Updating chromatogram libraries with metadata

Updating chromatogram libraries with metadata Andreas Hober  2019-08-19 07:52:32

I was only wondering if it would be possible to update chromatogram libraries on Panorama with metadata from e.g. a background proteome.
It would be very useful when looking at the overviews for protein coverage etc. I am currently working with quite a few Skyline files where all the proteins are named based on the standards that have been used for the method development and it would be great if I would be able to add a background proteome for grouping of the peptides once they have been added to assay project on Panorama, since now I have quite a few "proteins" which actually map towards the same actual protein.

Best regards

Vagisha Sharma responded:  2019-08-19 12:42:41

Hi Andreas,

Thanks for your question. Can you please send me a link to your library folder on PanoramaWeb so that I can better understand what you need? You can send it to me separately at vsharma@uw.edu if you prefer.

It sounds like you have several Skyline documents with the same protein (i.e. same sequence) but with a different label/name in each document. And when you are looking at the protein details in PanoramaWeb, for example, you want to be able to see coverage from peptides in all proteins in the library folder that have the same sequence. Does this sound right? Or are you looking at different protein isoforms? I assume this is a peptide-level (not protein-level) library folder on PanoramaWeb since protein uniqueness in a protein-library folder is determined by the protein sequence if the Skyline document has that information. And you should only be able to have one "version" of a protein (unique sequence) in the library.