Till Englert

@timosachsenberg So far, I have always used the Philosopher post-processing tools for open search, and reported the modifications without OpenMS. I can try to follow up on this issue with...

https://github.com/Vitek-Lab/MSstats/blob/3a3acbbd37f3cdebbb8db7bf165c96306f732e2d/R/converters.R#L234 Seems not to be in the code anymore, after they changed their code structure!

I tested with 3.22.1, which should be the latest version before v4. And yes v4 is not compatible in any case to be used in the nfcore/proteomicslfq docker... For testing...

[proteomicslfq_docker_build.log](https://github.com/nf-core/proteomicslfq/files/7650710/proteomicslfq_docker_build.log) Attached is the log of the dockerfile build of nf-core/proteomicslfq with the following environment.yml: name: nf-core-proteomicslfq-1.0.0 channels: - openms - conda-forge - bioconda dependencies: - openms::openms - openms::openms-thirdparty -...

After some testing I finally managed to include MSstats v4.2, but for this I needed to change the version of python (to v3.9) and ptxqc (to v1.0.12). Unfortunately, this leads...

The script I'm using is this nextflow script: https://github.com/tillenglert/proteomicslfq/blob/master/main.nf#L1304 with this config (testfiles): https://github.com/tillenglert/proteomicslfq/blob/master/conf/test.config#L20 As I'm still working on msfragger I tested the ptxqc process with comet. The logs and...

Ah perfect! I haven't tried this version, but it's working and compatible with the remaining packages. This is the current environment I'm using, which is working vor msstats and ptxqc:...

https://github.com/bigbio/quantms/pull/236