Version 0.11.0

• Windows and macOS signing
  • SynapSpec release builds are now signed on Windows and signed and notarized on macOS.
• Dimethyl modification identifications
  • Improved identification counts for analyses using dimethyl modifications.
• Methionine loss setting
  • Added support for configuring methionine loss.

• GPU version
  • Fixed an issue where the GPU version did not run correctly.
• GUI
  • Fixed queue and execution issues, including input validation, Run Now control, and cancel handling.

Version 0.10.4

• Analysis stability
  • Improved overall analysis stability for more reliable processing.
• Optimization workflow
  • Optimized analysis optimization steps for more efficient and consistent processing.

• Multiple modification analysis
  • Fixed an issue where analyses with multiple modifications did not run correctly.

Version 0.10.2

• Differential analysis for LFQ workflows
  • Added optional pairwise differential analysis across experimental conditions, with biological replicate modeling and technical-run aggregation.
  • Added GUI controls for condition and replicate metadata, condition-aware precursor correction, and the analysis quantity level.
  • Added condition-aware precursor correction to provide improved MS2 quantities for downstream differential analysis.
  • Differential analysis outputs include contrast statistics and report-ready DPC-preprocessed quantity matrices.

• Faster analysis performance
  • Improved analysis speed by optimizing computationally intensive workflows.
• Improved analysis stability
  • Improved overall workflow stability for more reliable and consistent analyses.

Version 0.9.2

• Experimental quantums (high precision) support
  • Added experimental support for quantums workflows using the high-precision mode.

• Faster analysis performance
  • Optimized computationally intensive code paths to reduce analysis time and improve overall workflow performance.

Version 0.9.1

• Configurable protein FDR
  • Added support for configuring protein-level FDR settings.

• Quantification stability
  • Improved quantification stability and performance for more consistent quantitative results.

• Protein information output
  • Fixed a bug where incorrect protein information was reported in the output.

Version 0.9.0

• More stable identification counts
  • Improved the FDR and candidate-ranking workflow to make identification counts more consistent across runs.
  • Search groups and precursor classes are handled more consistently during FDR estimation, reducing avoidable variation in reported IDs when the same dataset and configuration are analyzed repeatedly.
• Refined glycoproteomics scoring features
  • Added more glyco-specific scoring features for N-glycopeptide candidates.
  • The glyco workflow now captures diagnostic-ion coverage, Y-stub coverage, total library fragment coverage, all-fragment intensity and height correlations, oxonium-ion intensity fraction, Y-stub intensity fraction, and Y-stub-to-backbone intensity ratio.
  • These features give the FDR model more direct evidence about glycan-related signal, improving the distinction between plausible glycopeptide matches and weaker candidates.
• Improved glycoproteomics extraction workflow
  • Refined N-glyco fragment extraction so backbone, oxonium, and Y-stub evidence can be evaluated together instead of relying only on shared peptide-style fragment evidence.
  • Added more focused handling of observed glyco fragments and signal fractions, improving the feature set available for glycoproteomics review and scoring.
• Expanded modification coverage
  • Added Dimethyl modification chemistry support in the modification metadata used by the prediction and fingerprint workflows.
  • This improves compatibility for workflows that include dimethyl labeling or related modification-aware library generation.

• GUI required settings warning
  • Fixed a bug where the warning dialog did not appear when required GUI settings were missing.
• Protein name output
  • Fixed an issue where incorrect protein names were reported in the output.

Version 0.8.0

• Glycoproteomics support
  • Added N-glycopeptide library generation and search support for glycoproteomics workflows.
  • SynapSpec can generate glycopeptide candidates from N-glycosylation motifs, combine peptide backbone information with glycan compositions, and use glyco-aware fragments such as diagnostic ions and Y-stub ions during candidate generation and scoring.
  • Glyco search is integrated into the broader DIA workflow, including GUI settings, spectral library generation, prediction, extraction, and result handling.
• Feedback-driven N-glyco expansion
  • Added a bounded, tier-based glyco expansion strategy to avoid generating an unmanageable glycopeptide search space all at once.
  • Regular peptide evidence can unlock protein-level glyco candidates, and glyco hits can progressively unlock additional glycan tiers up to the configured limit.
  • This makes glycoproteomics search more practical for large FASTA inputs while keeping the workflow controlled and interpretable.
• Unspecific search support
  • Added support for unspecific search mode, where peptides are not required to follow enzyme cleavage rules at either terminus.
  • Supported search modes now include specific, semi-specific, N-terminal specific, C-terminal specific, and unspecific candidate generation.
  • This broadens SynapSpec's use cases for workflows where cleavage specificity is uncertain or where users want to explore noncanonical peptide evidence.
• Dynamic and simple search strategies
  • Added two search strategies for broad candidate generation.
  • Dynamic mode uses search feedback to expand the candidate space progressively, reducing memory pressure for semi-specific, unspecific, and glyco searches.
  • Simple mode generates candidates upfront for users who prefer a straightforward, predictable search plan.
• Improved prediction models and feature generation
  • Updated RT, MS2, charge, and coelution-related model support, including instrument-aware prediction assets and fingerprint caching.
  • Improved modified-sequence handling and model inputs so modified peptides and glycopeptides can be represented more consistently across library generation and prediction.
  • These updates support higher identification counts and better downstream scoring behavior in the expanded search modes.
• Expanded external library support
  • Added support for MaxQuant msms.txt as an external library source.
  • This makes it easier to reuse existing search outputs and combine external evidence with SynapSpec's in-silico and hybrid library generation workflows.
• Decoy strategy improvements
  • Added a unified decoy strategy framework with support for RT-shift, shuffle, glyco-aware, and unified decoy generation approaches.
  • This provides a more flexible foundation for FDR estimation across regular, broad-search, and glycoproteomics workflows.

