Hi David,

I think this actually breaks down into two questions:

1. Is there a way to export chromatogram images to PDF?
2. Is there a way to export images for all the chromatogram at one go?

The answer to both, unfortunately, is "no", but we'd be interested to hear more detail about the capability you are hoping to see (one per page? tiled? the same view as on your screen? etc).. Feedback from users is how Skyline keeps moving forward.

Thanks,

Brian Pratt

Though, the custom reports are capable of exporting all chromatograms in one report, and then someone could write an R script to plot them all in a PDF. It could even be posted to the Tool Store as an external tool. So, definitely not outside the realm of possibility for a moderately dedicated R programmer.

But, as Brian explains. There is no print to PDF feature in Skyline.

All the chromatograms in one report like the screen view after adjusting the peak boundaries, and much is what I'm looking for. I guess a R script to plot them all in PDF from the exported chromatogram file would work too, I will look into it.

Thanks, Brian and Brendan!

David

Can I ask what the purpose is? You can also upload a Skyline document to PanoramaWeb.org and even post it to Panorama Public for supplementary data. Once on PanoramaWeb.org, the chromatogram plots can be viewed for all peptides, filtered, searched and navigated in a much friendlier UI than a PDF. This is what we recommend for use as supplementary data for a publication, and it meets the MCP guidelines for targeted proteomics data. In fact, it can be considered the reference implementation for those guidelines (https://www.mcponline.org/content/16/3/327).

Hi Brendan,

I'd like to see a clear view of the overall experiment result, control vs treated, etc. for all proteins profiled. I've looked at the example data on PanoramaWeb.org, the results are still displayed for each individual peptide/protein. It's for reporting purpose, not really for publication.
Thanks,

BTW, slightly different subject, I know there is a way to generated a tab delimited ssl for spectral library in BibloSpec, but I still need to specify raw files in it. Can I just "tell" Skyline which fragment ions to use and what's relative intensity are for each fragment for a given peptide?

Thanks,

David