Combining own DDA library with SWATHatlas library

Combining own DDA library with SWATHatlas library SanL  2019-06-11

Good morning,

similar to a previous post submitted in 2016, I'd like to merge my own in-house DDA library with the Rosenberger library downloaded from here(phl004_canonical_s64_osw.tsv).

Now, I am trying to combine the two and align the retention times.

I know the process technically works the way it was suggested in the thread mentioned above. I did it before with a 'reduced' Rosenberger library similarly to the user in the thread.

Now, when I try to merge the in-house library with the 'full' Rosenberger library by importing the latter using the "import --> assay library" function, I get an "Index outside the bounds of the array" message (see screenshot attached with more details).

I cannot imagine the library being too big but I also could not figure out what the error message is telling me

Thank you in advance!


Nick Shulman responded:  2019-06-11
That error is happening while Skyline is trying to parse the modifications (e.g. "[+57.02]") in a peptide sequence.

This is definitely a bug in Skyline, but it might be that there is something wrong with the peptide sequence such as mismatched square brackets that our parsing function does not know how to handle.

Can you send us that file "phl004_canonical_s64_osw.tsv"?
If that file is less than 50MB, you can attach it to this support request.
Otherwise, you can upload it here:
-- Nick
SanL responded:  2019-06-11
Hey Nick,

I uploaded the file (description: SWATHatlas OpenSWATH library, only update I see from today) as it was too big.

There are some square brackets in there, some annotations (not all) are written as "[b7/0.007]". I suppose that could be the problem you are talking about?

Nick Shulman responded:  2019-06-12
Thanks for sending that file. Skyline is choking on the peptide sequence "[b10/-0.012]". I believe the one that it is choking on is on the line 515664.

There seems to be something wrong with the format of the data in the .tsv file. The ninth column is supposed to be "ProteinName", but starting on line 515618 those columns are in a different order. "[b10/-0.012]" is supposed to appear in the "Annotation" column, but because of this shift, it's now in the "FullUniModPeptideName" column.

Skyline has a bug that it can't handle a peptide sequence that starts with "[" and that's why the error happens on line 515664. I will try to fix it so that Skyline gives a more informative error message.

The real problem is that the columns in the .tsv file become messed up on line 515618.

Hope this helps.
-- Nick