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@nbollis nbollis released this 27 Apr 17:41
1.1.6
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MetaMorpheus 1.1.6

MetaMorpheus 1.1.6 is a substantial update that builds on the 1.1.5 release with major advances in RNA support, fragmentation and visualization, calibration flexibility, and search workflow robustness. It also includes a broad set of bug fixes and dependency updates that improve stability across routine proteomics, glycoproteomics, spectral-library, and MetaDraw workflows.

New Features & Enhancements

Expanded RNA and fragmentation support

  • Added broad RNA-mode support throughout the GUI, including RNA-aware calibrate, GPTMD, search, and custom modification workflows (#2579).
  • Introduced richer fragmentation parameter handling across the engine and GUI, including support for custom M-ion losses and improved RNA fragmentation controls (#2627).
  • Added a new option to write a combined target-decoy FASTA during search, which is especially useful for RNA and top-down style workflows (#2629).

Search, calibration, and quantification improvements

  • Added support for MS3 TMT workflows and improved reporter-ion quantification by extracting intensities more robustly from raw spectra (#2586).
  • Enabled spectrum-similarity scoring for decoys using library spectra when available, improving spectral-library search behavior and decoy handling (#2595).
  • Removed an internal PSM filter during protein inference, allowing more complete downstream inference behavior (#2603).
  • Added support for spectral-library use in non-specific searches so spectral-angle information is computed correctly for downstream PEP analysis (#2618).
  • Added support for choosing classic or modern search strategies during calibration, with corresponding engine and GUI updates (#2613).
  • Redesigned the calibration task window to better align with the main search-task workflow (#2612).
  • Added support for separate low-resolution fragment mass tolerance settings for child scans, improving mixed-resolution glycoproteomics workflows (#2635).
  • Replaced direct SSRCalc3 calls in PEP analysis with the IRetentionTimePredictor abstraction for cleaner and more extensible retention-time handling (#2639).

MetaDraw and visualization improvements

  • Added support for biopolymer coverage across multiple databases in MetaDraw (#2615).
  • Improved refragmentation handling so MetaDraw can persist refragmentation results on ambiguous PSMs (#2625).
  • Added whole-envelope annotation support in MetaDraw (#2634).
  • Expanded PlotModelStat and related MetaDraw visualization capabilities, including richer grouping and filtering behavior, as part of the fragmentation and M-ion work (#2627).

Bug Fixes

Search, scoring, and output correctness

  • Fixed a spectrum-library search bug affecting dalton-tolerance searches (#2594).
  • Cleaned up PSM writing and fixed related output-generation bugs (#2604).
  • Fixed a localization-probability bug (#2632).

GUI and workflow stability

  • Fixed checkbox bindings related to parsimony handling in the search task window (#2597).
  • Removed the SpectralRecovery/MBR analysis feature from the product surface (#2605).
  • Fixed environment issues introduced by a prior global.json change (#2614).
  • Fixed RNA/protein mode switching behavior in the UI (#2617).
  • Reworked GUI control flow to avoid relying on try/catch for routine logic, improving maintainability and reducing hidden failure paths (#2641).

File handling and vendor-data support

  • Fixed bugs encountered when adding timsTOF data files (#2636).

Dependency Updates

  • Updated mzLib to 1.0.572 (#2606).
  • Updated mzLib to 1.0.573 (#2620).
  • Updated mzLib to 1.0.574 (#2624).
  • Updated mzLib to 1.0.576 (#2633).
  • Updated mzLib to 1.0.577 (#2643).

Full Changelog

Full Changelog: 1.1.5...master

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