculating the second derivative, require that the chromatogram time points be evenly spaced.

Prior to Skyline 3.6, we would only save out this interpolated data.
Currently Skyline saves out the raw data, and does the interpolation again whenever Skyline needs to do anything related to peak integration.

You can switch between looking at the raw and interpolated chromatograms in Skyline by right-clicking on a chromatogram graph and choosing either "None" or "Interpolated" from the "Transform" submenu.