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+1. Tool name: iMonDB
+
+Description: Tool suite to automatically extract, store and visualize mass spectrometer instrument parameters from raw data files, particularly for Thermo instruments
+
+Repository/Link: https://github.com/bittremieux/iMonDB
+
+Publication Year: 2015
+
+Active Development: No
+
+Platform/Language: Java
+
+DDA: Yes
+
+DIA: Yes
+
+Targeted (SRM/MRM/PRM): No
+
+Metabolomics: No
+
+ID-based Metrics: No
+
+ID-free Metrics: Yes
+
+mzQC Support: No
+
+Real-time Monitoring: Yes
+
+Key Features: Extracts instrument parameters; Monitors hardware performance; Database storage
+
+---
+
+2. Tool name: MsQuality
+
+Description: Interoperable open-source R/Bioconductor package for calculation of standardized quality metrics, agnostic to underlying technology (proteomics, metabolomics, lipidomics)
+
+Repository/Link: https://github.com/tnaake/MsQuality and https://bioconductor.org/packages/release/bioc/html/MsQuality.html
+
+Publication Year: 2023
+
+Active Development: Yes
+
+Platform/Language: R/Bioconductor
+
+DDA: Yes
+
+DIA: Yes
+
+Targeted (SRM/MRM/PRM): Limited
+
+Metabolomics: Yes
+
+ID-based Metrics: Partial
+
+ID-free Metrics: Yes
+
+mzQC Support: No (planned)
+
+Real-time Monitoring: No
+
+Key Features: Multi-omics support; Standardized metrics; Low memory footprint; Multiple input formats
+
+---
+
+3. Tool name: MSstatsQC
+
+Description: R/Bioconductor package for longitudinal system suitability monitoring and quality control, initially for targeted SRM/MRM experiments, extended to DDA and DIA
+
+Repository/Link: https://github.com/eralpdogu/MSstatsQC and https://www.bioconductor.org/packages/release/bioc/html/MSstatsQC.html
+
+Publication Year: 2017 (v2: 2018)
+
+Active Development: Yes
+
+Platform/Language: R/Bioconductor
+
+DDA: Yes
+
+DIA: Yes (v2.0)
+
+Targeted (SRM/MRM/PRM): Yes
+
+Metabolomics: Limited
+
+ID-based Metrics: Yes
+
+ID-free Metrics: Partial
+
+mzQC Support: No
+
+Real-time Monitoring: Yes
+
+Key Features: Statistical process control; Control charts; Longitudinal monitoring; Change point analysis
+
+---
+
+4. Tool name: PeakQC
+
+Description: Omics-agnostic automated quality control software for mass spectrometry data, supporting proteomics, metabolomics, and lipidomics with ion mobility spectrometry
+
+Repository/Link: https://github.com/pnnl/IonToolPack
+
+Publication Year: 2024
+
+Active Development: Yes
+
+Platform/Language: Python (standalone)
+
+DDA: Yes
+
+DIA: Yes
+
+Targeted (SRM/MRM/PRM): Yes
+
+Metabolomics: Yes
+
+ID-based Metrics: Limited
+
+ID-free Metrics: Yes
+
+mzQC Support: No
+
+Real-time Monitoring: No
+
+Key Features: Automated outlier detection; Ion mobility support; Machine learning-based; Multi-omics
+
+---
+
+5. Tool name: pmartR
+
+Description: R package for quality control, exploratory data analysis, and statistical analysis of MS data, robust to missing data for proteomics, metabolomics, and lipidomics
+
+Repository/Link: https://github.com/pmartR/pmartR
+
+Publication Year: 2019
+
+Active Development: Yes
+
+Platform/Language: R
+
+DDA: Yes
+
+DIA: Yes
+
+Targeted (SRM/MRM/PRM): Limited
+
+Metabolomics: Yes
+
+ID-based Metrics: Yes
+
+ID-free Metrics: Limited
+
+mzQC Support: No
+
+Real-time Monitoring: No
+
+Key Features: Missing data handling; Statistical analysis; Filtering and normalization; Multi-omics
+
+---
+
+6. Tool name: PTXQC
+
+Description: R-based QC pipeline for bottom-up LC-MS data from MaxQuant, creates comprehensive QC reports with automated scoring and heatmap visualizations
+
+Repository/Link: https://github.com/cbielow/PTXQC
+
+Publication Year: 2016
+
+Active Development: Yes
+
+Platform/Language: R
+
+DDA: Yes
+
+DIA: Limited
+
+Targeted (SRM/MRM/PRM): No
+
+Metabolomics: No
+
+ID-based Metrics: Yes
+
+ID-free Metrics: Limited
+
+mzQC Support: Partial
+
+Real-time Monitoring: No
+
+Key Features: MaxQuant integration; Automated scoring; Comprehensive reports; Heat map visualization
+
+---
+
+7. Tool name: QC4Metabolomics
+
+Description: Real-time and retrospective quality control monitoring software for untargeted metabolomics data with web dashboard interface
