issue when importing peptide search from a MaxQuant msms.txt file - ignored modifications

issue when importing peptide search from a MaxQuant msms.txt file - ignored modifications marie locard-paulet21061  2020-09-08


I would like to use Skyline to generate a spectral library compatible with a library-based DIA search in DIA-NN.
My issue is that when I import an output from MaxQuant (1.6.14) using the "import peptide search" pipeline (msms.txt file in the same folder as the raw files, the mqpar.xml and the modifications.xml containing the list of variable modifications -I added the Ammonium and Ammonia loss in the bottom-), the only modifications that I find in the output are oxidation (M) and carbamydomethylation (C). So several modifications are missing.
I am pretty sure that I miss something but I cannot figure out what.

The idea is to then export a custom report from Skyline that would be in a format that I can make compatible with a DIA-NN input library. This bit works.

I work with Skyline (64-bit) (a0e7323e3).
I have uploaded the MaxQuant outputs I work with on the skyline upload site, with the name "".
Please let me know if you need more information.
Thank you for your help.
Kind regards,

Nick Shulman responded:  2020-09-08
What makes you say that these modifications are not being included?
When I create a .blib file from your search results, I do end up with many peptides that have an Ammonia loss (-17.0265 on N) and Ammonia (17.0265 on D, E).
Is there a particular peptide that you expected to see there in a modified form that you are not seeing?

-- Nick
marie locard-paulet21061 responded:  2020-09-08
Hi Nick,

thank you so much for spending the time. It is my mistake (sorry for spotting it late).
I exported the library using Export>Report and then using a template that I found on one of the threads of the Skyline help called "spectronautlibrary.skyr". This way, I did not manage to find back the Ammonia loss, Ammonium and Gln->pyroGlu modifications. It must be due to the Skyline document parameters (I am not super familiar with your tool).
Since I received your answer I looked at the .blib and indeed I find them.

So I am good. I will generate the library myself from the .blib from now on.
Is there any other way that you know of to generate the library in a .tsv or .csv format that would be directly compatible to tools such as DIA-NN?

Again, sorry for taking up your time.
Thanks a lot,