🚀 We're launching quantms.org — new hub for all #quantms related projects. Explore its components #pmultiqc & #ibaqpy, and check all reanalysis we're sharing with the community: quantms.org/datasets
Meet the Team and Labs behind the project
👉 quantms.org/about
#OpenSource #Proteomics #ASMS2025
Meet the Team and Labs behind the project
👉 quantms.org/about
#OpenSource #Proteomics #ASMS2025
quantms - Quantitative Mass Spectrometry Analysis
A bioinformatics best-practice analysis pipeline for Quantitative Mass Spectrometry (MS)
quantms.org
June 2, 2025 at 3:39 PM
🚀 We're launching quantms.org — new hub for all #quantms related projects. Explore its components #pmultiqc & #ibaqpy, and check all reanalysis we're sharing with the community: quantms.org/datasets
Meet the Team and Labs behind the project
👉 quantms.org/about
#OpenSource #Proteomics #ASMS2025
Meet the Team and Labs behind the project
👉 quantms.org/about
#OpenSource #Proteomics #ASMS2025
In the week of #ASMS2025, we release #quantms 1.5.0, a better structure for output folders, better error handling, and an upgrade of MSstats dependencies github.com/bigbio/quant... We called Zürich, thanks to amazing contributions from Fabian Egli, a new member of the quantms OS family.
Release 1.5.0 - Zürich · bigbio/quantms
What's Changed
Update for README.md by @imeMFK01 in #531
preparing for version 1.4.1dev by @ypriverol in #530
pmultiqc updated 0.0.27 version by @ypriverol in #537
quantms-utils 0.0.23 & sdrf-pipe...
github.com
June 2, 2025 at 1:46 PM
In the week of #ASMS2025, we release #quantms 1.5.0, a better structure for output folders, better error handling, and an upgrade of MSstats dependencies github.com/bigbio/quant... We called Zürich, thanks to amazing contributions from Fabian Egli, a new member of the quantms OS family.
🚀 Attention DIA/DDA proteomics users! Whether you're using #DIA-NN, #MaxQuant, #quantms, or any tool that outputs mzIdentML and mzML, the NEW pmultiqc v0.0.29 is here!
💡 Create stunning, shareable HTML reports for your collaborators in seconds.
✨ Try pmultiqc.quantms.org Examples👇
#Proteomics #QC
💡 Create stunning, shareable HTML reports for your collaborators in seconds.
✨ Try pmultiqc.quantms.org Examples👇
#Proteomics #QC
July 11, 2025 at 8:43 AM
🚀 Attention DIA/DDA proteomics users! Whether you're using #DIA-NN, #MaxQuant, #quantms, or any tool that outputs mzIdentML and mzML, the NEW pmultiqc v0.0.29 is here!
💡 Create stunning, shareable HTML reports for your collaborators in seconds.
✨ Try pmultiqc.quantms.org Examples👇
#Proteomics #QC
💡 Create stunning, shareable HTML reports for your collaborators in seconds.
✨ Try pmultiqc.quantms.org Examples👇
#Proteomics #QC
Im teaching here about DIANN (DIA analysis), OpenMS and quantms analysis for DDA. We have lectures about MaxQuant, PeptideShaker, ProteomeXchange, data reuse, standards, @pride-ebi.bsky.social One week fully packed with lectures about the fundamentals of computational proteomics.
If you’re looking to gain hands-on training in the basics of mass spectrometry and proteomics bioinformatics, then this course is for you! Make sure you’ve submitted your application by 6 April: www.ebi.ac.uk/training/eve...
Some financial assistance is available - see the course website.
🧪🧶🧬🖥️
Some financial assistance is available - see the course website.
🧪🧶🧬🖥️
March 27, 2025 at 12:57 PM
Im teaching here about DIANN (DIA analysis), OpenMS and quantms analysis for DDA. We have lectures about MaxQuant, PeptideShaker, ProteomeXchange, data reuse, standards, @pride-ebi.bsky.social One week fully packed with lectures about the fundamentals of computational proteomics.
🚀 #quantms 1.7.0 released (#Caracas)
MS2 transfer learning, #DeepLC, #MS2PIP, #AlphaPeptDeep, advanced rescoring, and onsite phosphorylation scoring are here! 🧵
> github.com/bigbio/quant...