+
+Repository/Link: https://github.com/stanstrup/QC4Metabolomics
+
+Publication Year: 2024
+
+Active Development: Yes
+
+Platform/Language: R/Shiny
+
+DDA: Limited
+
+DIA: Limited
+
+Targeted (SRM/MRM/PRM): Limited
+
+Metabolomics: Yes
+
+ID-based Metrics: Limited
+
+ID-free Metrics: Yes
+
+mzQC Support: No
+
+Real-time Monitoring: Yes
+
+Key Features: Real-time monitoring; User-defined compounds; Contaminant tracking; Web dashboard
+
+---
+
+8. Tool name: QCCalculator
+
+Description: OpenMS utility that calculates basic quality parameters from mass spectrometry runs and subsequent analysis data
+
+Repository/Link: https://tools.westgard.com/qccalculator.html
+
+Publication Year: 2014
+
+Active Development: Yes
+
+Platform/Language: C++ (OpenMS)
+
+DDA: Yes
+
+DIA: Yes
+
+Targeted (SRM/MRM/PRM): Limited
+
+Metabolomics: Yes
+
+ID-based Metrics: Yes
+
+ID-free Metrics: Yes
+
+mzQC Support: Yes (via OpenMS)
+
+Real-time Monitoring: No
+
+Key Features: Basic QC metrics; qcML export; OpenMS integration
+
+---
+
+9. Tool name: QCactus
+
+Description: Tool for DIA-PASEF data quality control from Bruker timsTOF instruments
+
+Repository/Link: https://github.com/csmc-vaneykjlab/qcactus
+
+Publication Year: 2023
+
+Active Development: Yes
+
+Platform/Language: Python
+
+DDA: Limited
+
+DIA: Yes
+
+Targeted (SRM/MRM/PRM): No
+
+Metabolomics: No
+
+ID-based Metrics: Yes
+
+ID-free Metrics: Limited
+
+mzQC Support: No
+
+Real-time Monitoring: No
+
+Key Features: timsTOF specific; DIA-PASEF support
+
+---
+
+10. Tool name: QCeltis
+
+Description: Python package for automated QC analysis across proteomics workflow, particularly for large-scale DIA experiments
+
+Repository/Link: https://github.com/csmc-vaneykjlab/Qceltis
+
+Publication Year: 2025
+
+Active Development: Yes
+
+Platform/Language: Python
+
+DDA: Limited
+
+DIA: Yes
+
+Targeted (SRM/MRM/PRM): No
+
+Metabolomics: No
+
+ID-based Metrics: Yes
+
+ID-free Metrics: Limited
+
+mzQC Support: No
+
+Real-time Monitoring: No
+
+Key Features: DIA-focused; Batch visualization; Interactive plots
+
+---
+
+11. Tool name: QCloud/QCloud2
+
+Description: Cloud-based quality control system for automatic data collection, processing, and longitudinal instrument evaluation with web interface
+
+Repository/Link: https://github.com/proteomicsunitcrg/Qcloud and https://github.com/proteomicsunitcrg/qcloud2-pipeline
+
+Publication Year: 2018 (v2: 2021)
+
+Active Development: Yes
+
+Platform/Language: Web-based/Cloud
+
+DDA: Yes
+
+DIA: Yes
+
+Targeted (SRM/MRM/PRM): Yes
+
+Metabolomics: No
+
+ID-based Metrics: Yes
+
+ID-free Metrics: Yes
+
+mzQC Support: No
+
+Real-time Monitoring: Yes
+
+Key Features: Cloud-based; Multi-instrument support; Automated processing; Web interface
+
+---
+
+12. Tool name: QuaMeter
+
+Description: Multivendor performance metrics tool for LC-MS/MS proteomics, provides ID-based and ID-free quality metrics
+
+Repository/Link: https://pubs.acs.org/doi/10.1021/ac300629p and part of https://proteowizard.sourceforge.io/projects.html
+
+Publication Year: 2012
+
+Active Development: Limited
+
+Platform/Language: C++/Command-line
+
+DDA: Yes
+
+DIA: Limited
+
+Targeted (SRM/MRM/PRM): Limited
+
+Metabolomics: No
+
+ID-based Metrics: Yes
+
+ID-free Metrics: Yes
+
+mzQC Support: No
+
+Real-time Monitoring: No
+
+Key Features: Multivendor support; ID-based and ID-free metrics; Widely cited reference tool
+
+---
+
+13. Tool name: Rapid QC-MS
+
+Description: Automated interactive dashboard for real-time assessment of LC-MS/MS data quality using internal, external, and reference standards
+
+Repository/Link: https://github.com/czbiohub-sf/Rapid-QC-MS
+
+Publication Year: 2024
+
+Active Development: Yes
+
+Platform/Language: Python/Web dashboard
+
+DDA: Yes
+
+DIA: Yes
+
+Targeted (SRM/MRM/PRM): Yes
+
+Metabolomics: Yes
+
+ID-based Metrics: Yes
+
+ID-free Metrics: Yes
+
+mzQC Support: No
+
+Real-time Monitoring: Yes
+
+Key Features: Real-time dashboard; Multiple standard types; Interactive visualizations
+
+---
+
+14. Tool name: SIMPATIQCO
+
+Description: Server-based software suite for monitoring LC-MS performance metrics on Orbitrap instruments with web-based visualization
