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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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MetaDraw Fragmentation Reanalysis #2361

Closed nbollis closed 2 weeks ago

nbollis commented 2 months ago

Enables the reanalysis of a fragmentation spectrum with additional fragment ion types.

The plotting methods use the MatchedIons of the psm that gets passed in to determine what to plot. To enable this functionality, I had to temporarily replace the fragment ions in the psm with the new matched ions, then put the original ions back in once the plotting has finished.

To use: have your normal MetaDraw Display image

Select the additional ions you want to search for image

His the search button. The persist check box will enable this research on all new PSMs you plot

image

codecov[bot] commented 2 months ago

Codecov Report

Attention: Patch coverage is 97.48744% with 5 lines in your changes missing coverage. Please review.

Project coverage is 92.89%. Comparing base (efa9b9d) to head (c9a5d79).

Additional details and impacted files [![Impacted file tree graph](https://app.codecov.io/gh/smith-chem-wisc/MetaMorpheus/pull/2361/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/2361?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 #2361 +/- ## ========================================== + Coverage 92.85% 92.89% +0.04% ========================================== Files 137 139 +2 Lines 21242 21435 +193 Branches 2931 2944 +13 ========================================== + Hits 19725 19913 +188 - Misses 1040 1043 +3 - Partials 477 479 +2 ``` | [Files](https://app.codecov.io/gh/smith-chem-wisc/MetaMorpheus/pull/2361?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/PsmTsv/PsmFromTsv.cs](https://app.codecov.io/gh/smith-chem-wisc/MetaMorpheus/pull/2361?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%> (ø)` | | | [...etaMorpheus/GuiFunctions/MetaDraw/DrawnSequence.cs](https://app.codecov.io/gh/smith-chem-wisc/MetaMorpheus/pull/2361?src=pr&el=tree&filepath=MetaMorpheus%2FGuiFunctions%2FMetaDraw%2FDrawnSequence.cs&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=smith-chem-wisc#diff-TWV0YU1vcnBoZXVzL0d1aUZ1bmN0aW9ucy9NZXRhRHJhdy9EcmF3blNlcXVlbmNlLmNz) | `99.36% <100.00%> (ø)` | | | [.../MetaDraw/FragmentResearching/FragmentViewModel.cs](https://app.codecov.io/gh/smith-chem-wisc/MetaMorpheus/pull/2361?src=pr&el=tree&filepath=MetaMorpheus%2FGuiFunctions%2FMetaDraw%2FFragmentResearching%2FFragmentViewModel.cs&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=smith-chem-wisc#diff-TWV0YU1vcnBoZXVzL0d1aUZ1bmN0aW9ucy9NZXRhRHJhdy9GcmFnbWVudFJlc2VhcmNoaW5nL0ZyYWdtZW50Vmlld01vZGVsLmNz) | `100.00% <100.00%> (ø)` | | | [...Morpheus/GuiFunctions/MetaDraw/MetaDrawSettings.cs](https://app.codecov.io/gh/smith-chem-wisc/MetaMorpheus/pull/2361?src=pr&el=tree&filepath=MetaMorpheus%2FGuiFunctions%2FMetaDraw%2FMetaDrawSettings.cs&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=smith-chem-wisc#diff-TWV0YU1vcnBoZXVzL0d1aUZ1bmN0aW9ucy9NZXRhRHJhdy9NZXRhRHJhd1NldHRpbmdzLmNz) | `99.37% <100.00%> (+0.21%)` | :arrow_up: | | [...etaMorpheus/GuiFunctions/MetaDraw/MetaDrawLogic.cs](https://app.codecov.io/gh/smith-chem-wisc/MetaMorpheus/pull/2361?src=pr&el=tree&filepath=MetaMorpheus%2FGuiFunctions%2FMetaDraw%2FMetaDrawLogic.cs&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=smith-chem-wisc#diff-TWV0YU1vcnBoZXVzL0d1aUZ1bmN0aW9ucy9NZXRhRHJhdy9NZXRhRHJhd0xvZ2ljLmNz) | `95.63% <80.00%> (-0.11%)` | :arrow_down: | | [...entResearching/FragmentationReanalysisViewModel.cs](https://app.codecov.io/gh/smith-chem-wisc/MetaMorpheus/pull/2361?src=pr&el=tree&filepath=MetaMorpheus%2FGuiFunctions%2FMetaDraw%2FFragmentResearching%2FFragmentationReanalysisViewModel.cs&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=smith-chem-wisc#diff-TWV0YU1vcnBoZXVzL0d1aUZ1bmN0aW9ucy9NZXRhRHJhdy9GcmFnbWVudFJlc2VhcmNoaW5nL0ZyYWdtZW50YXRpb25SZWFuYWx5c2lzVmlld01vZGVsLmNz) | `95.91% <95.91%> (ø)` | |
trishorts commented 2 months ago

pretty cool. i only ever see yAmmoniaLoss. maybe we need unit tests for each of the ion types? sounds like lots of work...... I wonder if we paste a couple of example spectra into proteinprospector if it sees any other fragments.

nbollis commented 2 months ago

That is a good idea and maybe a good starter project. Our current tests only truly test b, y, and c ions

trishorts commented 2 weeks ago

is the top supposed to look like this? image

trishorts commented 2 weeks ago

i think that export spectrum library should maybe contain the newly annotated fragments. image

nbollis commented 2 weeks ago

is the top supposed to look like this? image

This has been fixed