CSBiology/ProteomIQon

ProteomIQon is a mass spectrometry analysis suite that provides a comprehensive set of command-line tools for processing proteomics data. It handles the entire workflow from raw file conversion and preprocessing to peptide spectrum matching, protein inference, and various quantification methods including label-free, labeled, and SWATH analyses. The system also includes utilities for statistical analysis, alignment, and spectral library generation, all built on a modern .NET 10 F\# codebase.

14 changes.

This period focused on the initial release of the ProteomIQon library and its associated command-line tools for mass spectrometry data analysis, including preprocessing, peptide spectrum matching, and quantification. The work involved establishing the core domain models, adding comprehensive test suites, and migrating the build infrastructure to .NET 10. Legacy documentation and console projects were removed to streamline the codebase around the new modular toolset.

15 changes.

This period focused on expanding the ProteomIQon suite with numerous new command-line tools for mass spectrometry data processing, including spectral library generation, quantification, alignment, and table sorting. Significant work also involved creating converters between MzML and MzLite formats and implementing mzTab export capabilities. The period concluded with platform-specific packaging and an upgrade to the .NET 10 runtime.

9 changes.

This period focused on expanding the ProteomIQon suite with specialized command-line tools for ion mobility quantification, label efficiency analysis, and data format conversion. Concurrently, the project modernized its development infrastructure by replacing the build system with FAKE and updating core dependencies to target .NET 10.

The FsMzLite library is now available in the \lib/FsMzLite\ directory, including its compiled assembly, XML documentation files for FSharp.Core, Newtonsoft.Json, and System.Data.SQLite, and configuration files. The FsMzLite.dll.config file establishes a binding redirect for FSharp.Core version 4.4.1.0, ensuring compatibility with the .NET Framework 4.5 runtime.

lib/FsMzLite · high confidence

A new .NET template named 'pct' (ProteomIQonConsole) has been added to the ConsoleTemplate directory, allowing users to scaffold a new F\# console application for mass spectrometry analysis. The template includes a pre-configured CLI argument parser for specifying input instrument data, output directories, and parameter files, along with logging and JSON deserialization support. Users can install the template locally and generate new projects using the dotnet CLI.

ConsoleTemplate · high confidence

The documentation site now includes detailed guides for the MzMLToMzLite and MzLiteToMzML conversion tools, covering parameter configuration (such as compression and peak picking) and CLI execution examples. Additionally, developer notes have been added to explain how to install and use the ProteomIQon tool template for creating new standalone tools, alongside a getting started guide and a workflow overview for the PeptideDB tool.

_docs\WIP · high confidence

This change introduces the initial version of the ProteomIQon library, establishing the foundational types and processing logic for mass spectrometry data analysis. It defines the Domain and DTO models for peptide-spectrum matching, quantification, and protein inference, alongside core utilities for file I/O (supporting MzML, MzLite, Thermo, Bruker, and Wiff formats), logging, and JSON serialization. The library also includes specific algorithms for dynamic time warping alignment, PEP value calculation via IRLS, and Deedle frame extensions for data manipulation.

src/ProteomIQon · high confidence

Introduces a new command-line tool for label-free protein quantification that processes .quantAndProt input files to generate protein-level aggregation results. The tool supports optional aggregation of peptide charge states and modifications before summarizing data into protein groups, and includes configurable filtering based on alignment Q-values to control data inclusion in the final output.

src/LabelFreeProteinQuantification · high confidence

Introduces a new standalone tool for peptide spectrum matching within the ProteomIQon suite. The tool accepts mass spectrometry output files (via the -i flag, supporting directories or single mzlite files), a peptide database (-d), and a parameter file (-p) to perform spectrum scoring. It outputs results to a specified directory (-o) and supports parallel processing across multiple files using the -c flag. The implementation relies on BioFSharp.Mz for mass spectrometry data handling and includes logic for charge state determination and spectral scoring.

src/LabeledProteinQuantification, src/PeptideDB, src/PeptideSpectrumMatching · high confidence

A new command-line tool, AddDeducedPeptides, has been added to the ProteomIQon suite. It accepts protein inference results (.prot) and quantification alignment outputs (.quant) as input, filters the protein groups to include only those containing peptides present in the quantification files, and writes the combined results back to new .prot files in a specified output directory. The tool validates that protein inference was performed on combined files and uses the FSharpAux library for CSV reading and writing.

