1.0.566

mzLib v1.0.566 – Release Notes

This release introduces new spectral and chromatographic utilities, enhancements for negative ion and oligo analysis, improvements to performance and memory usage, and expanded file format support.

✨ New Features & Enhancements

📚 Spectrum & Library Management

• Transfer Spectrum Library Reading/Writing from MetaMorpheus (#914)
  Spectrum library I/O functionality has been moved from MetaMorpheus to mzLib for broader reuse and better modularity.

• MassIndexingEngine Added (#886)
  Introduced a new engine for efficient mass indexing across large datasets.

💾 File Format & Data Support

• Support for MRM Data in timsTOF Reader (#920)
  Extended timsTOF reader to support Multiple Reaction Monitoring (MRM) data.

• Read/Write Mandatory Sequence Attributes in Protein XML (#906)
  Improved protein XML support by handling required sequence attributes.

• Set Isolation Range in MsDataScan (#916)
  Enables definition of MS isolation range directly within the scan metadata.

⚗️ Fragmentation & Annotation

• Negative Ion Mode Annotation and Parsing (#915)
  Added support for interpreting spectra acquired in negative ion mode.

• Oligo Fragmentation with Null Parent Handling (#922)
  Improved robustness of oligonucleotide fragmentation when parent information is unavailable.

📈 Quantification & Chromatography

• FlashLFQ Fold Change Bug Fix (#918)
  Resolved an issue in fold change calculations within FlashLFQ.

• GetAllXICs Method Added (#902)
  New method to retrieve all extracted ion chromatograms across datasets.

• Cut Peaks for Extracted Ion Chromatograms (#903)
  Introduced peak-cutting logic to refine XIC representations.

⚙️ Performance & Infrastructure

• Memory Optimization via Target Mass List Pruning (#913)
  Reduced memory footprint by generating targetMassList only when needed during indexing.

• Fix to IQuantifiableResultFiles in MakeIdentifications (#919)
  Fixed a bug that affected result file quantifiability tracking in downstream tasks.

---

🔗 Full Changelog

1.0.565

What's Changed

• add UniProt required Xml entry attributes by @trishorts in #895
• Bug Fix: Internal Ion Parsing by @nbollis in #900
• Parse Auto Generated Prose from a MetaMorpheus result by @nbollis in #899
• Additional rna db types by @nbollis in #891
• PpmToleranceWithNotch by @zhuoxinshi in #892
• PeakTracing by @zhuoxinshi in #894
• if i create a branch from master will codecov actually have a base and generate a report by @trishorts in #908
• MsDataScan Negative mode precursor charges states are now negative by @nbollis in #911
• Added support for legacy Psmtsv files in Readers by @Alexander-Sol in #870
• Optimize Memory Usage in RAM for PeakIndexingEngine by @RayMSMS in #905
• Fixed ParseModification in SpectrumMatchFromTsv by @zhuoxinshi in #901
• AddPeaks Bug Fix by @zhuoxinshi in #912

Full Changelog: 1.0.564...1.0.565

1.0.564

What's Changed

• Tims tof reader fix to enable reading off of NAS by @Alexander-Sol in #897
• Added support for OneOverK0 column in PsmFromTsv by @Alexander-Sol in #896

Full Changelog: 1.0.563...1.0.564

1.0.563

What's Changed

File Reading

• MsAlign Mass Spec File Reading by @nbollis in #868
• Combine MsAlign Explainer by @nbollis in #875
• timsTOF files are now tolerant to corrupted scans @Alexander-Sol in #888
• timsTOF file dynamic connections can be repeatedly opened/closed, enabling MetaDraw @Alexander-Sol in #890

Quantification

• Enable IsoTracker to search specifically on certain PTM motifs @RayMSMS in #876
• IsoTracker will choose the XIC with the most IDs as the Reference XIC for alignment @RayMSMS in #874
• FlashLFQ Refactoring, addition of FlashLFQ Parameters, and making MbrScorer more robust (will slightly change MBR results) @Alexander-Sol in #861, #877, #887 #861

Misc.

