Update adducts regex

[Adafede]

Dear all,

I think the current regex does not allow to parse some complex types of adducts, being mixes of isotopomers and adducts.

Part of what I would like to address is described in the last lines of https://skyline.ms/wiki/home/software/Skyline/page.view?name=adduct_descriptions ("Charge-Only Examples with Isotope Labels Described Only by Mass")

and it would be great to account for things like [13C3]C3H12O6 at the same time.

I think many of us got some slight different flavors of regex internally, so eventually let's discuss about the perfect only one? 😄

I will start with an attempt: \\[(\\d*)M(?![a-z])(\\d*)([+-][\\w\\d].*)?.*\\](\\d*)([+-])?

@nilshoffmann

[nilshoffmann]

• Check that description about relation between adduct formula, charge and reported m/z (experimental) is clear in the specification.
• Create test cases to check the regular expression, the final experimental mass etc.
• Update the specification.
• Add Adriano as a contributor for mzTab-M 2.1.0

[Adafede]

@nilshoffmann If you point me to where you expect the tests to be, I am happy to help writing them (or their first version)

[nilshoffmann]

@Adafede
The Regexp is part of the constants in the JAVA parser/writer implementation:
https://github.com/lifs-tools/jmzTab-m/blob/master/api/src/main/java/uk/ac/ebi/pride/jmztab2/model/MZTabConstants.java#L75C1-L75C87

The corresponding test is here:
https://github.com/lifs-tools/jmzTab-m/blob/master/io/src/test/java/org/lifstools/mztab2/ParsingPrimitivesTest.java#L41

Happy to take any pull requests.
Please note that JAVA Regexps need additional escaping to work, e.g. \ instead of , but the code for the pattern in MZTabConstants should contain the original regexp along with the JAVA version.

[nilshoffmann]

Check mzSpecLib specification for a potential standard definition
Relates to #30

[philouail]

I know this is an old issue, but please go through the different steps of the template below, to make it easy for us to understand what to do next with this:

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Submitter Tasks

• Provide a pull request (Please add the link)
• Schema: Update mzTab_m_openapi.yml (View File)
• Specification: Update mzTab_format_specification_2_1-M.adoc with an example (View File)
• Example files: if possible, modify an existing or add a new example file (Existing example files)

Maintainer & WG Tasks

• Triage: Assign labels and Milestones to this issue.
• Discuss and review and approve PR.

Next Steps, once we reach an agreement on the changes above:

• Create a downstream issue in the jmzTab-m repo (https://github.com/lifs-tools/jmzTab-m/issues)
• Implement and test changes in jmzTab-M
• Implement changes in R & Python implementations