Version 0.7.0

• Improved tolerance optimization
  • Enhanced internal algorithm to find more appropriate tolerance values automatically
• Dynamic search space
  • Enables efficient semi-specific and unspecific searches through adaptive search space management
• Enhanced stability
  • Overall stability improvements for more reliable analysis

Version 0.6.2

• Enhanced timsTOF id count performance
• Reduced id count fluctuation
• Minor UI improvements

• Fixed error that occurred during application shutdown

Version 0.5.1

• GUI renewal (look and feel)
• Cycle correction for improved quantification stability

• Fixed CPU dispatch error

Version 0.4.2

• MacOS hardware acceleration support

• Fixed issue with reduced number of identified proteins

Version 0.4.1

• CPU and GPU Versions
  • SynapSpec is now available in separate CPU and GPU versions, allowing users to choose the version that best suits their hardware configuration.
• Display and Naming
  • Updated application name from "synapspec" to "SynapSpec" throughout the interface(macOS).
• Data Export Quality
  • Improved precision formatting in quantification output files for better readability.
• Analysis Workflow
  • Enhanced stability when starting analysis tasks.
• Memory Management
  • Improved memory usage to prevent out-of-memory issues during large-scale analyses.
• Library Information Display
  • When a library is selected as input, you can now see detailed information including library size and number of candidates.

• Match Between Runs (MBR)
  • Resolved MBR workflow issues that prevented library generation.
  • Improved handling of intermediate files during processing.

Version 0.3.6

• Improved Worker Efficiency
  • Optimized worker utilization, resulting in faster task execution and overall improved processing speed.

• Python.NET Initialization
  • Fixed an issue where pythonnet was being unnecessarily loaded on worker types that do not require it.
• Application Shutdown
  • Fixed issue where application shutdown did not work properly.
• Linux GUI
  • Fixed process execution failure in Linux GUI environment.

Version 0.3.4

• Windows Analysis
  • Fixed error cases that occurred during analysis on Windows.

Version 0.3.3

• macOS Compatibility
  • Fixed issue where application could not open on macOS.

Version 0.3.2

• Configuration and Output
  • Renamed output columns and configuration parameters to be more intuitive and self-explanatory.

• Distribution Package
  • Fixed Linux executable permissions to be preserved in distribution package (users no longer need to manually set execute permissions).

Version 0.3.1

• Hardware Acceleration
  • Fixed issue where GPU acceleration was enabled

• Logging
  • Enhanced log messages to provide more meaningful information for debugging and monitoring.
  • Removed unnecessary log outputs to reduce noise and improve clarity.

Version 0.3.0

• Hardware Acceleration
  • Implements GPU acceleration for improved processing performance and faster analysis workflows.

• Enhanced Logging System
  • Improved log message formatting and information detail for better debugging and workflow monitoring.
  • Provides more comprehensive execution status tracking.
• Match-Between-Runs (MBR) Reporting
  • Adds detailed reporting functionality for Match-Between-Runs results.
  • Enables better tracking and validation of cross-run peptide identification transfer.

• GUI Icon Display
  • Fixed Flet GUI application icon rendering issue.

Version 0.2.16

• Workflow Execution
  • Fixed workflow execution error caused by missing package dependencies.

Version 0.2.15

• DIA Analysis Workflow
  • Implements an initial workflow for processing and quantifying Data-Independent Acquisition (DIA) mass spectrometry data.
• Semi-Specific Analysis Support
  • Supports 'semi-specific' search options, where peptides are required to follow the enzyme cleavage rule at only one terminus (N-terminus or C-terminus).
• Graphical User Interface (GUI)
  • Provides a GUI to configure and execute analysis pipelines as an alternative to the command-line interface.
• Automatic Configuration
  • Includes a preliminary feature to suggest analysis parameters based on input data.
• Versatile Data Import
  • Provides initial compatibility for reading native (raw) file formats from major mass spectrometry vendors, including:
    • .raw
    • .d directories
    • .mzML, .mzXML
• Cross-Platform Support
  • Designed for operation on Windows, macOS, and Linux operating systems.