> docs.quantms.org/en/latest/in...
> quantms.org/home
#quantms #proteomics #massspectrometry
MS2 transfer learning, #DeepLC, #MS2PIP, #AlphaPeptDeep, advanced rescoring, and onsite phosphorylation scoring are here! 🧵
> github.com/bigbio/quant...
> docs.quantms.org/en/latest/in...
> quantms.org/home
#quantms #proteomics #massspectrometry
Release 1.7.0 - Caracas · bigbio/quantms
What's Changed
Increase dev version by @ypriverol in #579
fixing of bug in msstats_tmt.R (Issue: Error in the msstats_tmt.R function parse_contrasts #577) by @kai-lawsonmcdowall in #578
Pass corre...
github.com
January 9, 2026 at 2:42 PM
🚀 #quantms 1.7.0 released (#Caracas)
MS2 transfer learning, #DeepLC, #MS2PIP, #AlphaPeptDeep, advanced rescoring, and onsite phosphorylation scoring are here! 🧵
> github.com/bigbio/quant...
> docs.quantms.org/en/latest/in...
> quantms.org/home
#quantms #proteomics #massspectrometry
MS2 transfer learning, #DeepLC, #MS2PIP, #AlphaPeptDeep, advanced rescoring, and onsite phosphorylation scoring are here! 🧵
> github.com/bigbio/quant...
> docs.quantms.org/en/latest/in...
> quantms.org/home
#quantms #proteomics #massspectrometry
Thanks to the incredible work of @enryh.bsky.social, now #quantms is part of #ProteoBench. You can benchmark DDA LFQ data within ProteoBench using proteomicLFQ (#OpenMS algorithm) using quantms and ProteoBench. #OpenData #OpenSource @eubic-ms.org 🔥🚀
proteobench.readthedocs.io/en/stable/av...
proteobench.readthedocs.io/en/stable/av...
DDA quantification - precursor ions — ProteoBench documentation
proteobench.readthedocs.io
March 12, 2025 at 9:38 AM
Thanks to the incredible work of @enryh.bsky.social, now #quantms is part of #ProteoBench. You can benchmark DDA LFQ data within ProteoBench using proteomicLFQ (#OpenMS algorithm) using quantms and ProteoBench. #OpenData #OpenSource @eubic-ms.org 🔥🚀
proteobench.readthedocs.io/en/stable/av...
proteobench.readthedocs.io/en/stable/av...
We've been using the nf-core quantms for years, @willfondrie.com and @jspaezp.bsky.social contributed as we were getting it set up and debugged for our use cases. github.com/bigbio/quantms
April 30, 2026 at 1:55 PM
We've been using the nf-core quantms for years, @willfondrie.com and @jspaezp.bsky.social contributed as we were getting it set up and debugged for our use cases. github.com/bigbio/quantms
What a great tool. I use DeepLC in #quantms, in all our relanalysis, proteogenomics, and it works out of the box. Great work from @robbinbouwmeester.bsky.social and compomics team
New in DeepLC! Ability to deal with wild, weird, and wobbly LC setups or peptide modifications. This ability is possible with transfer learning; where only a minimal amount of training peptides are needed for accurate retention time predictions.
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
DeepLC introduces transfer learning for accurate LC retention time prediction and adaptation to substantially different modifications and setups
While LC retention time prediction of peptides and their modifications has proven useful, widespread adoption and optimal performance are hindered by variations in experimental parameters. These varia...
www.biorxiv.org
June 4, 2025 at 7:15 PM
What a great tool. I use DeepLC in #quantms, in all our relanalysis, proteogenomics, and it works out of the box. Great work from @robbinbouwmeester.bsky.social and compomics team
Running DIA-NN in the cloud? The quantms workflow is compatible with any cloud / HPC platform that supports nextflow, and recently also supports DIA-NN 2.0-series (huge thanks to @ypriverol.bsky.social and his team).
In the week of #ASMS2025, we release #quantms 1.5.0, a better structure for output folders, better error handling, and an upgrade of MSstats dependencies github.com/bigbio/quant... We called Zürich, thanks to amazing contributions from Fabian Egli, a new member of the quantms OS family.
