MSDIAL-v5.5.251021

What's Changed

Feature Updates

• Added GNPS exporter for molecular networking data output #596, #651, #645, #646 by @htsugawa, @YukiMatsuzawa
• Added the export function for mzTab-M format in the CUI application #623 by @htsugawa
• Implemented analysis pipeline and UI for TIMS-off imaging data #639 by @YukiMatsuzawa
• Implemented annotation process for minor lipid classes #628 by @mikikot113

Bug Fixes

• Fixed a bug where EAD annotation did not run in the initial analysis of EAD lipidomics projects #617 by @YukiMatsuzawa
• Fixed a peak switching error by adjusting the graph axis update order #620 by @YukiMatsuzawa
• Add user comment to mzTab-M format export #621 by @mikikot113
• Fixed GC-MS data processing and alignment issues #638, #643 by @htsugawa
• Modified isotope analysis process during alignment for improved accuracy #642 by @htsugawa
• Updated MS-FINDER batch processing, isotope view #618, #614 by @Bujee415
• Fixed a PDF compiling error of Notame report #652 by @Bujee415
• Fixed the RT correction function to reference the original RT value #648 by @YukiMatsuzawa

Full Changelog: Compare v5.5.250820...v5.5.250920:
MSDIAL-v5.5.250820...MSDIAL-v5.5.250920

MSDIAL-v5.5.250820

What's Changed

Feature Updates

• Added a new screen to visualize the similarity of MS/MS spectra among ions considered identical across samples #610 by @YukiMatsuzawa
• Reintroduced support for exporting results in the mzTab-M format—previously available in MS-DIAL 4—now with integrated GUI support #613 by @YukiMatsuzawa
• Added direct link-out to LIPID MAPS from annotated lipids in lipidomics projects for quick reference to structural and database information #599 by @YukiMatsuzawa
• Added an option in the proteomics project to perform peptide matching without enzymatic digestion, directly using the sequences listed in the FASTA file #598 by @htsugawa

Bug Fixes

• Restored MassQL functionality, which had previously become nonfunctional (Documentation) #597 by @htsugawa

Full Changelog: MSDIAL-v5.5.250627...MSDIAL-v5.5.250820

MSDIAL-v5.6.250820-alpha

What's Changed

Note: Some updates in this release overlap with those introduced in v5.5.250627. For consistency, the relevant descriptions are retained as-is.

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Feature Updates

• Added a new window to visualize the similarity of MS/MS spectra among ions considered identical across samples #610 by @YukiMatsuzawa
• Reintroduced support for exporting results in the mzTab-M format—previously available in MS-DIAL 4—now with integrated GUI support #613 by @YukiMatsuzawa
• Added direct link-out to LIPID MAPS from annotated lipids in lipidomics projects for quick reference to structural and database information #599 by @YukiMatsuzawa
• Added an option in the proteomics project to perform peptide matching without enzymatic digestion, directly using the sequences listed in the FASTA file #598 by @htsugawa
• Added an option to enable or disable chromatogram-based deconvolution #583 by @YukiMatsuzawa
• Updated the calculation formulas for dot product, weighted dot product, and reverse dot product used in spectrum similarity scoring #589, #591 by @YukiMatsuzawa

UI Updates

• Added a message to the sample file selection dialog to guide users #586 by @YukiMatsuzawa

Bug Fixes

• Fixed a bug where SHexCer compounds were not annotated in MS/MS characterization #575 by @mikikot113
• Updated project loading behavior to prioritize files in the new folder location #578 by @YukiMatsuzawa
• Fixed an error that occurred when using text-based libraries, which do not include spectral information #582 by @YukiMatsuzawa
• Restored MassQL functionality, which had previously become nonfunctional (Documentation) #597 by @htsugawa

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🚨 Breaking Changes (Introduced in v5.5.250627)

The calculation formulas for dot product, weighted dot product, and reverse dot product used in spectrum similarity scoring were updated in the previous release (v5.5.250627).

Previously, MS-DIAL used the squared value of the standard dot product as the similarity score. This has been changed to the conventional (non-squared) dot product, aligning with standard practice in spectral similarity evaluation.

⚠️ As a result, annotation results may differ even when using the same parameters as in earlier versions.

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📋 Full Changelog: MSDIAL-v5.6.250526-alpha...MSDIAL-v5.6.250820-alpha

MSDIAL-v5.5.250627

What's Changed

Feature Updates

• Added an option to enable or disable chromatogram-based deconvolution #583 by @YukiMatsuzawa
• Updated the calculation formulas for dot product, weighted dot product, and reverse dot product used in spectrum similarity scoring #589, #591 by @YukiMatsuzawa

UI Updates

• Added a message to the sample file selection dialog to guide users #586 by @YukiMatsuzawa

Bug Fixes

• Fixed a bug where SHexCer compounds were not annotated in MS/MS characterization #575 by @mikikot113
• Updated project loading behavior to prioritize files in the new folder location #578 by @YukiMatsuzawa
• Fixed an error that occurred when using text-based libraries, which do not include spectral information #582 by @YukiMatsuzawa

🚨 Breaking Changes

The calculation formulas for dot product, weighted dot product, and reverse dot product used in spectrum similarity scoring have been updated.

Previously, the squared value of the standard dot product was used as the similarity score. In this version, it has been changed to the conventional (non-squared) dot product formulation. As a result, annotation results may differ even when using the same parameters as in previous versions.

