modification parsing: missing ")" and "]"

[mlocardpaulet]

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

Desktop (please complete the following information):

• OS: MasOS Sonoma 14.2.1
• Browser Chrome Version 123.0.6312.122 (Official Build) (arm64)

[RobbinBouwmeester]

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]

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]

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

[mlocardpaulet]

Let's do that then.

[RobbinBouwmeester]

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

[RobbinBouwmeester]

Could you check #299 @mlocardpaulet