Release 1.5.0 - Zürich · bigbio/quantms
What's Changed
Update for README.md by @imeMFK01 in #531
preparing for version 1.4.1dev by @ypriverol in #530
pmultiqc updated 0.0.27 version by @ypriverol in #537
quantms-utils 0.0.23 & sdrf-pipe...
github.com
June 2, 2025 at 2:04 PM
Running DIA-NN in the cloud? The quantms workflow is compatible with any cloud / HPC platform that supports nextflow, and recently also supports DIA-NN 2.0-series (huge thanks to @ypriverol.bsky.social and his team).
🚀 quantmsdiann v2.0.0 ("Rome") is out!
- Support for ALL versions of #DIANN and DDA/DIA.
- All fancy/advanced parameters InfinDIA; fine-tuning
- 🛠️ github.com/bigbio/quant...
- 📃 quantmsdiann.quantms.org
Thanks to @vadim-demichev.bsky.social for the support and the entire #quantms family.
- Support for ALL versions of #DIANN and DDA/DIA.
- All fancy/advanced parameters InfinDIA; fine-tuning
- 🛠️ github.com/bigbio/quant...
- 📃 quantmsdiann.quantms.org
Thanks to @vadim-demichev.bsky.social for the support and the entire #quantms family.
April 20, 2026 at 9:14 AM
🚀 quantmsdiann v2.0.0 ("Rome") is out!
- Support for ALL versions of #DIANN and DDA/DIA.
- All fancy/advanced parameters InfinDIA; fine-tuning
- 🛠️ github.com/bigbio/quant...
- 📃 quantmsdiann.quantms.org
Thanks to @vadim-demichev.bsky.social for the support and the entire #quantms family.
- Support for ALL versions of #DIANN and DDA/DIA.
- All fancy/advanced parameters InfinDIA; fine-tuning
- 🛠️ github.com/bigbio/quant...
- 📃 quantmsdiann.quantms.org
Thanks to @vadim-demichev.bsky.social for the support and the entire #quantms family.
🚀 Release Day Alert! The brand-new #pmultiqc service is LIVE: www.ebi.ac.uk/pride/servic... 🎉 Instantly generate QC reports for #quantms, #DIANN, #MaxQuant & @pride-ebi.bsky.social datasets. Reviewing @pride-ebi.bsky.social quality data is super easy — all powered by pmultiqc: pmultiqc.quantms.org 🔥
PMultiQC - Proteomics MultiQC Analysis
www.ebi.ac.uk
August 11, 2025 at 12:32 PM
🚀 Release Day Alert! The brand-new #pmultiqc service is LIVE: www.ebi.ac.uk/pride/servic... 🎉 Instantly generate QC reports for #quantms, #DIANN, #MaxQuant & @pride-ebi.bsky.social datasets. Reviewing @pride-ebi.bsky.social quality data is super easy — all powered by pmultiqc: pmultiqc.quantms.org 🔥
We love quantms!! Amazing resource, and open source of course!
September 10, 2025 at 2:28 PM
We love quantms!! Amazing resource, and open source of course!
I have to say, none of this could have happened without DIANN. No moving to quantms + DIANN version 1.9.2
January 11, 2025 at 12:19 PM
I have to say, none of this could have happened without DIANN. No moving to quantms + DIANN version 1.9.2
For #quantms users: github.com/bigbio/quant...
quantmsdiann a new complete pipeline for DIA analysis. · Issue #697 · bigbio/quantms
Dear quantms community, The quantms team has been working hard to build a fully independent pipeline for DIA-NN and DIA analysis. This effort is driven by two main reasons: 1. Keeping pace with DIA...
github.com
April 13, 2026 at 5:26 PM
For #quantms users: github.com/bigbio/quant...
🚨 New feature alert!
pmultiqc.quantms.org now supports #DIA-NN! 🎉
Just drop in your diann_report.tsv, run quantms-utils, and boom 💥—beautiful summary reports for your spectra! 📊✨
Here an example: pmultiqc.quantms.org/DIANN/multiq...
Check out some sweet plots 👇 #proteomics #massspec
pmultiqc.quantms.org now supports #DIA-NN! 🎉
Just drop in your diann_report.tsv, run quantms-utils, and boom 💥—beautiful summary reports for your spectra! 📊✨
Here an example: pmultiqc.quantms.org/DIANN/multiq...
