QC tools overview

[fatemehmirzade]

This pull request adds a TSV file with an overview of QC tools.

[bittremieux]

todo: Can we format this a bit nicer, so that it looks good in the documentation? Now it's a very long page, not super useful for any reader to get an overview. Maybe use some kind of tiles, icons to indicate certain statuses, etc.

[fatemehmirzade]

You mean the .md file?
Sure
I will do it.

[cbielow]

sounds like an overview table would be nice to have?

[cbielow]

sorted by tool name:

Legend

• 🟢 Yes
• 🔴 No
• 🟡 Limited / Partial
• 🔧 In development / planned
• ⚪ Not specified

QC Tools Overview — Alphabetically Sorted

Tool	Year	Active Dev	Platform	DDA	DIA	Targeted	Metabolomics	ID-based	ID-free	mzQC	Real-time	Features
AutoQC	2016	🟢	C# /.NET (Skyline)	🟢	🟢	🟢	🟡	🟢	🟢	🔴	🟢	Automated QC for Skyline
DO-MS	2019	🟢	R / Web dashboard	🟢	🟢	🟡	🔴	🟢	🟢	🔴	🔴	QC for acquisition optimization
iDIA-QC	2025	🟢	Python	🟡	🟢	🔴	🔴	🟢	🟢	🔴	🔴	QC for DIA
iMonDB	2015	🔴	Java	🟢	🟢	🔴	🔴	🔴	🟢	🔴	🟢	QC dashboard for MS instruments
InfernoRDN	2008	🟢	Windows /.NET + R	🟢	🟡	🟡	🟢	🟢	🟡	🔴	🔴	General MS QC suite
LFQ_bout	2024	🟢	R	🟢	🟢	🟡	🔴	🟢	🟢	🔴	🔴	QC for LFQ workflows
LFQbench	2016	🟡	R/Bioconductor	🟢	🟡	🔴	🔴	🟢	🟢	🔴	🔴	LFQ benchmarking
McQuaC	⚪	🟢	Python / Web-based	🟢	🟢	🔴	🔴	🟢	🟡	🔧	🔴	QC dashboarding
Metriculator	2013	🟡	Ruby / Web interface	🟢	🟢	🟡	🔴	🟢	🟢	🔴	🔴	QC for proteomics
MsQuality	2023	🟢	R/Bioconductor	🟢	🟢	🟡	🟢	🟡	🟢	🔧	🔴	QC metrics for raw MS data
MSCohort	2025	🟢	Python / Web-based	🟢	🟢	🟡	🟡	🟢	🟢	🔴	🔴	Cohort-scale QC
MQmetrics	2021	🟢	R/Bioconductor	🟢	🟢	🟡	🔴	🟢	🟢	🔴	🔴	QC for MaxQuant
PACOM	2018	🟢	Java	🟢	🟢	🟡	🔴	🟢	🟡	🔴	🔴	QC metrics extraction
PeakQC	2024	🟢	Python	🟢	🟢	🟢	🟢	🟡	🟢	🔴	🔴	Peak-shape & chromatography QC
pmartR	2019	🟢	R	🟢	🟢	🟡	🟢	🟢	🟡	🔴	🔴	QC workflows for omics/PMI
pmultiqc	2023	🟢	Python (Nextflow)	🟢	🟢	🔴	🔴	🟢	🟡	🔴	🔴	Multi-QC reporting
ProteoBench	2024	🟢	Python / Web-based	🟢	🟢	🟡	🔴	🟢	🟡	🔧	🔴	Benchmarking framework
proteoQC	2014	🟡	R/Bioconductor	🟢	🟡	🔴	🟡	🟢	🟢	🔴	🔴	QC scoring
PTXQC	2016	🟢	R	🟢	🟡	🔴	🔴	🟢	🟡	🟡	🔴	MaxQuant QC reports
QC-ART	2018	🟡	Python / R	🟢	🟢	🟡	🔴	🟢	🟡	🔴	🟢	QC assessment toolkit
QCCalculator	2014	🟢	C++/OpenMS	🟢	🟢	🟡	🟢	🟢	🟢	🟢	🔴	Computes QC metrics in OpenMS
QCactus	2023	🟢	Python	🟡	🟢	🔴	🔴	🟢	🟡	🔴	🔴	QC metric extraction
QCeltis	2025	🟢	Python	🟡	🟢	🔴	🔴	🟢	🟡	🔴	🔴	QC processing pipeline
QC4Metabolomics	2024	🟢	R/Shiny	🟡	🟡	🟡	🟢	🟡	🟢	🔴	🟢	Metabolomics QC dashboards
QCloud / QCloud2	2018	🟢	Web-based / Cloud	🟢	🟢	🟢	🔴	🟢	🟢	🔴	🟢	Cloud-based QC monitoring
QuiC	2020	🟢	Commercial software	🟢	🟢	🟢	🔴	🟢	🟢	🔴	🟢	Vendor QC suite
QuaMeter	2012	🟡	C++ / Command-line	🟢	🟡	🟡	🔴	🟢	🟢	🔴	🔴	Legacy QC metrics
Rapid QC-MS	2024	🟢	Python / Web dashboard	🟢	🟢	🟢	🟢	🟢	🟢	🔴	🟢	Browser-based QC dashboard
RawBeans	2016	🔴	Standalone	🟢	🟢	🔴	🔴	🟡	🟢	🔴	🔴	Raw MS QC extraction
SIMPATIQCO	2013	🟡	Web-based (Thermo only)	🟢	🟢	🔴	🔴	🟢	🟢	🟢	🟢	QC for Thermo instruments
SProCoP	2014	🟡	R (Skyline plugin)	🟢	🟡	🟢	🔴	🔴	🟢	🔴	🟢	QC for SRM/PRM
Yamato	2020	🟢	C# /.NET	🟢	🟢	🟢	🔴	🟢	🟢	🟢	🔴	Visualization & QC