src/AddDeducedPeptides · high confidence

A new command-line tool is added to calculate statistics for alignment-based quantification, supporting both scoring and binary classification training. The tool accepts quantification, alignment, and aligned quantification files (and separate sets for training data), allowing users to match input files by name or position. It leverages Microsoft.ML for training a classifier to assign scores and Q-values, with options to output diagnostic charts and return the training dataset used.

src/AlignmentBasedQuantStatistics · high confidence

A new standalone tool, AlignmentBasedQuantification, is added to the ProteomIQon suite to perform quantification based on aligned peptide spectrum matches. This tool processes mass spectrometry data (mzlite files) alongside aligned PSMs, metrics, and quant files, supporting both single-file and directory-based batch processing. It introduces features such as ion mobility filtering, diagnostic chart generation, and name-based file matching to align input datasets. The implementation leverages BioFSharp.Mz for data handling and includes logic for baseline correction and spline fitting to refine intensity traces, outputting detailed quantification metrics including alignment scores and isotopic patterns.

src/AlignmentBasedQuantification · high confidence

A new command-line tool, JoinQuantPepIonsWithProteins, is introduced to join quantified peptide ions with inferred protein data. The tool accepts quantified peptide files (.quant) and inferred protein files (.prot) as input, matching them either by filename or by list position, and produces a combined output file (.quantAndProt). The output integrates peptide quantification metrics (such as light/heavy intensities, precursor mass, and ion mobility) with protein-level information (ProteinGroup, QValue), enabling users to analyze peptide-protein relationships in a single dataset.

src/JoinQuantPepIonsWithProteins · high confidence

Adds a new command-line tool for calculating label efficiency in mass spectrometry data. The tool accepts input files, an output directory, and a parameter file, then processes peptide data to simulate isotopic distributions and compare them against measured patterns using Kullback-Leibler divergence. It leverages BioFSharp for chemical formula and isotopic distribution calculations and Plotly.NET for generating visualization charts of the measured versus simulated isotopic patterns.

src/LabelEfficiencyCalculator · high confidence

A new command-line utility has been added to convert validated MSFragger PSM files and MzLite mass spectrometry data into a standardized PSM format. The tool accepts input paths for MSFragger outputs, MzLite files, and a peptide database, then matches spectra by retention time and precursor m/z to generate output files. It supports parallel processing across multiple cores and logs detailed execution information.

src/MsFraggerToPSM · high confidence

A new command-line tool, MzMLToMzLite, is added to convert MzML mass spectrometry data into the MzLite format. The tool supports processing single or multiple input files with optional parallelization, allows filtering spectra by retention time, and includes a flag to fix malformed MzML files containing invalid HTML entities. It utilizes sequential reading to reduce memory usage and supports various peak-picking modes, including wavelet-based centroidization.

src/MzMLToMzLite · high confidence

A new MzMLToMzLiteIonMobility tool is added to the ProteomIQon suite, enabling the conversion of mass spectrometry data that includes ion mobility dimensions into the MzLite format. The converter handles ion mobility data by zipping mobility values with standard mz/intensity peaks and supports wavelet-based centroidization for profile data. It includes a new -f (FixFiles) command-line flag that strips invalid characters from input files before processing, matching the behavior of the existing MzMLToMzLite tool. The implementation also features parallel processing capabilities for handling multiple input files and integrates with the MzIO library for reading and writing the converted data.

src/MzMLToMzLiteIonMobility · high confidence

A new command-line tool (MzTAB) has been added to ProteomIQon to generate mzTab output files. The tool accepts input files for table sorting, protein inference, quantification, and peptide-spectrum matches, then aligns this data and writes structured mzTab sections (metadata, protein, peptide, and PSM). It supports both labeled and unlabeled experiments, reporting heavy and light abundances where applicable, and handles relative path resolution for input and output locations.

src/MzTAB · high confidence

A new command-line tool, MzliteToMzML, is added to the ProteomIQon suite to convert mass spectrometry data from the MzLite format into the standard mzML format. The tool accepts an input path (file or directory), an output directory, and a JSON parameter file for peptide spectrum matching configuration. It supports parallel processing across multiple files when an input directory is specified, allowing users to control the number of cores used via a command-line flag. The converter filters mass spectra based on retention time ranges defined in the parameter file and writes the resulting spectra to mzML files.

src/MzliteToMzML · high confidence

A new standalone command-line tool for PSM-based quantification is now available. Users can run the tool via the CLI, providing mandatory inputs for instrument output files, scored PSMs, a peptide database, and a parameter file, with an optional output directory. The tool supports optional flags to enable name-based file matching, generate diagnostic charts, zip those charts, and control parallelism levels. It processes mass spectrometry data to produce quantification results, handling both single-file and multi-file inputs with configurable logging and verbosity.