Check out some sweet plots 👇 #proteomics #massspec
May 20, 2025 at 11:00 AM
🚨 New feature alert!
pmultiqc.quantms.org now supports #DIA-NN! 🎉
Just drop in your diann_report.tsv, run quantms-utils, and boom 💥—beautiful summary reports for your spectra! 📊✨
Here an example: pmultiqc.quantms.org/DIANN/multiq...
Check out some sweet plots 👇 #proteomics #massspec
pmultiqc.quantms.org now supports #DIA-NN! 🎉
Just drop in your diann_report.tsv, run quantms-utils, and boom 💥—beautiful summary reports for your spectra! 📊✨
Here an example: pmultiqc.quantms.org/DIANN/multiq...
Check out some sweet plots 👇 #proteomics #massspec
Next year will start on 🔥 A lot of things are happening in #quantms and new developments especially to make the workflow faster and get improved resource allocation CPU/MEM/IO.
December 24, 2024 at 5:12 PM
Next year will start on 🔥 A lot of things are happening in #quantms and new developments especially to make the workflow faster and get improved resource allocation CPU/MEM/IO.
Thanks to both Ben @proteomicsnews.bsky.social & @benneely.com for a great chat on ProteomeXchange, HUPO-PSI, #quantms, formats, and PRIDE. I shared my personal view on open data, availability & standards. Feeling privileged to work at EMBL-EBI/PRIDE and grateful to keep learning from my colleagues.
This week’s #THEProteomicsShow continues to explore #AltProteomics, but this time more about the data. Ben @proteomicsnews.bsky.social and I sat down with Yasset @ypriverol.bsky.social and talked about non-mass spec data and related aspects. Find it wherever you find fine podcasts and enjoy!
August 15, 2025 at 2:37 PM
Thanks to both Ben @proteomicsnews.bsky.social & @benneely.com for a great chat on ProteomeXchange, HUPO-PSI, #quantms, formats, and PRIDE. I shared my personal view on open data, availability & standards. Feeling privileged to work at EMBL-EBI/PRIDE and grateful to keep learning from my colleagues.
Another #quantms dataset out www.ebi.ac.uk/pride/archiv... in @pride-ebi.bsky.social check how nice the SDRF looks in #PRIDE, a part of the results quantms forces the users to use well-annotated experimental designs, good for data #FAIR. Here is the paper on that dataset doi.org/10.1016/j.en...
PRIDE - PRoteomics IDEntifications Database
EMBL-EBI
www.ebi.ac.uk
May 8, 2025 at 2:46 PM
Another #quantms dataset out www.ebi.ac.uk/pride/archiv... in @pride-ebi.bsky.social check how nice the SDRF looks in #PRIDE, a part of the results quantms forces the users to use well-annotated experimental designs, good for data #FAIR. Here is the paper on that dataset doi.org/10.1016/j.en...
quantms-rescoring enables deep proteome coverage across protein quantification, immunopeptidomics, and post-translational modifications experiments. https://www.biorxiv.org/content/10.64898/2026.01.12.698877v1
January 12, 2026 at 7:46 PM
quantms-rescoring enables deep proteome coverage across protein quantification, immunopeptidomics, and post-translational modifications experiments. https://www.biorxiv.org/content/10.64898/2026.01.12.698877v1
#quantms doubles down on #SDRF, eliminating non-standardized input parameters for greater consistency. github.com/bigbio/quant...
Deprecate OpenMS experimental design format, enforce SDRF-only input by Copilot · Pull Request #639 · bigbio/quantms
Deprecate OpenMS schema as input and allow CSV/TSV/SDRF formats
Completed Changes
Update input_check subworkflow to always treat input as SDRF (remove conditional logic)
Update create_input_chan...
github.com
January 17, 2026 at 12:39 PM
#quantms doubles down on #SDRF, eliminating non-standardized input parameters for greater consistency. github.com/bigbio/quant...
This is Big for #quantms team. Let me explain some of the big improvements:
- Sage integration thanks to @michaellazear.bsky.social
- Bruker and library based DIA support thanks to @jspaezp.bsky.social
- Major improvements in LFQ pipeline and pmultiqc reports.
- Lot of bugs fixed from version 1.1.1.
