Hi T,
It should not be that hard, no. It is already enabled for custom list, but explicitly disabled for proteins that originated in FASTA files. I guess that was a mistake. Embarrassingly, this was requested not long after my first release, and remains in the issues list:

https://skyline.gs.washington.edu/labkey/issues/home/issues/details.view?issueId=41

I will try to make sure it gets fixed for the next release.

Always good to hear what people want to see changed. Thanks for taking the time to make this request.

--Brendan

Hey Brendan,

Just bumping this again, I'm not sure if the new version has a way to change names quickly. But for next release it would be awesome if there was some way to change names of large protein sets real quick. The real reason is because of the different accessions, and to go back and forth can be pain especially with a list of hundreds of proteins. Thanks again for the great software !

-T

Hi T,
Did you have something in mind? A form with a two column grid: Current Name, New Name?

Just curious what you might be hoping to see for this operation, and what would work for you.

Thanks.

--Brendan

Hey Brendan,

That would suffice. It doesn't need to be complicated, if someway to export and reimport names for proteins (couple hundred in our case). Something to let us be flexible with the naming if need be, without needing to change skyline method or re-pick transitions/peptides. Problem arises once we build out a large number of transitions based on fasta's from uniprot, but the accession and abbreviation might be different from what other researchers might be used to or we want to make it more relevant to our needs. We can do it manually after we export the data, but would need to do that all the time, since we're constantly swapping in, swapping out proteins, and often large amounts at time, it can take a while .

Thanks for the quick response !

-tsbatth

Hi T,
Exporting the names of the proteins in your document should be pretty easy with the custom reports. I think adding a simple two column grid form (with menu item Edit > Refine > Rename Proteins...) that you can paste to from Excel shouldn't be that hard.

The workflow would be:
- Export current protein names in a report
- Assign new names in Excel
- Edit > Refine > Rename Proteins...
- Copy-paste from Excel to the 2-column grid form

That should work for your case, right?

Thanks for your feedback.

--Brendan

Yup that would be prefect! Thanks again for awesome software !

Regards,

T

Also one more thing, I'm not sure if it's been mentioned but with the latest skyline release, it adds two "." before .dam (x..dam) so if I export multiple methods it will name them "x_.0001.dam" . Analyst being analyst will mess up randomly at times and give errors, but not always. Just an FYI.

Thanks again!

PS

Easy way to fix is select "All files" under Save as type and type in "x.dam" manually.

Hi T,
Can you tell me what build version you are using when you see the .dam file issue? Thanks for reporting it.

--Brendan

1.3.0.3735