Added new features to Top-Down PEP

[nbollis]

Added the following features

• Peaks in precursor envelope
• Count of identifications per scan
• Intensity of most abundant precursor peak
• Fractional intensity of precursor in isolation window

Removed the normalization for top down PEP

Current Master is green This PR is cyan PrSM and Proteoform count are determined by those with <= 0.01 PEP_QValue

[codecov[bot]]

Codecov Report

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

Project coverage is 92.97%. Comparing base (519dd2d) to head (4082f0b).

Additional details and impacted files

[](https://app.codecov.io/gh/smith-chem-wisc/MetaMorpheus/pull/2377?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 #2377 +/- ## ========================================== + Coverage 92.95% 92.97% +0.02% ========================================== Files 139 139 Lines 21605 21668 +63 Branches 2979 2983 +4 ========================================== + Hits 20083 20146 +63 Misses 1043 1043 Partials 479 479 ``` | [Files](https://app.codecov.io/gh/smith-chem-wisc/MetaMorpheus/pull/2377?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 | | |---|---|---| | [...EngineLayer/FdrAnalysis/PEPValueAnalysisGeneric.cs](https://app.codecov.io/gh/smith-chem-wisc/MetaMorpheus/pull/2377?src=pr&el=tree&filepath=MetaMorpheus%2FEngineLayer%2FFdrAnalysis%2FPEPValueAnalysisGeneric.cs&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=smith-chem-wisc#diff-TWV0YU1vcnBoZXVzL0VuZ2luZUxheWVyL0ZkckFuYWx5c2lzL1BFUFZhbHVlQW5hbHlzaXNHZW5lcmljLmNz) | `95.83% <100.00%> (+0.11%)` | :arrow_up: | | [MetaMorpheus/EngineLayer/FdrAnalysis/PsmData.cs](https://app.codecov.io/gh/smith-chem-wisc/MetaMorpheus/pull/2377?src=pr&el=tree&filepath=MetaMorpheus%2FEngineLayer%2FFdrAnalysis%2FPsmData.cs&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=smith-chem-wisc#diff-TWV0YU1vcnBoZXVzL0VuZ2luZUxheWVyL0ZkckFuYWx5c2lzL1BzbURhdGEuY3M=) | `100.00% <100.00%> (ø)` | | | [...etaMorpheus/EngineLayer/Ms2ScanWithSpecificMass.cs](https://app.codecov.io/gh/smith-chem-wisc/MetaMorpheus/pull/2377?src=pr&el=tree&filepath=MetaMorpheus%2FEngineLayer%2FMs2ScanWithSpecificMass.cs&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=smith-chem-wisc#diff-TWV0YU1vcnBoZXVzL0VuZ2luZUxheWVyL01zMlNjYW5XaXRoU3BlY2lmaWNNYXNzLmNz) | `97.16% <100.00%> (+0.05%)` | :arrow_up: | | [MetaMorpheus/EngineLayer/SpectralMatch.cs](https://app.codecov.io/gh/smith-chem-wisc/MetaMorpheus/pull/2377?src=pr&el=tree&filepath=MetaMorpheus%2FEngineLayer%2FSpectralMatch.cs&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=smith-chem-wisc#diff-TWV0YU1vcnBoZXVzL0VuZ2luZUxheWVyL1NwZWN0cmFsTWF0Y2guY3M=) | `99.72% <100.00%> (+<0.01%)` | :arrow_up: | | [MetaMorpheus/TaskLayer/MetaMorpheusTask.cs](https://app.codecov.io/gh/smith-chem-wisc/MetaMorpheus/pull/2377?src=pr&el=tree&filepath=MetaMorpheus%2FTaskLayer%2FMetaMorpheusTask.cs&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=smith-chem-wisc#diff-TWV0YU1vcnBoZXVzL1Rhc2tMYXllci9NZXRhTW9ycGhldXNUYXNrLmNz) | `88.49% <100.00%> (ø)` | |