- Sage integration thanks to @michaellazear.bsky.social
- Bruker and library based DIA support thanks to @jspaezp.bsky.social
- Major improvements in LFQ pipeline and pmultiqc reports.
- Lot of bugs fixed from version 1.1.1.
Pipeline release! nf-core/quantms v1.2.0 - nfcore/quantms v1.2.0 - Thimphu!
Please see the changelog: https://github.com/nf-core/quantms/releases/tag/1.2.0
Please see the changelog: https://github.com/nf-core/quantms/releases/tag/1.2.0
November 2, 2023 at 8:15 PM
This is Big for #quantms team. Let me explain some of the big improvements:
- Sage integration thanks to @michaellazear.bsky.social
- Bruker and library based DIA support thanks to @jspaezp.bsky.social
- Major improvements in LFQ pipeline and pmultiqc reports.
- Lot of bugs fixed from version 1.1.1.
- Sage integration thanks to @michaellazear.bsky.social
- Bruker and library based DIA support thanks to @jspaezp.bsky.social
- Major improvements in LFQ pipeline and pmultiqc reports.
- Lot of bugs fixed from version 1.1.1.
Some researchers get their boost from papers or grants.
My adrenaline rush comes from pull requests and seeing others use our tools.
I got two happiness shots today:
- www.nature.com/articles/s41... using #quantms
- github.com/PRIDE-Archiv... new PR to #pridepy tool
☕🔥
My adrenaline rush comes from pull requests and seeing others use our tools.
I got two happiness shots today:
- www.nature.com/articles/s41... using #quantms
- github.com/PRIDE-Archiv... new PR to #pridepy tool
☕🔥
Activity-targeted metaproteomics uncovers rare syntrophic bacteria central to anaerobic community metabolism - Nature Microbiology
An approach combining BONCAT, stable isotope probing and metaproteomics showcases the hidden metabolic interconnectivity of microorganisms within an anaerobic digestion community.
www.nature.com
October 22, 2025 at 6:55 PM
Some researchers get their boost from papers or grants.
My adrenaline rush comes from pull requests and seeing others use our tools.
I got two happiness shots today:
- www.nature.com/articles/s41... using #quantms
- github.com/PRIDE-Archiv... new PR to #pridepy tool
☕🔥
My adrenaline rush comes from pull requests and seeing others use our tools.
I got two happiness shots today:
- www.nature.com/articles/s41... using #quantms
- github.com/PRIDE-Archiv... new PR to #pridepy tool
☕🔥
Nice introduction in Chinese about quantms and what you can do with it in the quantms channel. www.youtube.com/watch?v=w3_b... #proteomics #massspectrometry #bigdata
November 27, 2023 at 8:42 AM
Nice introduction in Chinese about quantms and what you can do with it in the quantms channel. www.youtube.com/watch?v=w3_b... #proteomics #massspectrometry #bigdata
quantms-rescoring enables deep proteome coverage across protein quantification, immunopeptidomics, and post-translational modifications experiments. www.biorxiv.org/cont...
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#proteomics #prot-preprint
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#proteomics #prot-preprint
January 13, 2026 at 12:20 PM
quantms-rescoring enables deep proteome coverage across protein quantification, immunopeptidomics, and post-translational modifications experiments. www.biorxiv.org/cont...
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#proteomics #prot-preprint
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#proteomics #prot-preprint
I just saw this manuscript from @lindsaykpino.com @willfondrie.com @jspaezp.bsky.social Native, Spatiotemporal Profiling of the Global Human Regulome www.biorxiv.org/content/10.1... using #quantms. It just made my day!!! So glad hours of coding are used by others. Thanks guys
Native, Spatiotemporal Profiling of the Global Human Regulome
The regulome, comprising transcription factors, cofactors, chromatin remodelers, and other regulatory proteins, forms the core machinery by which cells interpret signals and execute gene expression pr...
www.biorxiv.org
September 10, 2025 at 2:13 PM
I just saw this manuscript from @lindsaykpino.com @willfondrie.com @jspaezp.bsky.social Native, Spatiotemporal Profiling of the Global Human Regulome www.biorxiv.org/content/10.1... using #quantms. It just made my day!!! So glad hours of coding are used by others. Thanks guys