MetaMorpheusDIA

[zhuoxinshi]

This is the first part of incorporating DIA analysis into MetaMorpheus. The DIA workflow being implemented here reconstructs DIA MS2 scans into pseudo Ms2WithSpecificMass that can be searched directly by our DDA search engines. This includes the following steps:

1. Reading in raw scans and dividing MS2 scans with different isolation windows into different DIA window groups.
2. Constructing XICs for all peaks in the MS1 scans and MS2 scans in the same window.
3. Grouping the precursor XICs with fragment XICs in the same window into precursor-fragments groups based on their correlations.
4. Converting precursor-fragments groups into pseudo Ms2WithSpecificMass.

The DIAEngine class contains this complete workflow and outputs the final list of pseudo Ms2WithSpecificMass. Inside DIAEngine, the process of constructing XICs and grouping precursors and fragments are represented by abstract classes XicConstructor and PfGroupingEngine that can take in different strategies.

[codecov]

Codecov Report

❌ Patch coverage is 99.05363% with 3 lines in your changes missing coverage. Please review.
✅ Project coverage is 96.86%. Comparing base (2e579dc) to head (a67c466).
⚠️ Report is 4 commits behind head on master.

Files with missing lines	Patch %	Lines
...Morpheus/EngineLayer/DIA/PrecursorFragmentGroup.cs	97.32%	3 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##           master    #2546      +/-   ##
==========================================
+ Coverage   96.75%   96.86%   +0.11%     
==========================================
  Files         157      167      +10     
  Lines       23410    23886     +476     
  Branches     3252     3315      +63     
==========================================
+ Hits        22650    23138     +488     
+ Misses        755      743      -12     
  Partials        5        5              

Flag	Coverage Δ
unittests	94.95% <97.81%> (+0.11%)	⬆️

Flags with carried forward coverage won't be shown. Click here to find out more.

Files with missing lines	Coverage Δ
MetaMorpheus/EngineLayer/DIA/DIAEngine.cs	100.00% <100.00%> (ø)
MetaMorpheus/EngineLayer/DIA/DIAparameters.cs	100.00% <100.00%> (ø)
.../DIA/PrecursorFragmentGrouping/PfGroupingEngine.cs	100.00% <100.00%> (ø)
...DIA/PrecursorFragmentGrouping/XicGroupingEngine.cs	100.00% <100.00%> (ø)
...aMorpheus/EngineLayer/DIA/PrecursorFragmentPair.cs	100.00% <100.00%> (ø)
...eLayer/DIA/XicConstruction/MzPeakXicConstructor.cs	100.00% <100.00%> (ø)
...r/DIA/XicConstruction/NeutralMassXicConstructor.cs	100.00% <100.00%> (ø)
.../EngineLayer/DIA/XicConstruction/XicConstructor.cs	100.00% <100.00%> (ø)
...Morpheus/EngineLayer/DIA/PrecursorFragmentGroup.cs	97.32% <97.32%> (ø)

... and 14 files with indirect coverage changes

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[Copilot]

Pull Request Overview

This PR introduces DIA (Data-Independent Acquisition) analysis capabilities to MetaMorpheus by implementing a workflow that reconstructs DIA MS2 scans into pseudo Ms2WithSpecificMass objects that can be searched by existing DDA search engines.

Key changes:

• Implements a complete DIA workflow including MS2 scan grouping by isolation windows, XIC construction, precursor-fragment grouping, and pseudo MS2 scan generation
• Introduces abstract base classes (XicConstructor, PfGroupingEngine) with concrete implementations for different XIC construction strategies
• Adds comprehensive test coverage for all major DIA workflow components

Reviewed Changes

Copilot reviewed 13 out of 14 changed files in this pull request and generated 4 comments.

Show a summary per file

File	Description
Test.csproj	Adds test data file for DIA testing
TestXicGrouping.cs	Comprehensive tests for XIC correlation, overlap calculations, and grouping logic
DIAEngineTest.cs	End-to-end tests for the complete DIA workflow including scan window mapping and pseudo scan conversion
XicConstructor.cs	Abstract base class defining XIC construction interface
NeutralMassXicConstructor.cs	Concrete implementation for neutral mass-based XIC construction
MzPeakXicConstructor.cs	Concrete implementation for m/z peak-based XIC construction
PrecursorFragmentPair.cs	Data structure representing precursor-fragment XIC pairs
XicGroupingEngine.cs	Implementation of precursor-fragment grouping based on correlation and overlap thresholds
PfGroupingEngine.cs	Abstract base class for precursor-fragment grouping strategies
PrecursorFragmentGroup.cs	Core logic for XIC correlation/overlap calculations and pseudo MS2 scan generation
PseudoMs2ConstructionType.cs	Enum defining different pseudo MS2 construction strategies
DIAparameters.cs	Configuration class for DIA workflow parameters
DIAEngine.cs	Main engine orchestrating the complete DIA workflow

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[nbollis]

This should be updated after new mzlib is merged and before we merge this PR.

[nbollis]

There are many places in which this class can be optimized. The main slowdowns here will be collection handling. Many new lists are created throughout this process and immediately discarded. We can optimize this by using object pools and IEnumerable return.

I am happy to work with you on this if you would like, either before or after this PR is merged