What's Changed

Summary

This release provides a corrective update to the previous version, focusing on parameter scope adjustment and spectrum similarity scoring behavior.

Bug Fixes

• Restricted the scope of the MS1 tolerance default value change to GC-MS projects only, preventing unintended application to other project types by @YukiMatsuzawa in #719

• Fixed an issue where weighted dot product could be overestimated in certain cases, improving the reliability of spectrum similarity scoring by @YukiMatsuzawa in #720

Full Changelog: MSDIAL-v5.5.260319...MSDIAL-v5.5.260323

What's Changed

Summary

This release primarily focuses on enhancements and fixes for GC-MS workflows, including improvements to alignment, annotation handling, and quantification features. Several new capabilities have also been introduced to improve usability and data handling across the platform.

⚠️ Important Notice

Due to recent changes in GC-MS alignment settings, the default MS tolerance for alignment has been set to 0.5 Da. This value may also be applied to non-GC-MS projects unintentionally.

Users working with LC-MS or other high-resolution data are advised to verify and adjust the MS tolerance parameter accordingly.

A corrective update addressing this issue will be released soon.

Feature Updates

• Enabled comparison by displaying the raw spectrum as a background layer behind the deconvoluted spectrum in DIA analysisPR #718 by @YukiMatsuzawa
• Implemented the quant mass manager feature, previously available in MS-DIAL 4, for GC-MS projectsPR #657 by @YukiMatsuzawa
• Added function to export results in SDF format PR #709, #713, #716 by @mikikot113
• Added HCO₃⁻ adduct annotation method for lipidomics PR #673 by @mikikot113
• Added function to include metadata in CSV files in the console application (v5) PR #665 by @htsugawa

Improvements

• Improved performance of the compound search feature PR #667 by @YukiMatsuzawa
• Enabled correction of fill percentage after peak alignment to account for peaks that are present but not initially detected in some samples PR #659 by @YukiMatsuzawa
• Updated text parameter export behavior (v4, LC-MS)PR #302 by @ondrej-kuda
• Adjusted peak detection parameters to be less stringent, increasing the number of detected peaks PR #688 by @htsugawa
• Reduced the minimum fatty acyl chain length to 8 in EAD-based lipidomics annotation to expand detectable lipid species PR #690 by @YukiMatsuzawa
• Updated the default MS similarity tolerance for alignment to 0.5 Da for GC-MS nominal mass data PR #710 by @htsugawa
• Added a notification message when Hive spectral data cannot be loaded due to API limitations, guiding users to update to a newer MS-DIAL version PR #678 by @YukiMatsuzawa
• Improved graph update behavior in the peak view so that graphs properly refresh after manual data updates in certain cases PR #655 by @YukiMatsuzawa

Bug Fixes

• Fixed incorrect standard deviation calculation in LOWESS cross-validation PR #664 by @YukiMatsuzawa
• Fixed validation logic for ion mobility parameters where valid values could be incorrectly rejected PR #669 by @YukiMatsuzawa
• Fixed mzTab export format issues and unified file extension to ".mzTab" PR #679, #683, #695 by @mikikot113, @htsugawa
• Fixed handling of duplicate annotations in GC-MS analysis PR #674, #703 by @htsugawa
• Fixed an issue in the CUI version where valid file paths were not correctly recognized PR #681 by @htsugawa
• Fixed GC-MS alignment and processing bugs, including quant mass assignment issues PR #708, #712 by @htsugawa
• Adjusted lipidomics annotation logic PR #686, #701 by @mikikot113
• Fixed an issue in GC-MS alignment where an unintended parameter was referenced instead of the expected one PR #711, #714, #717 by @htsugawa, @YukiMatsuzawa

📋 Full Changelog: Compare v5.5.251021...v5.5.260319:MSDIAL-v5.5.251021...MSDIAL-v5.5.260319

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

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

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.

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

🚨 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.

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

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

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

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

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