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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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Xl spectral library #2292

Closed Alexander-Sol closed 6 months ago

Alexander-Sol commented 1 year ago

This PR adds support for Crosslink Spectral Libraries.

While performing a XL search, there is a Write Spectral Library checkbox. Toggling it results in a spectral library .msp file being written to the results folder.

This spectral library contains single peptide results, intra-link peptide results, and intra-link peptide results. Peptide names take the following form: PEPTIDEK(8)EDITPEPK(8), where the numbers in parentheses represent the location of the crosslink on each peptide. Internally, these are represented as CrosslinkLibrarySpectrum objects.

To enable library lookup, a new property was added to CrosslinkSpectralMatch and PsmFromTsv: UniqueSequence. For crosslinks, the unique sequence is identical to the spectral library name ( PEPTIDEK(8)EDITPEPK(8) ). For non crosslinked peptides, it is identical to the full sequence.

codecov[bot] commented 1 year ago

Codecov Report

Merging #2292 (1ba45bf) into master (984505d) will increase coverage by 0.02%. The diff coverage is 94.24%.

Additional details and impacted files [![Impacted file tree graph](https://app.codecov.io/gh/smith-chem-wisc/MetaMorpheus/pull/2292/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/2292?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 #2292 +/- ## ========================================== + Coverage 92.67% 92.69% +0.02% ========================================== Files 135 136 +1 Lines 20994 21280 +286 Branches 2880 2926 +46 ========================================== + Hits 19456 19726 +270 - Misses 1063 1072 +9 - Partials 475 482 +7 ``` | [Files](https://app.codecov.io/gh/smith-chem-wisc/MetaMorpheus/pull/2292?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=smith-chem-wisc) | Coverage Δ | | |---|---|---| | [...ineLayer/CrosslinkSearch/CrosslinkSpectralMatch.cs](https://app.codecov.io/gh/smith-chem-wisc/MetaMorpheus/pull/2292?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=smith-chem-wisc#diff-TWV0YU1vcnBoZXVzL0VuZ2luZUxheWVyL0Nyb3NzbGlua1NlYXJjaC9Dcm9zc2xpbmtTcGVjdHJhbE1hdGNoLmNz) | `96.35% <100.00%> (+0.54%)` | :arrow_up: | | [MetaMorpheus/EngineLayer/PsmTsv/PsmTsvReader.cs](https://app.codecov.io/gh/smith-chem-wisc/MetaMorpheus/pull/2292?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=smith-chem-wisc#diff-TWV0YU1vcnBoZXVzL0VuZ2luZUxheWVyL1BzbVRzdi9Qc21Uc3ZSZWFkZXIuY3M=) | `89.10% <100.00%> (+0.10%)` | :arrow_up: | | [...gineLayer/SpectralLibrarySearch/LibrarySpectrum.cs](https://app.codecov.io/gh/smith-chem-wisc/MetaMorpheus/pull/2292?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=smith-chem-wisc#diff-TWV0YU1vcnBoZXVzL0VuZ2luZUxheWVyL1NwZWN0cmFsTGlicmFyeVNlYXJjaC9MaWJyYXJ5U3BlY3RydW0uY3M=) | `98.41% <100.00%> (ø)` | | | [...etaMorpheus/GuiFunctions/MetaDraw/MetaDrawLogic.cs](https://app.codecov.io/gh/smith-chem-wisc/MetaMorpheus/pull/2292?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=smith-chem-wisc#diff-TWV0YU1vcnBoZXVzL0d1aUZ1bmN0aW9ucy9NZXRhRHJhdy9NZXRhRHJhd0xvZ2ljLmNz) | `95.74% <100.00%> (+0.04%)` | :arrow_up: | | [...pheus/TaskLayer/XLSearchTask/XLSearchParameters.cs](https://app.codecov.io/gh/smith-chem-wisc/MetaMorpheus/pull/2292?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=smith-chem-wisc#diff-TWV0YU1vcnBoZXVzL1Rhc2tMYXllci9YTFNlYXJjaFRhc2svWExTZWFyY2hQYXJhbWV0ZXJzLmNz) | `100.00% <100.00%> (ø)` | | | [...taDraw/SpectrumMatch/CrosslinkSpectrumMatchPlot.cs](https://app.codecov.io/gh/smith-chem-wisc/MetaMorpheus/pull/2292?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=smith-chem-wisc#diff-TWV0YU1vcnBoZXVzL0d1aUZ1bmN0aW9ucy9NZXRhRHJhdy9TcGVjdHJ1bU1hdGNoL0Nyb3NzbGlua1NwZWN0cnVtTWF0Y2hQbG90LmNz) | `96.10% <92.30%> (-0.78%)` | :arrow_down: | | [...TaskLayer/XLSearchTask/PostXLSearchAnalysisTask.cs](https://app.codecov.io/gh/smith-chem-wisc/MetaMorpheus/pull/2292?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=smith-chem-wisc#diff-TWV0YU1vcnBoZXVzL1Rhc2tMYXllci9YTFNlYXJjaFRhc2svUG9zdFhMU2VhcmNoQW5hbHlzaXNUYXNrLmNz) | `79.56% <97.36%> (+4.56%)` | :arrow_up: | | [MetaMorpheus/EngineLayer/PsmTsv/PsmFromTsv.cs](https://app.codecov.io/gh/smith-chem-wisc/MetaMorpheus/pull/2292?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=smith-chem-wisc#diff-TWV0YU1vcnBoZXVzL0VuZ2luZUxheWVyL1BzbVRzdi9Qc21Gcm9tVHN2LmNz) | `96.84% <72.22%> (-0.98%)` | :arrow_down: | | [.../SpectralLibrarySearch/CrosslinkLibrarySpectrum.cs](https://app.codecov.io/gh/smith-chem-wisc/MetaMorpheus/pull/2292?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=smith-chem-wisc#diff-TWV0YU1vcnBoZXVzL0VuZ2luZUxheWVyL1NwZWN0cmFsTGlicmFyeVNlYXJjaC9Dcm9zc2xpbmtMaWJyYXJ5U3BlY3RydW0uY3M=) | `94.38% <94.38%> (ø)` | | | [...gineLayer/SpectralLibrarySearch/SpectralLibrary.cs](https://app.codecov.io/gh/smith-chem-wisc/MetaMorpheus/pull/2292?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=smith-chem-wisc#diff-TWV0YU1vcnBoZXVzL0VuZ2luZUxheWVyL1NwZWN0cmFsTGlicmFyeVNlYXJjaC9TcGVjdHJhbExpYnJhcnkuY3M=) | `87.14% <94.78%> (+2.11%)` | :arrow_up: |