src/PSMBasedQuantification · high confidence

Adds the PSMStatistics application, a new command-line tool that processes peptide spectrum matches (PSMs) to calculate statistics, posterior error probabilities (PEP), and q-values. The tool accepts input PSM files and a peptide database, applies configurable parameters for scoring and filtering, and outputs results including diagnostic charts. It supports parallel processing across multiple files and integrates with SQLite for database lookups.

src/PSMStatistics · high confidence

This change introduces the QuantBasedAlignment module, which aligns quantified peptide files (.quant) by leveraging machine learning (Microsoft.ML FastTree) and dynamic time warping to predict corresponding scan times. The tool processes input files to generate alignment results that include ion mobility data and PEP values, and provides a CLI interface to specify target and source files, output directories, and diagnostic chart generation.

src/QuantBasedAlignment · high confidence

A new RatioLFQ executable and library have been added to the ProteomIQon suite, enabling users to perform ratio-based label-free quantification (LFQ) on proteomics data. The tool accepts input files, output paths, and column specifications via command-line arguments, processes the data using FSharp.Stats for statistical operations like median calculations and least-squares fitting, and outputs a tab-separated file with LFQ-normalized ratios. This release also updates the underlying dependency stack to BioFSharp.Mz 0.2.0 and BioFSharp 2.0.0, and targets .NET 10.

src/RatioLFQ · high confidence

Adds a new command-line tool (SWATHAnalysis) that processes SWATH mass spectrometry data against consensus libraries and peptide databases. The tool supports single-file or directory-based input, name-based or positional file matching, parallel processing, and diagnostic chart generation, with output including quantified peptide and fragment information.

src/SWATHAnalysis · high confidence

A new SpectralLibrary project has been added, providing a command-line tool that constructs spectral libraries from mass spectrometry output, PSM statistics, and quantification results. The tool accepts input paths for instrument data, peptide databases, and quant files, supporting both single-file and directory-based processing with optional name-based file matching. It integrates quantification data to filter and process peptides, calculates ion information including relative intensities and m/z deltas, and outputs the resulting spectral libraries to a specified directory.

src/SpectralLibrary · high confidence

A new PSMBasedQuantificationTIMs module has been added to the ProteomIQon platform, enabling peptide quantification using Ion Mobility Spectrometry (TIMS) data. This feature introduces the Gabor3D algorithm for improved peak detection and integrates ion mobility values into the quantification results (PSM and alignment-based). The module includes a new command-line interface for parsing instrument outputs, scored PSMs, and parameter files, and supports parallel processing across multiple files. It also implements a fallback mechanism for sparse mz correction and ensures robustness against empty results and non-finite intensities in quality filters.

src/PSMBasedQuantificationTIMs · high confidence

Adds the TableSort application, a command-line tool for processing and sorting proteomics quantification and protein tables. The tool accepts input paths for quantification and protein data files, along with a parameter file, to perform operations such as file matching, filtering based on field bounds, statistical aggregation (sum, mean, median), and outlier detection using Tukey's method. It supports configurable transformations (log10, log2, ln) and outputs the processed tables to a specified directory, including calculation of statistical measurements like coefficient of variation (CV), standard deviation (StDev), and standard error of the mean (SEM).

src/TableSort · high confidence

Adds a new command-line application in src/ConsensusSpectralLibrary that generates consensus spectral libraries from instrument output and existing spectral libraries. The tool accepts input paths for instrument data and spectral libraries, an output directory, and a parameter file, and supports a diagnostic chart flag for visualization. It handles both single-file and directory-based inputs, processes MzLite files, and retains global modification information and peptide sequence IDs during the consensus generation process.

src/ConsensusSpectralLibrary · high confidence

A new standalone Preprocessing tool has been added to the ProteomIQon suite, enabling users to convert mass spectrometry data (Bruker .d, Thermo .raw, ABSciex .wiff, and existing .mzlite files) into the MzIO format. This tool introduces support for Thermo raw files via the MzIO library, replacing the previous MzLite dependency, and allows for parallel execution across multiple files using the new -p (parallelism level) command-line argument. It also supports advanced centroidization options, including wavelet-based peak picking, and manages input/output paths using relative path resolution.

