Bibliospec version 3 does not support my DIA-NN library file

Bibliospec version 3 does not support my DIA-NN library file bora onat  2024-06-12 11:00


I'm trying to build a new library in Skyline using a DIA-NN predicted library output. I get the error, saying Bibliospec supports up to version 3, but my library file is version 8. How do I correct this issue? Thank you.

Nick Shulman responded:  2024-06-12 11:14
We are trying to figure out an answer to that right now.

What we have heard is that in addition to the version 8 format .speclib file that you are seeing there is also supposed to be another file whose name ends in ".skyline.speclib", but we have not yet figured out how that file is supposed to be created when you run dia-nn.

The latest DIA-NN user interface does have a "Skyline" button, which we have determined only works if you have the latest Skyline-daily administrator version installed which you can install from here:

Hopefully we will have an answer in a day or two.
-- Nick
Nick Shulman responded:  2024-06-13 10:48
It is currently not possible for BiblioSpec to build a library from the *.predicted.speclib file that you get from DIA-NN version 1.9 because that file is in the version 8 format which BiblioSpec does not understand.

DIA-NN version 1.9 sometimes produces a file whose name ends in ".skyline.speclib" which BiblioSpec is able to read.

The requirements for getting that file seem to be:
1. You are starting from an existing .speclib, and you are not asking DIA-NN to generate a prediction library from a FASTA file. That is, you have something specified in the textbox next to "Spectral Library" and you do not have any FASTA specified.
2. The "MBR" (match between runs) checkbox is checked
3. You are searching two or more raw files.

If all of these things are true, and everything succeeds it seems you end up with a *.skyline.speclib file which you can then use with Skyline or BiblioSpec.

I hope this helps you until we can figure out how to add support for the version 8 format to BiblioSpec.
-- Nick