Put those mods back where they came from or so help me #827
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Updating Master
Me - 0
This reverts commit f06cbc0.
Improved logic in `DigestionProduct.cs` to ensure correct application of N-terminal and C-terminal modifications to biopolymers, preventing overwriting unless the new modification is more specific. Updated assertions and modification order in test cases to reflect changes, enhancing accuracy and robustness of the digestion process.
Codecov ReportAll modified and coverable lines are covered by tests ✅
Additional details and impacted files@@ Coverage Diff @@
## master #827 +/- ##
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+ Coverage 77.75% 77.76% +0.01%
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Files 230 230
Lines 34144 34166 +22
Branches 3534 3540 +6
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+ Hits 26547 26569 +22
Misses 6991 6991
Partials 606 606
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Does this only apply to the behaviour of fixed mods? If you have peptide-N-term and protein-N-term variable mods, does one take precedence? |
trishorts
requested review from
Alexander-Sol,
pcruzparri,
zhuoxinshi and
RayMSMS
trishorts
approved these changes
Jan 22, 2025
Alexander-Sol
approved these changes
Jan 22, 2025
nbollis
changed the title
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My last PR made an incorrect assumption: modification localization restriction "peptide N-terminal" is meant to refer to ANY N-term, not just those that are generated during digestion.
In the last digestion PR, I made peptide N-terminal mod and N-terminal modification localization mutually exclusive.
This incorrect change results in no isobaric quantification labels being added to the peptide which contains the protein terminus.
The only integration test failing is due to the calibration change. This PR is safe
Changes
DigestionProduct.cs: Ensured correct application and management of protease-associated and terminal modifications. By maintining current overwriting behavior, but ensuring that protein n-term overwrites peptide and not the other way around when applicable.ModificationLocalization.cs: "Peptide N-terminal." mods are now valid on ALL N-termini.TestProteinDigestion.cs: Updated and added test cases to reflect new terminal modification logic.TestDigestion.cs: Adjusted tests for expected digestion products and sequences with terminal modifications.