Hi Rob,

It will probably be helpful to have screen shots of any settings you selected along the way. When I use your files, accepting all the defaults, everything proceeds more or less instantaneously.

Thanks,

Brian Pratt

I think the problem is that if you tell Skyline to accept all of the modifications (there are about 60 of them) that were discovered in the peptide search results, then Skyline has too many permutations that it needs to work through when Skyline is trying to figure out what modifications to put on the peptides from the FASTA file.

One thing that you can do instead is cancel out of the "Import Peptide Search" wizard once you get to the part where it's asking for the FASTA file.
Then, in Skyline, use the menu item:
View > Spectral Libraries
and then use the "Add All" button to add the peptides from the spectral library into your document.

I am not sure whether we can speed up all of the work that Skyline is doing during "Import Fasta". It seems like something that ought to be straightforward to fix ("instead of generating all possible peptides and then checking whether they are in the library, instead iterate over the peptides that are in the library") but there might be a reason that it is implemented the way that it is.

Thanks to you both, indeed when I don't select any mods, the import is very quick. We're writing PTM discovery software though, so we're going to often have a fairly large variety of PTMs observed in a sample.

The cancel and then view->spectral library tricked worked, thanks Nick. Great talking to you at ASMS at my poster, too.

Our search output is largely in .tsv format and we're excited to use Skyline for visualizing our search results (from mzID). It's a great help to us and we're of course fans of open-source software. Thanks for contributing so much to the MS community.