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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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Added precursor intensity to PSM, peptide proteoform output file #2365

Closed zhuoxinshi closed 5 months ago

zhuoxinshi commented 6 months ago

The current psm, peptide and proteoform output reports the scan TIC as the intensity. This value is replaced in this PR by the intensity of the most abundant mz for the peptide.

codecov[bot] commented 6 months ago

Codecov Report

Attention: Patch coverage is 88.88889% with 3 lines in your changes are missing coverage. Please review.

Project coverage is 92.76%. Comparing base (5ee8567) to head (998c1b4).

Additional details and impacted files [![Impacted file tree graph](https://app.codecov.io/gh/smith-chem-wisc/MetaMorpheus/pull/2365/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/2365?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 #2365 +/- ## ========================================== - Coverage 92.76% 92.76% -0.01% ========================================== Files 137 137 Lines 21166 21179 +13 Branches 2924 2930 +6 ========================================== + Hits 19635 19646 +11 - Misses 1049 1050 +1 - Partials 482 483 +1 ``` | [Files](https://app.codecov.io/gh/smith-chem-wisc/MetaMorpheus/pull/2365?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 | | |---|---|---| | [...etaMorpheus/EngineLayer/Ms2ScanWithSpecificMass.cs](https://app.codecov.io/gh/smith-chem-wisc/MetaMorpheus/pull/2365?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) | `97.11% <100.00%> (+0.14%)` | :arrow_up: | | [MetaMorpheus/EngineLayer/PsmTsv/PsmFromTsv.cs](https://app.codecov.io/gh/smith-chem-wisc/MetaMorpheus/pull/2365?src=pr&el=tree&filepath=MetaMorpheus%2FEngineLayer%2FPsmTsv%2FPsmFromTsv.cs&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=smith-chem-wisc#diff-TWV0YU1vcnBoZXVzL0VuZ2luZUxheWVyL1BzbVRzdi9Qc21Gcm9tVHN2LmNz) | `96.86% <100.00%> (+0.01%)` | :arrow_up: | | [MetaMorpheus/EngineLayer/PsmTsv/PsmTsvReader.cs](https://app.codecov.io/gh/smith-chem-wisc/MetaMorpheus/pull/2365?src=pr&el=tree&filepath=MetaMorpheus%2FEngineLayer%2FPsmTsv%2FPsmTsvReader.cs&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=smith-chem-wisc#diff-TWV0YU1vcnBoZXVzL0VuZ2luZUxheWVyL1BzbVRzdi9Qc21Uc3ZSZWFkZXIuY3M=) | `89.21% <100.00%> (+0.10%)` | :arrow_up: | | [MetaMorpheus/EngineLayer/PsmTsv/PsmTsvWriter.cs](https://app.codecov.io/gh/smith-chem-wisc/MetaMorpheus/pull/2365?src=pr&el=tree&filepath=MetaMorpheus%2FEngineLayer%2FPsmTsv%2FPsmTsvWriter.cs&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=smith-chem-wisc#diff-TWV0YU1vcnBoZXVzL0VuZ2luZUxheWVyL1BzbVRzdi9Qc21Uc3ZXcml0ZXIuY3M=) | `97.54% <100.00%> (+0.01%)` | :arrow_up: | | [MetaMorpheus/EngineLayer/SpectralMatch.cs](https://app.codecov.io/gh/smith-chem-wisc/MetaMorpheus/pull/2365?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=) | `99.44% <75.00%> (-0.28%)` | :arrow_down: | | [MetaMorpheus/TaskLayer/MetaMorpheusTask.cs](https://app.codecov.io/gh/smith-chem-wisc/MetaMorpheus/pull/2365?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) | `88.48% <84.61%> (-0.13%)` | :arrow_down: |
codecov-commenter commented 6 months ago

Codecov Report

Attention: Patch coverage is 95.12195% with 2 lines in your changes missing coverage. Please review.

Project coverage is 92.81%. Comparing base (6a35c8c) to head (70ebe42).

Additional details and impacted files [![Impacted file tree graph](https://app.codecov.io/gh/smith-chem-wisc/MetaMorpheus/pull/2365/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/2365?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 #2365 +/- ## ======================================= Coverage 92.81% 92.81% ======================================= Files 137 137 Lines 21171 21188 +17 Branches 2924 2929 +5 ======================================= + Hits 19650 19666 +16 Misses 1042 1042 - Partials 479 480 +1 ``` | [Files](https://app.codecov.io/gh/smith-chem-wisc/MetaMorpheus/pull/2365?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 | | |---|---|---| | [MetaMorpheus/EngineLayer/CommonParameters.cs](https://app.codecov.io/gh/smith-chem-wisc/MetaMorpheus/pull/2365?src=pr&el=tree&filepath=MetaMorpheus%2FEngineLayer%2FCommonParameters.cs&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=smith-chem-wisc#diff-TWV0YU1vcnBoZXVzL0VuZ2luZUxheWVyL0NvbW1vblBhcmFtZXRlcnMuY3M=) | `95.58% <100.00%> (+0.06%)` | :arrow_up: | | [...etaMorpheus/EngineLayer/Ms2ScanWithSpecificMass.cs](https://app.codecov.io/gh/smith-chem-wisc/MetaMorpheus/pull/2365?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) | `97.11% <100.00%> (+0.14%)` | :arrow_up: | | [MetaMorpheus/EngineLayer/PsmTsv/PsmFromTsv.cs](https://app.codecov.io/gh/smith-chem-wisc/MetaMorpheus/pull/2365?src=pr&el=tree&filepath=MetaMorpheus%2FEngineLayer%2FPsmTsv%2FPsmFromTsv.cs&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=smith-chem-wisc#diff-TWV0YU1vcnBoZXVzL0VuZ2luZUxheWVyL1BzbVRzdi9Qc21Gcm9tVHN2LmNz) | `97.69% <100.00%> (+<0.01%)` | :arrow_up: | | [MetaMorpheus/EngineLayer/PsmTsv/PsmTsvReader.cs](https://app.codecov.io/gh/smith-chem-wisc/MetaMorpheus/pull/2365?src=pr&el=tree&filepath=MetaMorpheus%2FEngineLayer%2FPsmTsv%2FPsmTsvReader.cs&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=smith-chem-wisc#diff-TWV0YU1vcnBoZXVzL0VuZ2luZUxheWVyL1BzbVRzdi9Qc21Uc3ZSZWFkZXIuY3M=) | `89.21% <100.00%> (+0.10%)` | :arrow_up: | | [MetaMorpheus/EngineLayer/PsmTsv/PsmTsvWriter.cs](https://app.codecov.io/gh/smith-chem-wisc/MetaMorpheus/pull/2365?src=pr&el=tree&filepath=MetaMorpheus%2FEngineLayer%2FPsmTsv%2FPsmTsvWriter.cs&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=smith-chem-wisc#diff-TWV0YU1vcnBoZXVzL0VuZ2luZUxheWVyL1BzbVRzdi9Qc21Uc3ZXcml0ZXIuY3M=) | `97.54% <100.00%> (+0.01%)` | :arrow_up: | | [MetaMorpheus/EngineLayer/SpectralMatch.cs](https://app.codecov.io/gh/smith-chem-wisc/MetaMorpheus/pull/2365?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/2365?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% <91.30%> (-0.11%)` | :arrow_down: |