Filtering a Skyline document for protein length

Filtering a Skyline document for protein length cabarnescabarnes  2021-07-12

Hi. I have a Skyline document of something like 5000 protein entries and I'd like to filter it based on the amino acid sequence length of the proteins in the document. Specifically, I want it to only be the proteins under 150 aa. I can obviously export results to a table and do it there, but I'd like the Skyline document to only include this subset. Is that possible?

Nick Shulman responded:  2021-07-15
I cannot think of a way to do this in Skyline.
We certainly could add "Protein Length" and "Protein Molecular Weight" columns to the Document Grid in a future version of Skyline.

If you needed to do this in Skyline today, this is what I would do:
1. Go to "Settings > Document Settings > Annotations" and define an annotation called "Protein Length" which applies to "Proteins".
2. View > Document Grid and choose the report "Proteins".
3. Use the "Copy All" button in the toolbar of the Document Grid to copy all the rows of data including the column headers
4. Paste that into a new Excel Document.
5. The first value in the "Protein Length" column in Excel will say "#N/A". Change that to the formula:
since "G" is the column for "Protein Sequence"
6. Select all of the cells in the "Protein Sequence" column from row 2 to the end of the data, and choose "Fill > Down" on the ribbon.
7. The protein lengths will all be filled in and selected in Excel. You can copy that to the clipboard.
8. Move to the "Protein Length" cell in the first row in the Document Grid in Skyline and then do "Ctrl + V" to paste what you copied from Excel.

Hope this works for you.
-- Nick
cabarnescabarnes responded:  2021-07-16
That works great. That's a simple work around and great trick for the future. Thanks.