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...

#quantms doubles down on #SDRF, eliminating non-standardized input parameters for greater consistency. github.com/bigbio/quant...

Thanks to all collaborators and contributors, especially to @vadim-demichev.bsky.social #OpenMS team, @compomics.com team, and all the core contributors of #quantms. We now have more than 23 contributors, including @microsoft-copilot.bsky.social and other LLM tools.

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...

🚀 #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

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.

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
☕🔥

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...

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

One day at the Cell-Matrix workshop in London. So many discussions about FAIR principles, Cell Atlases, and metadata. A lot of interest in #quantms, our formats #SDRF #quantms.io. Thanks to Alexandra Naba for the invitation. I took a lot of comments and feedback about @pride-ebi.bsky.social .

Activity-targeted metaproteomics enhances the ecophysiological characterization of cryptic syntrophic metabolisms Syntrophic microbial consortia can contribute significantly to the activity and function of anoxic ecosystems, yet are often too rare to study their in situ physiologies using traditional molecular me...

#quantms used in metaproteomics studies www.biorxiv.org/content/10.1.... 🚀 We continue to be committed to maintaining the tool, #opensource #openaccess #openeverything. !!! So happy to see our work used by others.

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.

PMultiQC - Proteomics MultiQC Analysis

🚀 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 🔥

🚀 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

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

quantms - Quantitative Mass Spectrometry Analysis A bioinformatics best-practice analysis pipeline for Quantitative Mass Spectrometry (MS)

🚀 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

The new structure of #quantms outputs is clean, simple and highly customisable.

pipeline info, #pmultiqc reports; quant tables, SDRF configs, and spectra statistics and MS features.

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...

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.

PRIDE - PRoteomics IDEntifications Database EMBL-EBI

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...

Getting on track after a week at HUPO-PSI. Many things happening in the team at the same time. We are about to release a new version of #pmultiqc (pmultiqc.quantms.org) that supports @maxquant.bsky.social #mzIdentml + mzML and #quantms workflows. Nice MQ pmultiqc.quantms.org/PXD003133/mu...

📈 @ypriverol.bsky.social shared his experience in scalability of reprocessing with #quantms and Wout Bittremieux taught us to handle quality control. (3/5)

DDA quantification - precursor ions — ProteoBench documentation

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...

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.

Just talk for 2 hours with Timo from #OpenMS about CI/CD and #quantms integration, OpenMS timsTOFF support, our results with proteogenomics and #SAGE, and some data compression ideas. What a nice way to start the day.

In #quantms we have a final step with #MSstats (Olga Vitek) to perform downstream analysis. By default, we had some parameters in MSstas to remove low-quality features, features in few replicates etc. We now have a few complaints from users that their data doesn't produce diff proteins. 🧵

We are now more connected to other resources, including #Uniprot #ENSEMBL #ExpressionAtlas and the new one @opentargets.bsky.social. We continue performing multiple reanalyses and push data to all these resources. #quantms allow us to do a lot of these large-scale reanalyses.

If you ask chatgpt to give you 5 proteins highly expressed in the human heart it responds: P12883, P45379, P01160, P68032, P10916. #quantms absolute expression profiles agreed 100% with chatgpt. quantms.org/ae/tissues?p...

But I want to be clear about something while you can run #quantms in your PC, it is mainly desing for cloud and HPC and really large datasets. For PC analyses you can run DIANN or OpenMS, or SAGE and is better I guess.

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.