+
+Repository/Link: http://ms.imp.ac.at/?goto=simpatiqco
+
+Publication Year: 2013
+
+Active Development: Limited
+
+Platform/Language: Web-based (Thermo only)
+
+DDA: Yes
+
+DIA: Yes
+
+Targeted (SRM/MRM/PRM): No
+
+Metabolomics: No
+
+ID-based Metrics: Yes
+
+ID-free Metrics: Yes
+
+mzQC Support: Yes
+
+Real-time Monitoring: Yes
+
+Key Features: Orbitrap-specific; Web visualization; Automated uploads; Longitudinal tracking
+
+---
+
+15. Tool name: Yamato
+
+Description: SWATH-QC metrics tool for monitoring data-independent acquisition (DIA/SWATH) data quality, focusing on peptide-level quality control metrics
+
+Repository/Link: https://github.com/PaulBrack/Yamato
+
+Publication Year: 2020
+
+Active Development: Yes
+
+Platform/Language: C#/.NET
+
+DDA: Yes
+
+DIA: Yes
+
+Targeted (SRM/MRM/PRM): Yes
+
+Metabolomics: No
+
+ID-based Metrics: Yes
+
+ID-free Metrics: Yes
+
+mzQC Support: Yes
+
+Real-time Monitoring: No
+
+Key Features: Fast forward-only XML parsing; mzQC serialization; Transition library deserialization (Thermo, Skyline, TraML); SwaMe and Prognosticator metric libraries
+
+---
+
+16. Tool name: QC-ART
+
+Description: Real-time quality control assessment tool for MS-based proteomics data to dynamically flag instrument or sample quality issues
+
+Repository/Link: https://pmc.ncbi.nlm.nih.gov/articles/PMC6126382/
+
+Publication Year: 2018
+
+Active Development: Limited
+
+Platform/Language: Python/R
+
+DDA: Yes
+
+DIA: Yes
+
+Targeted (SRM/MRM/PRM): Limited
+
+Metabolomics: No
+
+ID-based Metrics: Yes
+
+ID-free Metrics: Limited
+
+mzQC Support: No
+
+Real-time Monitoring: Yes
+
+Key Features: Real-time flagging; Machine learning; Drift detection
+
+---
+
+17. Tool name: QuiC
+
+Description: LC-MS proteomics monitoring software from Biognosys that generates real-time quality control readouts with iRT peptides
+
+Repository/Link: https://biognosys.com/software/quic/ and https://biognosys.com/resources/quic-manual/
+
+Publication Year: 2020
+
+Active Development: Yes
+
+Platform/Language: Commercial software
+
+DDA: Yes
+
+DIA: Yes
+
+Targeted (SRM/MRM/PRM): Yes
+
+Metabolomics: No
+
+ID-based Metrics: Yes
+
+ID-free Metrics: Yes
+
+mzQC Support: No
+
+Real-time Monitoring: Yes
+
+Key Features: iRT peptides; Commercial support; Integration with Biognosys products
+
+---
+
+18. Tool name: pmultiqc
+
+Description: Quality control tool integrated in quantms pipeline for DDA and DIA proteomics experiments
+
+Repository/Link: https://github.com/bigbio/pmultiqc
+
+Publication Year: 2023
+
+Active Development: Yes
+
+Platform/Language: Python (Nextflow)
+
+DDA: Yes
+
+DIA: Yes
+
+Targeted (SRM/MRM/PRM): No
+
+Metabolomics: No
+
+ID-based Metrics: Yes
+
+ID-free Metrics: Limited
+
+mzQC Support: No
+
+Real-time Monitoring: No
+
+Key Features: Nextflow integration; Multi-platform
+
+---
+
+19. Tool name: Metriculator
+
+Description: Web-based software for long-term storage and visualization of extensive performance metrics based on NIST standards
+
+Repository/Link: http://github.com/princelab/metriculator
+
+Publication Year: 2013
+
+Active Development: Limited
+
+Platform/Language: Ruby/Web interface
+
+DDA: Yes
+
+DIA: Yes
+
+Targeted (SRM/MRM/PRM): Limited
+
+Metabolomics: No
+
+ID-based Metrics: Yes
+
+ID-free Metrics: Yes
+
+mzQC Support: No
+
+Real-time Monitoring: No
+
+Key Features: NIST metrics; Web interface; Long-term storage; Outlier detection
+
+---
+
+20. Tool name: RawBeans
+
+Description: Tool for rapid visual HTML-based QC reports focused on monitoring LC-MS system performance within experiments
+
+Repository/Link: https://bitbucket.org/incpm/prot-qc/downloads
+
+Publication Year: 2016
+
+Active Development: No
+
+Platform/Language: Standalone
+
+DDA: Yes
+
+DIA: Yes
+
+Targeted (SRM/MRM/PRM): No
+
+Metabolomics: No
+
+ID-based Metrics: Limited
+
+ID-free Metrics: Yes
+
+mzQC Support: No
+
+Real-time Monitoring: No
+
+Key Features: Rapid HTML reports; Raw data focus; Visual QC
+
+---
+
+21. Tool name: McQuaC
+
+Description: Cloud-based quality control system for mass spectrometry with automated data processing and mzQC export