• Reorganize the IDs from IsoTracker and MBR to avoid the crashing @RayMSMS in #885
• Averagine Generalization by @nbollis in #883
• Change the access modifier of Modification from private set to protected set. by @RayMSMS in #893

Full Changelog: 1.0.562...1.0.563

1.0.562

What's Changed

File Reading

• MetaMorpheus Crosslink PsmTsv and Spectral Library Reading by @nbollis in #845
• Readers spectral match Restructuring by @Alexander-Sol in #858
• FlashLFQ can now turn and IQuantifaibleResultFile into a list of Identifications by @mzhastings in #857
• Updated MetaMorpheus PsmTsv reader to match current MetaMorpheus output by @nbollis in #866
• Reader extensions: ReadResultFile and ReadIQuantifiableResult @Alexander-Sol in #864
• MsPathFinderT Modifications now read as MzLib modifications by @nbollis in #853
• Implemented IQuantifiableRecord/File for SpectrumMatchFromTsv/File by @Alexander-Sol in https://github.com/smith-chem-wisc/mzLib/

Quantification

• Created enum instead of boolean for quantification detection type by @RayMSMS in #852
• Refactoring FlashLFQ: Created MbrChromatographicPeak child calss by @Alexander-Sol in #860

QOL

• Enabled custom delimiters to remove mods when getting Base Sequence from Full Sequence - Custom Delimiters by @nbollis in #854

Transcriptomics

• Added support for Rna Sequence Variants and Truncation Products by @nbollis in #848
• Extended decoy scrambling on homologous sequence to RNA by @nbollis in #859

Full Changelog: 1.0.561...1.0.562

1.0.561

What's Changed

New Features

• IsoTracker: The quantification tool for isobaric peaks in Match-between-runs by @RayMSMS in #832

Maintenance/Bug Fixes

• Fixed bug in FlashLFQ, eliminated unneccessary namespace by @Alexander-Sol in #836
• Fixed issue where timsTOF reader would have null scans in the Scan array by @Alexander-Sol in #834
• Eliminate Need to call Loaders.LoadElements by @nbollis in #833
• Changed a few methods in FlashLFQ to work with DIA by @zhuoxinshi in #835
• MatchedFragmentIon and Product enhancement by @nbollis in #838
• Refactored peakIndexing in flashLFQ to work with interfaces by @Alexander-Sol in #841
• Xml DB Writing from one method by @nbollis in #846
• Decoy Identifier in RNA decoys with optional custom Identier by @nbollis in #847
• Result File Operators by @nbollis in #843

New Contributors

• @zhuoxinshi made their first contribution in #835
• @RayMSMS made their first contribution in #832

Full Changelog: 1.0.559...1.0.560

1.0.559

What's Changed

New Features

• enable reading of lipid mods from protein xml by @trishorts in #828

Maintenance/Bug Fixes

• Mzml writer no longer rounds mz values, reverts change made in 1.0.558 by @Alexander-Sol in #831
• Github action workflow now uploads artifacts - a MetaMorpheus installer and a zipped folder containing the MM GUI .exe @Alexander-Sol in #829
• Included CsvHelper as dependency in nuspec, as CsvHelper is a dependency of SqLite in Readers @Alexander-Sol in #830

Full Changelog: 1.0.558...1.0.559

1.0.558

Hot Fix from last release

• Fixed a terminal mod bug by @nbollis in #827
• Changed rounding method in mzml writer by @Alexander-Sol in #826

Full Changelog: 1.0.557...1.0.558

1.0.557

What's Changed

New Features

• Added object pooling utility classes by @nbollis in #822
• Added ability to read TimsTof into the standard MsDataFile by @Alexander-Sol in #812

Maintenance

• Condensed and optimized digestion code in parent DigestionProduct class by @nbollis in #823

Bug Fixes

• Digestion: Ensured consistent variable modification ordering and eliminated bug where protein N-Terminal mod were added to peptides by @nbollis in #825
• Rounded m/z values to 4 decimal places when writing mzML file as values past this are insignificant for standard FTMS data by @Alexander-Sol in #821

Full Changelog: 1.0.556...1.0.557

1.0.556

What's Changed

• Ensured consistent ordering of modifications when writing protein databases by @Alexander-Sol in #820
• Added IsoDec, a high resolution proteomic deconvolution algorithm by @nbollis in #791

Full Changelog: 1.0.555...1.0.556