Changes to MBR within FlashLFQ

[Alexander-Sol]

Major changes to MBR within FlashLFQ.

Peak Decoys

When performing MBR, we attempt to locate a decoy peak for each acceptor peak. Acceptor peaks are located by predicting a retention time and looking for the theoretical peptide mass at that retention time. Decoy peaks are located by choosing a "random" retention time and looking for the theoretical peptide mass at the random retention time.

PEP Calculation for MBR Peak

All MBR peaks are fed into a binary classifier (similar to the one used within MetaMorpheus) and semi-supervised learning is performed to calculate a PEP for each peak.

MBR Q-Values

For each file, Q-Values are calculated for each MBR peak by ranking them in PEP order and performing target-decoy competition

[codecov[bot]]

Codecov Report

Attention: Patch coverage is 92.06501% with 83 lines in your changes missing coverage. Please review.

Project coverage is 77.08%. Comparing base (6c18e9f) to head (46cc07f).

Files with missing lines	Patch %	Lines
mzLib/FlashLFQ/FlashLfqEngine.cs	91.89%	25 Missing and 8 partials :warning:
mzLib/FlashLFQ/PEP/PepAnalysisEngine.cs	93.10%	19 Missing and 11 partials :warning:
mzLib/FlashLFQ/PEP/ChromatographicPeakData.cs	80.32%	12 Missing :warning:
mzLib/FlashLFQ/PEP/DonorGroup.cs	75.00%	4 Missing :warning:
mzLib/FlashLFQ/MbrScorer.cs	94.91%	1 Missing and 2 partials :warning:
mzLib/FlashLFQ/ChromatographicPeak.cs	96.42%	0 Missing and 1 partial :warning:

Additional details and impacted files

[](https://app.codecov.io/gh/smith-chem-wisc/mzLib/pull/802?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 #802 +/- ## ========================================== + Coverage 76.48% 77.08% +0.59% ========================================== Files 211 214 +3 Lines 31960 32795 +835 Branches 3286 3388 +102 ========================================== + Hits 24446 25280 +834 + Misses 6954 6949 -5 - Partials 560 566 +6 ``` | [Files with missing lines](https://app.codecov.io/gh/smith-chem-wisc/mzLib/pull/802?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 | | |---|---|---| | [mzLib/FlashLFQ/FlashLFQResults.cs](https://app.codecov.io/gh/smith-chem-wisc/mzLib/pull/802?src=pr&el=tree&filepath=mzLib%2FFlashLFQ%2FFlashLFQResults.cs&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=smith-chem-wisc#diff-bXpMaWIvRmxhc2hMRlEvRmxhc2hMRlFSZXN1bHRzLmNz) | `92.04% <100.00%> (+0.20%)` | :arrow_up: | | [mzLib/FlashLFQ/Identification.cs](https://app.codecov.io/gh/smith-chem-wisc/mzLib/pull/802?src=pr&el=tree&filepath=mzLib%2FFlashLFQ%2FIdentification.cs&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=smith-chem-wisc#diff-bXpMaWIvRmxhc2hMRlEvSWRlbnRpZmljYXRpb24uY3M=) | `100.00% <100.00%> (ø)` | | | [mzLib/FlashLFQ/IndexedMassSpectralPeak.cs](https://app.codecov.io/gh/smith-chem-wisc/mzLib/pull/802?src=pr&el=tree&filepath=mzLib%2FFlashLFQ%2FIndexedMassSpectralPeak.cs&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=smith-chem-wisc#diff-bXpMaWIvRmxhc2hMRlEvSW5kZXhlZE1hc3NTcGVjdHJhbFBlYWsuY3M=) | `100.00% <100.00%> (ø)` | | | [mzLib/FlashLFQ/IsotopicEnvelope.cs](https://app.codecov.io/gh/smith-chem-wisc/mzLib/pull/802?src=pr&el=tree&filepath=mzLib%2FFlashLFQ%2FIsotopicEnvelope.cs&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=smith-chem-wisc#diff-bXpMaWIvRmxhc2hMRlEvSXNvdG9waWNFbnZlbG9wZS5jcw==) | `83.33% <100.00%> (+1.51%)` | :arrow_up: | | [mzLib/FlashLFQ/RtInfo.cs](https://app.codecov.io/gh/smith-chem-wisc/mzLib/pull/802?src=pr&el=tree&filepath=mzLib%2FFlashLFQ%2FRtInfo.cs&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=smith-chem-wisc#diff-bXpMaWIvRmxhc2hMRlEvUnRJbmZvLmNz) | `100.00% <100.00%> (ø)` | | | [mzLib/FlashLFQ/SpectraFileInfo.cs](https://app.codecov.io/gh/smith-chem-wisc/mzLib/pull/802?src=pr&el=tree&filepath=mzLib%2FFlashLFQ%2FSpectraFileInfo.cs&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=smith-chem-wisc#diff-bXpMaWIvRmxhc2hMRlEvU3BlY3RyYUZpbGVJbmZvLmNz) | `100.00% <100.00%> (ø)` | | | [mzLib/Proteomics/PSM/PsmFromTsv.cs](https://app.codecov.io/gh/smith-chem-wisc/mzLib/pull/802?src=pr&el=tree&filepath=mzLib%2FProteomics%2FPSM%2FPsmFromTsv.cs&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=smith-chem-wisc#diff-bXpMaWIvUHJvdGVvbWljcy9QU00vUHNtRnJvbVRzdi5jcw==) | `92.11% <ø> (ø)` | | | [mzLib/FlashLFQ/ChromatographicPeak.cs](https://app.codecov.io/gh/smith-chem-wisc/mzLib/pull/802?src=pr&el=tree&filepath=mzLib%2FFlashLFQ%2FChromatographicPeak.cs&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=smith-chem-wisc#diff-bXpMaWIvRmxhc2hMRlEvQ2hyb21hdG9ncmFwaGljUGVhay5jcw==) | `98.29% <96.42%> (+12.34%)` | :arrow_up: | | [mzLib/FlashLFQ/MbrScorer.cs](https://app.codecov.io/gh/smith-chem-wisc/mzLib/pull/802?src=pr&el=tree&filepath=mzLib%2FFlashLFQ%2FMbrScorer.cs&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=smith-chem-wisc#diff-bXpMaWIvRmxhc2hMRlEvTWJyU2NvcmVyLmNz) | `81.20% <94.91%> (+2.98%)` | :arrow_up: | | [mzLib/FlashLFQ/PEP/DonorGroup.cs](https://app.codecov.io/gh/smith-chem-wisc/mzLib/pull/802?src=pr&el=tree&filepath=mzLib%2FFlashLFQ%2FPEP%2FDonorGroup.cs&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=smith-chem-wisc#diff-bXpMaWIvRmxhc2hMRlEvUEVQL0Rvbm9yR3JvdXAuY3M=) | `75.00% <75.00%> (ø)` | | | ... and [3 more](https://app.codecov.io/gh/smith-chem-wisc/mzLib/pull/802?src=pr&el=tree-more&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=smith-chem-wisc) | |

[Alexander-Sol]