+
+Repository/Link: https://github.com/mpc-bioinformatics/McQuaC
+
+Publication Year: Not specified
+
+Active Development: Yes
+
+Platform/Language: Python/Web-based
+
+DDA: Yes
+
+DIA: Yes
+
+Targeted (SRM/MRM/PRM): No
+
+Metabolomics: No
+
+ID-based Metrics: Yes
+
+ID-free Metrics: Limited
+
+mzQC Support: In development
+
+Real-time Monitoring: No
+
+Key Features: Cloud-based; mzQC in development; Automated processing
+
+---
+
+22. Tool name: ProteoBench
+
+Description: Open, community-curated web platform for benchmarking and quality control of proteomics data analysis workflows with multiple modules for DDA/DIA quantification
+
+Repository/Link: https://github.com/Proteobench/ProteoBench
+
+Publication Year: 2024
+
+Active Development: Yes
+
+Platform/Language: Python/Web-based
+
+DDA: Yes
+
+DIA: Yes
+
+Targeted (SRM/MRM/PRM): Limited
+
+Metabolomics: No
+
+ID-based Metrics: Yes
+
+ID-free Metrics: Limited
+
+mzQC Support: In development
+
+Real-time Monitoring: No
+
+Key Features: Community-driven benchmarking; Multiple modules; Public results repository; Multispecies support; Workflow comparison
+
+---
+
+23. Tool name: LFQ_bout
+
+Description: R-based benchmark analysis software for validation and performance evaluation of LC-MS/MS workflows using hybrid proteome samples
+
+Repository/Link: https://pubs.acs.org/doi/pdf/10.1021/acs.jproteome.3c00531?ref=article_openPDF
+
+Publication Year: 2024
+
+Active Development: Yes
+
+Platform/Language: R
+
+DDA: Yes
+
+DIA: Yes
+
+Targeted (SRM/MRM/PRM): Limited
+
+Metabolomics: No
+
+ID-based Metrics: Yes
+
+ID-free Metrics: Yes
+
+mzQC Support: No
+
+Real-time Monitoring: No
+
+Key Features: Multispecies benchmarking; Summary statistics; Detects quantification errors; Workflow comparison
+
+---
+
+24. Tool name: LFQbench
+
+Description: R package computational benchmarking framework for label-free quantitative proteomics using hybrid proteome samples to calculate precision and accuracy metrics
+
+Repository/Link: https://github.com/IFIproteomics/LFQbench
+
+Publication Year: 2016
+
+Active Development: Limited (last update 2020)
+
+Platform/Language: R/Bioconductor
+
+DDA: Yes
+
+DIA: Limited
+
+Targeted (SRM/MRM/PRM): No
+
+Metabolomics: No
+
+ID-based Metrics: Yes
+
+ID-free Metrics: Yes
+
+mzQC Support: No
+
+Real-time Monitoring: No
+
+Key Features: Precision and accuracy metrics; Hybrid proteome analysis; Multi-tool comparison; Benchmark framework; ROC curves
+
+---
+
+25. Tool name: AutoQC
+
+Description: Automated quality control system integrated with Skyline and PanoramaWeb for longitudinal instrument performance monitoring
+
+Repository/Link: https://skyline.ms/project/home/software/Skyline/begin.view
+
+Publication Year: 2016
+
+Active Development: Yes
+
+Platform/Language: C#/.NET (Skyline)
+
+DDA: Yes
+
+DIA: Yes
+
+Targeted (SRM/MRM/PRM): Yes
+
+Metabolomics: Limited
+
+ID-based Metrics: Yes
+
+ID-free Metrics: Yes
+
+mzQC Support: No
+
+Real-time Monitoring: Yes
+
+Key Features: Vendor-neutral; Multiple acquisition techniques support; Multi-instrument tracking; Automated Skyline and Panorama integration; Statistical process control; Web browser access
+
+---
+
+26. Tool name: MSCohort
+
+Description: Comprehensive QC system for large-scale urinary proteomics data with 81 metrics for individual experiment and cohort quality evaluation
+
+Repository/Link: https://github.com/BUAA-LiuLab/MSCohort
+
+Publication Year: 2025
+
+Active Development: Yes
+
+Platform/Language: Python/Web-based
+
+DDA: Yes
+
+DIA: Yes
+
+Targeted (SRM/MRM/PRM): Limited
+
+Metabolomics: Limited
+
+ID-based Metrics: Yes
+
+ID-free Metrics: Yes
+
+mzQC Support: No
+
+Real-time Monitoring: No
+
+Key Features: 81 QC metrics; Integrates metrics from NIST, QuaMeter, DO-MS, RawBeans and others; Intra- and inter-experiment evaluation; Multi-platform comparison
+
+---
+
+27. Tool name: iDIA-QC
+
+Description: AI-empowered DIA-based quality control tool with machine learning models for automated LC and MS system evaluation
+
+Repository/Link: https://github.com/guomics-lab/iDIA-QC
+
+Publication Year: 2025
+
