QC tools

docs/pages/QC_Tools.tsv

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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