fasta2speclib feature requests

[JB91451]

Dear ms2pip developers,

Thank you for the new version of your tool. It works really well.

I have rather a question than an issue: Is there any way to include semi-specific or even unspecific enzymatically cleaved peptides in the fasta2speclib tool?
In the earlier versions of ms2pip I bypassed fasta2speclib for this purpose by using a script to generate the peptide list via generate-peptides from crux (btw. this did allow to filter peptides also by m/z which was a huge advantage -> I agree with issue #187 that this would be a nice option in the future) and modifying this list to obtain suitable peprec files including a 'max variable modifications per peptide' option. However, it would be nice if it is possible to use the offical way.

Best regards,
Juergen

[RalfG]

Dear Juergen, thanks for your interest in fasta2speclib! We are currently working on optimizing fasta2speclib, so we should be able to implement your suggestions in the next version.

[RalfG]

fasta2speclib feature requests:

• Semi-specific cleavage
• Unspecific cleavage
• Min and max precursor m/z
• Max variable modifications per peptide

[RalfG]

@JB91451, @willems533,

All requested features are now available in MS²PIP v3.11.0. Please let us know if everything works as expected. If you would run into any issues, let us know and we'll be happy to help.

Best,
Ralf

[JB91451]

Dear Ralf,

Thank you and the entire MS2PIP team for this really fast implementation! I will test it as soon as possible. Unfortunately, this week I am buisy with some lab courses.

Best,
Juergen

[patrick-willems]

Hey Ralf,

Thanks! I will also test it soon in one of the coming days,

Patrick

[JB91451]

Hi Ralf,

I tried the new features today and they seem to work. However, when I set more than one cpu in the config file, the process seems to get stuck in the multiprocessing step at the very beginning. For the tests I used a VM-Server with win10 and python 3.7 (I can not change the version there due to access restrictions). Even with only one cpu the process seems to stop at a step "generated new fontManager".
When I run the very same config file from my desktop computer (python 3.10) multiprocessing works as expected but I have to reduce the chunk-size.

On the computer where the process does not finish, I also have to use a virtual environment in order to call fasta2speclib while on my desktop I installed ms2pip globally and could run both commands directly.

Best,
Juergen

[RalfG]

Moved to new issue: #195