+Active Development: Yes
+
+Platform/Language: Python
+
+DDA: Limited
+
+DIA: Yes
+
+Targeted (SRM/MRM/PRM): No
+
+Metabolomics: No
+
+ID-based Metrics: Yes
+
+ID-free Metrics: Yes
+
+mzQC Support: No
+
+Real-time Monitoring: No
+
+Key Features: AI/ML-based QC; 15 DIA metrics; timsTOF, TripleTOF and Orbitrap support; Automated LC/MS performance prediction; DIA-NN integration; Notification system; HTML longitudinal reports
+
+---
+
+28. Tool name: SProCoP
+
+Description: Statistical Process Control in Proteomics tool integrated into Skyline for monitoring QC metrics with control charts and Pareto analysis
+
+Repository/Link: https://skyline.ms/skyts/home/software/Skyline/tools/details.view?name=SProCoP
+
+Publication Year: 2014
+
+Active Development: Limited
+
+Platform/Language: R (Skyline plugin)
+
+DDA: Yes
+
+DIA: Limited
+
+Targeted (SRM/MRM/PRM): Yes
+
+Metabolomics: No
+
+ID-based Metrics: No
+
+ID-free Metrics: Yes
+
+mzQC Support: No
+
+Real-time Monitoring: Yes
+
+Key Features: Statistical process control charts; Five ID-free metrics; Skyline integration; Real-time monitoring; Multi-peptide tracking; Vendor-neutral dashboard
+
+---
+
+29. Tool name: DO-MS
+
+Description: Data-driven Optimization of MS methods tool for interactive visualization and optimization of DDA/DIA data
+
+Repository/Link: https://github.com/SlavovLab/DO-MS
+
+Publication Year: 2019 (v2.0: 2023)
+
+Active Development: Yes
+
+Platform/Language: R/Web dashboard
+
+DDA: Yes
+
+DIA: Yes
+
+Targeted (SRM/MRM/PRM): Limited
+
+Metabolomics: No
+
+ID-based Metrics: Yes
+
+ID-free Metrics: Yes
+
+mzQC Support: No
+
+Real-time Monitoring: No
+
+Key Features: Interactive GUI; MaxQuant and DIA-NN support; Bottleneck diagnosis; Parameter optimization; Single-cell and plexDIA support; Modular and extensible
+
+---
+
+30. Tool name: PACOM
+
+Description: Proteomics Assay COMparator - Java tool for importing, comparing, and visualizing multiple proteomics experiments for data integrity and quality verification
+
+Repository/Link: https://github.com/smdb21/pacom
+
+Publication Year: 2018
+
+Active Development: Yes
+
+Platform/Language: Java
+
+DDA: Yes
+
+DIA: Yes
+
+Targeted (SRM/MRM/PRM): Limited
+
+Metabolomics: No
+
+ID-based Metrics: Yes
+
+ID-free Metrics: Limited
+
+mzQC Support: No
+
+Real-time Monitoring: No
+
+Key Features: Multi-dataset comparison; Data integration; Rich graphical representations; MIAPE/HUPO-PSI compliant; Multiple search engine support; Java standalone
+
+---
+
+31. Tool name: MQmetrics
+
+Description: R/Bioconductor package for analyzing quality and reproducibility of MaxQuant proteomics data with comprehensive PDF reports
+
+Repository/Link: https://github.com/svalvaro/MQmetrics
+
+Publication Year: 2021
+
+Active Development: Yes
+
+Platform/Language: R/Bioconductor
+
+DDA: Yes
+
+DIA: Yes
+
+Targeted (SRM/MRM/PRM): Limited
+
+Metabolomics: No
+
+ID-based Metrics: Yes
+
+ID-free Metrics: Yes
+
+mzQC Support: No
+
+Real-time Monitoring: No
+
+Key Features: MaxQuant-specific; PDF report generation; iRT peptide tracking; Contamination analysis; Reproducibility assessment; Easy single-function workflow; Bioconductor package
+
+---
+
+32. Tool name: proteoQC
+
+Description: R/Bioconductor package providing integrated pipeline for MS-based proteomics QC with HTML reports using X!Tandem search
+
+Repository/Link: https://github.com/wenbostar/proteoQC
+
+Publication Year: 2014
+
+Active Development: Limited
+
+Platform/Language: R/Bioconductor
+
+DDA: Yes
+
+DIA: Limited
+
+Targeted (SRM/MRM/PRM): No
+
+Metabolomics: Limited
+
+ID-based Metrics: Yes
+
+ID-free Metrics: Yes
+
+mzQC Support: No
+
+Real-time Monitoring: No
+
+Key Features: HTML report generation; X!Tandem integration; iTRAQ/TMT labeling efficiency; Mass accuracy summaries; Separation efficiency plots; Raw-to-report pipeline; Bioconductor package
+
+---
+
+33. Tool name: InfernoRDN
+
+Description: Windows application with R backend for comprehensive downstream data analysis including normalization, statistics, clustering, and visualization
+
+Repository/Link: https://github.com/PNNL-Comp-Mass-Spec/InfernoRDN
+
