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Proteobench / ProteoBench

ProteoBench is an open and collaborative platform for community-curated benchmarks for proteomics data analysis pipelines. Our goal is to allow a continuous, easy, and controlled comparison of proteomics data analysis workflows.
https://proteobench.readthedocs.io
Apache License 2.0
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modification parsing: missing ")" and "]" #282

Open mlocardpaulet opened 2 months ago

mlocardpaulet commented 2 months ago

Describe the bug The parsing of the modification and reporting in the intermediate table is not right (in the field precursor ion).

To Reproduce Steps to reproduce the behavior:

  1. load a MQ evidence file
  2. Click on "parse and bench"

Expected behavior the modifications in the following screenshot should be "[Oxidation (M)]"

Screenshots image

Desktop (please complete the following information):

RobbinBouwmeester commented 1 month ago

So, this is due to differences in how to format this, this is what it was in the "old" file format:

(ac)ADDIDIEAM(ox)LEAPYK

So best solution is when selecting a software tool we have two entries for MQ, with both formatting options.

mlocardpaulet commented 1 month ago

I see, yes. This is a bit annoying! How do you want to proceed? Shall we:

  1. have several "MaxQuant" options in the drop-down menue of the upload: like "MaxQuant version 1.5 to 2.4" and "MaxQuant version 2.5 or above"
  2. make a more general "modification sequence format" dropdown menu that comes up after the workflow tool selection. This option is more flexible but means that the user has to check him/herself.
  3. check automatically what format the modified sequence is using, but not sure how easy/reliable this can be.
  4. or any other idea?
RobbinBouwmeester commented 1 month ago

I think option one is the easiest. But the other options are definitely also possible.

mlocardpaulet commented 1 month ago

Let's do that then.

RobbinBouwmeester commented 1 month ago

Ok, I think I have a different better solution in mind, with a "greedy" regex. Will try this and keep you posted.

RobbinBouwmeester commented 1 month ago

Could you check #299 @mlocardpaulet