src/Preprocessing · high confidence

The \src/ProteomIQon/Scripts\ directory now includes a comprehensive set of F\# scripts (e.g., \createLabelFreeQuantificationParams.fsx\, \createLabeledQuantificationParams.fsx\, \createPreprocessingParamsThermo.fsx\) that generate and serialize default configuration files for various analysis modules. These scripts cover label-free and labeled quantification, preprocessing for Bruker/Thermo/Wiff instruments, peptide spectrum matching, protein inference, and spectral library creation, ensuring that each module has a standardized, serializable set of initial parameters.

src/ProteomIQon/Scripts · high confidence

The ProteomIQonConsole project has been removed from the codebase. This change deletes the command-line interface implementation, including the command-line argument parsing logic (CommandLine.fs), the entry point (Program.fs), and the associated dependency references (paket.references). Users will no longer have access to this specific console application component.

src/ProteomIQonConsole · high confidence

The \src/ProteomIQon/pepValue\ directory now includes an Apache License 2.0 file and the \pepValueCalculation.fs\ source file, which implements the false discovery rate (FDR) and peptide error probability (PEP) calculations derived from the Percolator algorithm. This addition clarifies the licensing for this specific component, which is based on work by Lukas Käll, and provides the implementation logic for calculating PEP values using iterative reweighted least squares (IRLS).

src/ProteomIQon/pepValue · high confidence

The QuantBasedAlignment tool is now available as a dedicated Linux x64 package, separated from the Windows variant to allow independent versioning and packaging. This release upgrades the runtime to .NET 10 and updates key dependencies, including BioFSharp to 2.0.0 and Plotly.NET to 6.0.0-preview.2, ensuring compatibility with the latest platform features.

_src/QuantBasedAlignment\linux-x64 · high confidence

The project has replaced the legacy FAKE build script (build.fsx) and Paket dependency manager with a modern .NET SDK-based build project (build/build.fsproj). This change requires the .NET 10.0.101 SDK (specified in global.json) and updates the solution file to target Visual Studio 17. Additionally, the license has been changed from the Unlicense to the MIT License, and the CI configuration has been updated to use the .NET CLI for package restoration and build execution.

(repo-wide) · high confidence

The build process has been replaced with a new FAKE script (build/Build.fs) that orchestrates the entire lifecycle for the ProteomIQon suite. This system introduces structured tasks for cleaning, building, and packaging all listed projects (including MsFraggerToPSM, MzMLToMzLite, PeptideDB, and others) into NuGet packages. It supports both stable and prerelease release workflows, automatically handling versioning based on RELEASE\_NOTES.md, creating Git tags, and publishing packages to NuGet. Additionally, it integrates documentation generation using FsDocs, ensuring docs are built and deployed to GitHub Pages alongside the code releases.

build · high confidence

The ProteinInference command-line tool has been updated to accept both individual files and directories as input via the -i flag. Previously, the tool likely required specific file paths; now, users can point the tool to a folder containing input files (e.g., \*.qpsm), and the tool will automatically parse and process all matching files within that directory. This change simplifies batch processing by allowing users to specify entire directories rather than listing every file individually.

src/ProteinInference · high confidence

The previous documentation source files have been removed from the repository. This includes the main index and tutorial content files (index.fsx, tutorial.fsx), the custom CSS styling (CSBStyles.css), and the HTML template (template.cshtml) used for generating the documentation site. Users relying on these specific legacy assets for local documentation generation will need to update their build processes or templates.

docsrc · high confidence

The QuantBasedAlignment tool for Windows x64 has been separated into its own project, with the entry point now explicitly targeting the .NET 10 runtime and updated dependencies including BioFSharp 2.0.0 and Plotly.NET 6.0.0-preview.2.

_src/QuantBasedAlignment\win-x64 · high confidence

Added test fixtures for legacy table sorting validation; Initial test suite for ProteomIQon pipeline and quantification modules.

The ProteomIQon tool suite has been upgraded to target .NET 10.0, replacing the previous .NET 5.0 target. This change is accompanied by updates to key dependencies, including MzIO (up to 0.1.10), BioFSharp (to 2.0.0), BioFSharp.Mz (to 0.2.1), FSharpAux (to 2.1.0), and Plotly.NET (to 6.0.0-preview.2). The build system itself has also been migrated to .NET 10.0.

(dependencies) · high confidence

Written by watchdog.canine.dev from the codebase's own history, inside the signed delivery this page is composed from.

• CAI 62 → 60 (-1.8)
• Rubric changed (rubric-2026.09.15 → rubric-2026.10.1) — scores are not directly comparable.