+Publication Year: 2008, Updated 2021
+
+Active Development: Yes
+
+Platform/Language: Windows/.NET with R
+
+DDA: Yes
+
+DIA: Limited
+
+Targeted (SRM/MRM/PRM): Limited
+
+Metabolomics: Yes
+
+ID-based Metrics: Yes
+
+ID-free Metrics: Limited
+
+mzQC Support: No
+
+Real-time Monitoring: No
+
+Key Features: Comprehensive statistical analysis; Diagnostic plots; Multiple normalization methods; ANOVA and clustering; Heatmaps; Peptide-to-protein rollup
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+Tool Name	Description	Repository/Link	Publication Year	Active Development	Platform/Language	DDA	DIA	Targeted (SRM/MRM/PRM)	Metabolomics	ID-based Metrics	ID-free Metrics	mzQC Support	Real-time Monitoring	Key Features
+iMonDB	"Tool suite to automatically extract, store and visualize mass spectrometer instrument parameters from raw data files, particularly for Thermo instruments"	https://github.com/bittremieux/iMonDB	2015	No	Java	Yes	Yes	No	No	No	Yes	No	Yes	Extracts instrument parameters; Monitors hardware performance; Database storage
+MsQuality	"Interoperable open-source R/Bioconductor package for calculation of standardized quality metrics, agnostic to underlying technology (proteomics, metabolomics, lipidomics)"	https://github.com/tnaake/MsQuality and https://bioconductor.org/packages/release/bioc/html/MsQuality.html	2023	Yes	R/Bioconductor	Yes	Yes	Limited	Yes	Partial	Yes	No (planned)	No	Multi-omics support; Standardized metrics; Low memory footprint; Multiple input formats
+MSstatsQC	"R/Bioconductor package for longitudinal system suitability monitoring and quality control, initially for targeted SRM/MRM experiments, extended to DDA and DIA"	https://github.com/eralpdogu/MSstatsQC and https://www.bioconductor.org/packages/release/bioc/html/MSstatsQC.html	2017 (v2: 2018)	Yes	R/Bioconductor	Yes	Yes (v2.0)	Yes	Limited	Yes	Partial	No	Yes	Statistical process control; Control charts; Longitudinal monitoring; Change point analysis
+PeakQC	"Omics-agnostic automated quality control software for mass spectrometry data, supporting proteomics, metabolomics, and lipidomics with ion mobility spectrometry"	https://github.com/pnnl/IonToolPack	2024	Yes	Python (standalone)	Yes	Yes	Yes	Yes	Limited	Yes	No	No	Automated outlier detection; Ion mobility support; Machine learning-based; Multi-omics
+pmartR	"R package for quality control, exploratory data analysis, and statistical analysis of MS data, robust to missing data for proteomics, metabolomics, and lipidomics"	https://github.com/pmartR/pmartR	2019	Yes	R	Yes	Yes	Limited	Yes	Yes	Limited	No	No	Missing data handling; Statistical analysis; Filtering and normalization; Multi-omics
+PTXQC	"R-based QC pipeline for bottom-up LC-MS data from MaxQuant, creates comprehensive QC reports with automated scoring and heatmap visualizations"	https://github.com/cbielow/PTXQC	2016	Yes	R	Yes	Limited	No	No	Yes	Limited	 Partial	No	MaxQuant integration; Automated scoring; Comprehensive reports; Heat map visualization
+QC4Metabolomics	Real-time and retrospective quality control monitoring software for untargeted metabolomics data with web dashboard interface	https://github.com/stanstrup/QC4Metabolomics	2024	Yes	R/Shiny	Limited	Limited	Limited	Yes	Limited	Yes	No	Yes	Real-time monitoring; User-defined compounds; Contaminant tracking; Web dashboard
+QCCalculator	OpenMS utility that calculates basic quality parameters from mass spectrometry runs and subsequent analysis data	https://tools.westgard.com/qccalculator.html	2014	Yes	C++ (OpenMS)	Yes	Yes	Limited	Yes	Yes	Yes	Yes (via OpenMS)	No	Basic QC metrics; qcML export; OpenMS integration
+QCactus	Tool for DIA-PASEF data quality control from Bruker timsTOF instruments	https://github.com/csmc-vaneykjlab/qcactus	2023	Yes	Python	Limited	Yes	No	No	Yes	Limited	No	No	timsTOF specific; DIA-PASEF support
+QCeltis	"Python package for automated QC analysis across proteomics workflow, particularly for large-scale DIA experiments"	https://github.com/csmc-vaneykjlab/Qceltis	2025	Yes	Python	Limited	Yes	No	No	Yes	Limited	No	No	DIA-focused; Batch visualization; Interactive plots
