Exporting Skyline document as report to include modified amino acid position on protein

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Exporting Skyline document as report to include modified amino acid position on protein paul.derbyshire  2021-01-29
 

Hi Skyline Team,

I have a question regarding document export as a report, i.e., File > Export > Report. Is it possible to extract the modified position of an amino acid within a protein sequence? In the jpg example attached, this protein is phosphorylated at position S134. Can such information (S134) be included in the report and if so which of the various option(s) should be selected?

Thanks in advance.

Paul

 
 
Nick Shulman responded:  2021-01-29
Someone else asked for this feature a while ago, and we should probably add it.
https://skyline.ms/issues/home/issues/details.view?issueId=247

The way I imagine it would work would be that there would be a single column in the Document Grid which contained a comma-separated list of the amino acid symbols and positions.
If you might want to have that list in different formats, we could potentially add sub-properties in the Document Grid (similar to how under the "Peptide Modified Sequence" column there are different things depending on whether you want the modifications described by their masses or their full names).

Do you have a preference for whether this thing uses the one letter or three letter amino acid codes?
Are there situations where you might need to know the name of the modification? If so, what would you want that to look like?

-- Nick
 
paul.derbyshire responded:  2021-01-30
Hi Nick,

Single letter codes should be fine. This would be a very useful feature, especially for large datasets made up of modified sequences. I don't think there will be a need to know the name of the modification. At least not for the work we are doing.

Many thanks

Paul
 
Nick Shulman responded:  2021-01-31
Can you send me a Skyline document that contains peptides you'd like to see this for?
I realize that I could test with any modified peptide in a protein, but it's always nice to be able to see that the feature looks nice with real world data.

In Skyline you can use the menu item:
File > Share
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.

-- Nick
 
paul.derbyshire responded:  2021-02-02
Hi Nick,

I have created .zip file containing the Skyline document and supporting files that includes one .raw file collected on a Thermo Fusion and it's Mascot search results in .dat format. I also include the Araport11 .fasta file (background proteome). Note this is PRM work.

Thanks

Paul