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smith-chem-wisc / MetaMorpheus

Proteomics search software with integrated calibration, PTM discovery, bottom-up, top-down and LFQ capabilities
MIT License
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Increased QValue cutoff for calibrating PSMs to 0.01 #2392

Closed Alexander-Sol closed 4 months ago

Alexander-Sol commented 4 months ago

Recent changes to the way Q-Value is calculate have increased Q-Values across the board.

This caused calibration to fail on files that MetaMorpheus used to calibrate successfully.

To address this, I increased the Q-value Notch cut-off for PSMs that are used for calibration from 0.001 to 0.01. I also created a property within CalibrationParameters that reflects this cutoff threshold. Previously it was just a magic number buried in CalibrationTask.

codecov[bot] commented 4 months ago

Codecov Report

All modified and coverable lines are covered by tests :white_check_mark:

Project coverage is 93.69%. Comparing base (f48d118) to head (226b418).

Additional details and impacted files [![Impacted file tree graph](https://app.codecov.io/gh/smith-chem-wisc/MetaMorpheus/pull/2392/graphs/tree.svg?width=650&height=150&src=pr&token=m0HXyK8tFy&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=smith-chem-wisc)](https://app.codecov.io/gh/smith-chem-wisc/MetaMorpheus/pull/2392?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=smith-chem-wisc) ```diff @@ Coverage Diff @@ ## master #2392 +/- ## ======================================= Coverage 93.69% 93.69% ======================================= Files 139 139 Lines 21720 21725 +5 Branches 3004 3003 -1 ======================================= + Hits 20351 20356 +5 Misses 910 910 Partials 459 459 ``` | [Files](https://app.codecov.io/gh/smith-chem-wisc/MetaMorpheus/pull/2392?dropdown=coverage&src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=smith-chem-wisc) | Coverage Δ | | |---|---|---| | [...TaskLayer/CalibrationTask/CalibrationParameters.cs](https://app.codecov.io/gh/smith-chem-wisc/MetaMorpheus/pull/2392?src=pr&el=tree&filepath=MetaMorpheus%2FTaskLayer%2FCalibrationTask%2FCalibrationParameters.cs&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=smith-chem-wisc#diff-TWV0YU1vcnBoZXVzL1Rhc2tMYXllci9DYWxpYnJhdGlvblRhc2svQ2FsaWJyYXRpb25QYXJhbWV0ZXJzLmNz) | `100.00% <100.00%> (ø)` | | | [...pheus/TaskLayer/CalibrationTask/CalibrationTask.cs](https://app.codecov.io/gh/smith-chem-wisc/MetaMorpheus/pull/2392?src=pr&el=tree&filepath=MetaMorpheus%2FTaskLayer%2FCalibrationTask%2FCalibrationTask.cs&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=smith-chem-wisc#diff-TWV0YU1vcnBoZXVzL1Rhc2tMYXllci9DYWxpYnJhdGlvblRhc2svQ2FsaWJyYXRpb25UYXNrLmNz) | `89.73% <100.00%> (+0.13%)` | :arrow_up: |