+QCloud/QCloud2	"Cloud-based quality control system for automatic data collection, processing, and longitudinal instrument evaluation with web interface"	https://github.com/proteomicsunitcrg/Qcloud and https://github.com/proteomicsunitcrg/qcloud2-pipeline	2018 (v2: 2021)	Yes	Web-based/Cloud	Yes	Yes	Yes	No	Yes	Yes	No	Yes	Cloud-based; Multi-instrument support; Automated processing; Web interface
+QuaMeter	"Multivendor performance metrics tool for LC-MS/MS proteomics, provides ID-based and ID-free quality metrics"	https://pubs.acs.org/doi/10.1021/ac300629p and  part of https://proteowizard.sourceforge.io/projects.html	2012	Limited	C++/Command-line	Yes	Limited	Limited	No	Yes	Yes	No	No	Multivendor support; ID-based and ID-free metrics; Widely cited reference tool
+Rapid QC-MS	"Automated interactive dashboard for real-time assessment of LC-MS/MS data quality using internal, external, and reference standards"	https://github.com/czbiohub-sf/Rapid-QC-MS	2024	Yes	Python/Web dashboard	Yes	Yes	Yes	Yes	Yes	Yes	No	Yes	Real-time dashboard; Multiple standard types; Interactive visualizations
+SIMPATIQCO	Server-based software suite for monitoring LC-MS performance metrics on Orbitrap instruments with web-based visualization	http://ms.imp.ac.at/?goto=simpatiqco	2013	Limited	Web-based (Thermo only)	Yes	Yes	No	No	Yes	Yes	Yes	Yes	Orbitrap-specific; Web visualization; Automated uploads; Longitudinal tracking
+Yamato	"SWATH-QC metrics tool for monitoring data-independent acquisition (DIA/SWATH) data quality, focusing on peptide-level quality control metrics"	https://github.com/PaulBrack/Yamato	2020		C#/.NET	Yes	Yes	Yes	No	Yes	Yes	Yes	No	"Fast forward-only XML parsing; mzQC serialization; Transition library deserialization (Thermo, Skyline, TraML); SwaMe and Prognosticator metric libraries"
+QC-ART	Real-time quality control assessment tool for MS-based proteomics data to dynamically flag instrument or sample quality issues	https://pmc.ncbi.nlm.nih.gov/articles/PMC6126382/	2018	Limited	Python/R	Yes	Yes	Limited	No	Yes	Limited	No	Yes	Real-time flagging; Machine learning; Drift detection
+QuiC	LC-MS proteomics monitoring software from Biognosys that generates real-time quality control readouts with iRT peptides	https://biognosys.com/software/quic/ and https://biognosys.com/resources/quic-manual/	2020	Yes	Commercial software	Yes	Yes	Yes	No	Yes	Yes	No	Yes	iRT peptides; Commercial support; Integration with Biognosys products
+pmultiqc	Quality control tool integrated in quantms pipeline for DDA and DIA proteomics experiments	https://github.com/bigbio/pmultiqc	2023	Yes	Python (Nextflow)	Yes	Yes	No	No	Yes	Limited	No	No	Nextflow integration; Multi-platform
+Metriculator	Web-based software for long-term storage and visualization of extensive performance metrics based on NIST standards	http://github.com/princelab/metriculator	2013	Limited	Ruby/Web interface	Yes	Yes	Limited	No	Yes	Yes	No	No	NIST metrics; Web interface; Long-term storage; Outlier detection
+RawBeans	Tool for rapid visual HTML-based QC reports focused on monitoring LC-MS system performance within experiments	https://bitbucket.org/incpm/prot-qc/downloads	2016	No	Standalone	Yes	Yes	No	No	Limited	Yes	No	No	Rapid HTML reports; Raw data focus; Visual QC
+McQuaC	Cloud-based quality control system for mass spectrometry with automated data processing and mzQC export	https://github.com/mpc-bioinformatics/McQuaC	-	Yes	Python/Web-based	Yes	Yes	No	No	Yes	Limited	In development	No	Cloud-based; mzQC in development; Automated processing
+ProteoBench	"Open, community-curated web platform for benchmarking and quality control of proteomics data analysis workflows with multiple modules for DDA/DIA quantification"	https://github.com/Proteobench/ProteoBench	2024	Yes	Python/Web-based	Yes	Yes	Limited 	No	Yes	Limited	In development	No	Community-driven benchmarking; Multiple modules; Public results repository; Multispecies support; Workflow comparison
+LFQ_bout	R-based benchmark analysis software for validation and performance evaluation of LC-MS/MS workflows using hybrid proteome samples	https://pubs.acs.org/doi/pdf/10.1021/acs.jproteome.3c00531?ref=article_openPDF	2024	Yes	R	Yes	Yes	Limited 	No 	Yes	Yes	No	No	Multispecies benchmarking; Summary statistics; Detects quantification errors; Workflow comparison