Full Changelog: MSDIAL-v5.5.250530...MSDIAL-v5.5.250627

MSDIAL-v5.5.250530

What's Changed

Feature Updates

• Added HCO₃⁻ adduct annotation method #534, #540 by @mikikot113, @Bujee415
• Fixed WE annotation method #539 by @mikikot113
• Added HCO₃⁻ support for other lipid classes #542 by @Bujee415
• Added option to perform alignment using only reference-matched peaks #549 by @YukiMatsuzawa
• Added support for multiple intensity axis titles in MS/MS spectrum view #551 by @YukiMatsuzawa
• Internal MS-FINDER update #555, #570, #571 by @Bujee415
• Added RelativeAmplitudeCutoff parameter for spectrum filtering in deconvolution #560,  #566 by @YukiMatsuzawa
• Updated Notame logo #563 by @Bujee415
• Increased score digit precision for result files #569 by @Bujee415

Bug Fixes

• Fixed a bug of aligned eic not showing #541 by @YukiMatsuzawa
• Fixed bug where EIC was not displayed after alignment and improved chart UI #550 by @YukiMatsuzawa
• Fixed typo in XAML: "Exp. vs. Rep." to "Exp. vs. Ref." #552 by @YukiMatsuzawa
• Fixed MSP file parser #553 by @Bujee415
• Fixed Vitamin E annotation method #557 by @mikikot113
• Updated GC-MS alignment process #574 by @YukiMatsuzawa

Full Changelog: MSDIAL-v5.5.250404...MSDIAL-v5.5.250530

MSDIAL-v5.6.250526-alpha

What's changed

Feature Updates

• Added support for ZT Scan DIA data
• Enabled dynamic MS2 data loading for SCIEX wiff2 format
• Supported Q1-axis based spectrum deconvolution in analyzing ZT Scan DIA
• Introduced a new visualization function to display spectrum similarities across samples in alignment results (try to click Peak spectra alignment function in the alignment spot viewer)
• RT- and Q1-axis peak features can be visualized by Show PIs function (see MS/MS spectrum ribbon)

Notes

This is an alpha version under development. Several features are not yet implemented:

• RT correction is not available in this branch when analyzing wiff2 format
• Projects created with previous MS-DIAL versions can be opened, but performance may degrade when loading wiff2 data. If you used wiff2 format previously, we recommend to reanalyze your data from "new project", or use MS-DIAL v5.5 instead.
• Projects analyzed with MS-DIAL v5.6 may not be backward-compatible with earlier versions like v5.5

MSFINDER v3.73

What's Changed

• Release Msfinder 3.72 by @Bujee415 in #546
• Fix msp file parcer by @Bujee415 in #553
• fixed file generator in msfinder by @YukiMatsuzawa in #565
• Msfinder fix version popup by @Bujee415 in #568

Full Changelog: MSFINDER-v3.72...MSFINDER-v3.73

MSFINDER-v3.72

What's Changed

• Independent msfinder bug fix by @Bujee415 in #544

Full Changelog: MSFINDER-v3.61...MSFINDER-v3.72

MSDIAL-v5.5.250404

What's Changed

Feature Updates

Added MGMG, DGMG, and FAHFA as new lipid classes for analysis#517 by @htsugawa

• Improved graph zoom behavior#529 by @YukiMatsuzawa

• Modified the alignment chromatogram table to reflect class-based colors in the chromatogram display#530 by @YukiMatsuzawa

Bug Fixes

• Fixed an issue that caused MS-DIAL to crash during alignment#518 by @YukiMatsuzawa

• Fixed a bug that prevented export of results in the proteomics project#523 by @YukiMatsuzawa

• Fixed a bug where saving would fail after performing retention time correction on many samples#524 by @YukiMatsuzawa

• Fixed an issue where CCS values were not properly reflected for Waters and Agilent data, and refactored LC-IM-MS alignment algorithm#531 by @YukiMatsuzawa

Full Changelog: MSDIAL-v5.5.250221...MSDIAL-v5.5.250404

MSDIAL-v5.5.250221

What's Changed

• fixed console app process by @htsugawa in #453
• Minor Bug Fixes and Updates by @YukiMatsuzawa in #455
• Fixed Bug Preventing Spectrum Saving in Raw vs. Purified View by @YukiMatsuzawa in #463
• Add PeakAreaAboveBaseline calculation by @YukiMatsuzawa in #465
• updated exporter of molecular networking for generating linkages (ege… by @htsugawa in #464
• Fixed Bug with Misaligned Selection Range in Alignment EIC Curation and Enabled Curation for Specific Samples by @YukiMatsuzawa in #466
• Add ErrorMessageBox on TextLibraryReader by @mikikot113 in #468
• Update Msfinder function by @Bujee415 in #460
• Enhanced File Type Support Messaging in Dataset File Settings by @YukiMatsuzawa in #470
• Add mnexporter4lcimms by @htsugawa in #472
• Refactor chromatogram logic and reorganize namespaces by @YukiMatsuzawa in #473
• Add full path for console app by @Bujee415 in #474
• Add stack trace for error message by @Bujee415 in #475
• Fixed Loop Variable Capture Issue in Multi-Threaded Annotation Process by @YukiMatsuzawa in #476
• Fix proteomics by @htsugawa in #477
• Replace Zip with ZipInternal across codebase by @YukiMatsuzawa in #479
• Refactor and add null checks in spectra processing by @YukiMatsuzawa in #480
• Standardization of Build Configurations and Introduction of Unified Build Scripts by @YukiMatsuzawa in #482
• Fix hex cer annotation methods by @mikikot113 in #484
• Add PC[H+HCO3]- annotation metnods by @mikikot113 in #494
• Add LPI and LPG NH4adduct spectrum by @mikikot113 in #499
• Fixed Retention Index Calculation Issues and Added Validation Checks by @YukiMatsuzawa in #504
• added serialized msp to ascii msp by @htsugawa in #498
• Oad spec generator update by @Bujee415 in #503
• OAD spectrum generator update by @Bujee415 in #508

Full Changelog: MSDIAL-v5.5.241118-beta...MSDIALv5.5