Protein description in skyline

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Protein description in skyline Sylvie Bourassa  2016-03-02
 
Hi, I would like to know if there is a setting somewhere in skyline to change the protein description.
With my complete proteome mouse databank of 2016, I only see the accesssion number and the gene name but not the complete description (Only see the description in the yellow square) (see attached). When I export the results, I do not see the complete description. I did not have this problem before. (I use the same database with mascot and scaffold and I see everything as usual). Briefly, for the example attached, I would like to have the decription"macrophage-expressed gene 1 protein in the targets first line (idem for each protein). I tried : view targets: by name, accesssion, by preferred name by gene and none gives the complete description. My library is a dat file obtained with same databank and my background proteome is also the same databank.

Thank you for your help, Sylvie
 
 
Brendan MacLean responded:  2016-03-02
Hi Sylvie,
The only other way to show this in the Skyline user interface is to use the Document Grid (in the View menu). The default Proteins view has the Protein Description as the second column. You can also add it to any custom view or report by using the view and report customization form and choosing the column Proteins > Protein Description, which should allow you to export it to Excel with the rest of your results. For more information on the Skyline Live Reports, please consult the following tutorial, which has a full reference of available columns at the end:

https://skyline.gs.washington.edu/labkey/wiki/home/software/Skyline/page.view?name=tutorial_custom_reports

Hope this helps. Good luck with your research.

--Brendan
 
moe responded:  2016-03-21
Hi Sylvie,

I found a workaround the other day that you could try (no guarantees though :)
Hope that the steps below are clear. Since this is very "manual" it is possible to introduce errors but if you are careful it should work. Would be keen to hear other people's opinion.

1) Go to Edit - Refine - Rename Proteins

2) click populate and accession number

3) select all and copy both columns (current name and New Name) to a txt or xls file to get the uniprot IDs

4) copy only the uniprot IDs and go to uniprot (http://www.uniprot.org/uploadlists/) and paste the column containing the uniprot ids into the form and click go

5) click the download button on the resulting page and choose excel or tab or txt and "uncompressed"

6) open the downloaded file and copy the column with protein names into the the xls file from step 3) so that you have the current name in the left column and the new name in the right column.

7) copy the two columns together and go back to the rename dialog in skyline

8) delete all info in the two columns and paste the new two columns from step 7) into the form

9) click ok and you're done, the proteins are all renamed to the actual protein names

Cheers
Moritz