+LFQbench	R package computational benchmarking framework for label-free quantitative proteomics using hybrid proteome samples to calculate precision and accuracy metrics	https://github.com/IFIproteomics/LFQbench	2016	Limited (last update 2020)	R/Bioconductor	Yes	Limited	No 	No 	Yes	Yes	No	No	Precision and accuracy metrics; Hybrid proteome analysis; Multi-tool comparison; Benchmark framework; ROC curves
+AutoQC	Automated quality control system integrated with Skyline and PanoramaWeb for longitudinal instrument performance monitoring.	https://skyline.ms/project/home/software/Skyline/begin.view	2016	Yes	C#/.NET (Skyline)	Yes	Yes	Yes	Limited	Yes	Yes	No	Yes	Vendor-neutral; Multiple acquisition techniques support; Multi-instrument tracking; Automated Skyline and Panorama integration; Statistical process control; Web browser access
+MSCohort	Comprehensive QC system for large-scale urinary proteomics data with 81 metrics for individual experiment and cohort quality evaluation	https://github.com/BUAA-LiuLab/MSCohort	2025	Yes	Python/Web-based	Yes	Yes	Limited	Limited	Yes	Yes	No	No	"81 QC metrics; Integrates metrics from NIST, QuaMeter, DO-MS, RawBeans and others; Intra- and inter-experiment evaluation; Multi-platform comparison"
+iDIA-QC	AI-empowered DIA-based quality control tool with machine learning models for automated LC and MS system evaluation	https://github.com/guomics-lab/iDIA-QC	2025	Yes	Python	Limited	Yes	No	No	Yes	Yes	No	No	"AI/ML-based QC; 15 DIA metrics; timsTOF, TripleTOF and Orbitrap support; Automated LC/MS performance prediction; DIA-NN integration; Notification system; HTML longitudinal reports"
+SProCoP	Statistical Process Control in Proteomics tool integrated into Skyline for monitoring QC metrics with control charts and Pareto analysis	https://skyline.ms/skyts/home/software/Skyline/tools/details.view?name=SProCoP	2014	Limited	R (Skyline plugin)	Yes	Limited	Yes	No	No	Yes	No	Yes	Statistical process control charts; Five ID-free metrics; Skyline integration; Real-time monitoring; Multi-peptide tracking; Vendor-neutral dashboard
+DO-MS	Data-driven Optimization of MS methods tool for interactive visualization and optimization of DDA/DIA data	https://github.com/SlavovLab/DO-MS	2019 (v2.0: 2023)	Yes	R/Web dashboard	Yes	Yes	Limited	No	Yes	Yes	No	No	Interactive GUI; MaxQuant and DIA-NN support; Bottleneck diagnosis; Parameter optimization; Single-cell and plexDIA support; Modular and extensible
+PACOM	"Proteomics Assay COMparator - Java tool for importing, comparing, and visualizing multiple proteomics experiments for data integrity and quality verification"	https://github.com/smdb21/pacom	2018	Yes	Java 	Yes	Yes	Limited	No	Yes	Limited	No	No	Multi-dataset comparison; Data integration; Rich graphical representations; MIAPE/HUPO-PSI compliant; Multiple search engine support; Java standalone
+MQmetrics	R/Bioconductor package for analyzing quality and reproducibility of MaxQuant proteomics data with comprehensive PDF reports	https://github.com/svalvaro/MQmetrics	2021	Yes	R/Bioconductor	Yes	Yes	Limited	No	Yes	Yes	No	No	MaxQuant-specific; PDF report generation; iRT peptide tracking; Contamination analysis; Reproducibility assessment; Easy single-function workflow; Bioconductor package
+proteoQC	R/Bioconductor package providing integrated pipeline for MS-based proteomics QC with HTML reports using X!Tandem search	https://github.com/wenbostar/proteoQC	2014	Limited	R/Bioconductor	Yes	Limited	No	Limited	Yes	Yes	No	No	HTML report generation; X!Tandem integration; iTRAQ/TMT labeling efficiency; Mass accuracy summaries; Separation efficiency plots; Raw-to-report pipeline; Bioconductor package
+InfernoRDN	"Windows application with R backend for comprehensive downstream data analysis including normalization, statistics, clustering, and visualization"	https://github.com/PNNL-Comp-Mass-Spec/InfernoRDN	"2008, Updated 2021"	Yes	Windows/.NET with R	Yes	Limited	Limited	Yes	Yes	Limited	No	No	Comprehensive statistical analysis; Diagnostic plots; Multiple normalization methods; ANOVA and clustering; Heatmaps; Peptide-to-protein rollup