• Code Health 60 (new)
• Architecture 100 → 100 (+0.0)
• Maturity 60 → 61 (+1.0)
• Readiness 55 → 55 (+0.0)
• Security 65 → 65 (+0.0)

• Documentation: no installation or build instructions (README.md)
• Off-boarding risk: anonymized user #1

• AlignmentBasedQuantStatistics.createTrainingsData (cognitive 44) (src/AlignmentBasedQuantStatistics/AlignmentBasedQuantStatistics.fs)
• AlignmentBasedQuantStatistics.createTrainingsData (cyclomatic 22) (src/AlignmentBasedQuantStatistics/AlignmentBasedQuantStatistics.fs)
• AlignmentBasedQuantification.quantifyPeptides (cognitive 166) (src/AlignmentBasedQuantification/AlignmentBasedQuantification.fs)
• AlignmentBasedQuantification.quantifyPeptides (cyclomatic 64) (src/AlignmentBasedQuantification/AlignmentBasedQuantification.fs)
• DTW'.bestPath (cognitive 17) (src/ProteomIQon/BioFSharp.Mz_Temp.fs)
• DTW'.warp (cognitive 41) (src/ProteomIQon/BioFSharp.Mz_Temp.fs)
• DTW'.warp (cyclomatic 26) (src/ProteomIQon/BioFSharp.Mz_Temp.fs)
• Documentation: no architecture or design documentation (docs/_template.html)
• Documentation: no installation or build instructions (ConsoleTemplate/readme.txt)
• Documentation: no usage examples (ConsoleTemplate/readme.txt)
• Duplicated block (10 lines × 2) (ConsoleTemplate/template/Program.fs)
• Duplicated block (10 lines × 2) (src/ConsensusSpectralLibrary/ConsensusSpectralLibrary.fs)
• Duplicated block (10 lines × 2) (src/LabelEfficiencyCalculator/LabelEfficiencyCalculator.fs)
• Duplicated block (10 lines × 2) (src/ProteinInference/Program.fs)
• Duplicated block (10 lines × 3) (src/PSMBasedQuantification/Program.fs)
• Duplicated block (10 lines × 4) (src/AlignmentBasedQuantification/AlignmentBasedQuantification.fs)
• Duplicated block (11 lines × 2) (src/AlignmentBasedQuantification/AlignmentBasedQuantification.fs)
• Duplicated block (11 lines × 2) (src/MzMLToMzLite/MzMLToMzLite.fs)
• Duplicated block (11 lines × 2) (src/PSMBasedQuantificationTIMs/PSMBasedQuantificationTIMs.fs)
• Duplicated block (11 lines × 3) (src/AlignmentBasedQuantification/AlignmentBasedQuantification.fs)
• …and 219 more

• Containers 0 added · 0 removed · contexts 14 added · 0 removed · edges 11 added · 0 removed

• ProteomIQon
• ProteomIQon.AlignmentBasedQuantStatistics
• ProteomIQon.AlignmentBasedQuantification
• ProteomIQon.ConsensusSpectralLibrary
• ProteomIQon.LabelEfficiencyCalculator
• ProteomIQon.MzTAB
• ProteomIQon.PSMBasedQuantification
• ProteomIQon.PSMBasedQuantificationTIMs
• ProteomIQon.PSMStatistics
• ProteomIQon.ProteinInference
• ProteomIQon.QuantBasedAlignment
• ProteomIQon.SWATHAnalysis
• ProteomIQon.SpectralLibrary
• build

• ProteomIQon.AlignmentBasedQuantStatistics → ProteomIQon (coupling)
• ProteomIQon.AlignmentBasedQuantification → ProteomIQon (coupling)
• ProteomIQon.ConsensusSpectralLibrary → ProteomIQon (coupling)
• ProteomIQon.MzTAB → ProteomIQon (coupling)
• ProteomIQon.PSMBasedQuantification → ProteomIQon (coupling)
• ProteomIQon.PSMBasedQuantificationTIMs → ProteomIQon (coupling)
• ProteomIQon.PSMStatistics → ProteomIQon (coupling)
• ProteomIQon.ProteinInference → ProteomIQon (coupling)
• ProteomIQon.QuantBasedAlignment → ProteomIQon (coupling)
• ProteomIQon.SWATHAnalysis → ProteomIQon (coupling)
• ProteomIQon.SpectralLibrary → ProteomIQon (coupling)

Written by watchdog.canine.dev from the codebase's own history, inside the signed delivery this page is composed from.

CSBiology/ProteomIQon was measured the same way every project in this corpus was: the same rubric, at a pinned commit, with the result published in full. Point a surveyor at a repository you know and see whether you agree with it.