New release of pmultiqc v0.0.34 🚀🎉. github.com/bigbio/pmult..., highlights: - A new contributor, Chris Bielow - MaxDIA support, thanks @maxquant.bsky.social pmultiqc.quantms.org/MaxDIA/multi... - DIANN reports way deeper thanks @vadim-demichev.bsky.social pmultiqc.quantms.org/DIANN/multiq...

We love quantms!! Amazing resource, and open source of course!

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

First results from Olink Reveal: pubs.acs.org/doi/10.1021/.... Ground-truth data in PRIDE (www.ebi.ac.uk/pride/archiv...) and analysis code on OSF (osf.io/as4gv).

Major release of @pride-ebi.bsky.social submission tool: - Smarter Java setup — bundled JRE - Reliable file transfer logging with Aspera, FTP. - Clearer instructions and troubleshooting in the README - Automated releases through GitHub Actions, so updates are consistent github.com/PRIDE-Archiv...

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 .

#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.

Sneakpeak at this week's episode!

🚀 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 🔥

The @pride-ebi.bsky.social infrastructure will undergo scheduled maintenance from 19th to 21st August 2025. During this period, data submissions will remain available, but project accessions will not be released until the maintenance is complete on 21st August.

🚀 We’ve launched the new MassBank! Now live at massbank.eu & massbank.jp — redesigned with a faster backend, better search, and powerful tools for exploring & sharing mass spectral data. Enjoy the fresh experience! Feedback and ideas welcome, please post them on github.com/MassBank/Mas...

Excited to be one of the guest editors! We’re calling for papers on cutting-edge #proteomics and #metabolomics in #multiomics research. Looking forward to your submissions!

I'm co-editing a special issue at Genome Biology with @fcyucn.bsky.social: "Advances in Proteomics and Metabolomics." We're seeking innovative research that enhances the visibility and impact of #proteomics & #metabolomics in the context of #Multiomics. www.biomedcentral.com/collections/...

Im wondering if, for data that would be used for training AI models, people are annotating in peptidoforms Carboxymethyl (C)? I see some tools adding them to the peptidoforms and others not; interesting that other fixed modifications are added like TMT tags. What do you suggest?

🚀 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

Poster 37, #BSPR2025. An open-source LIMS based on SDRF by @naotgnuhp.bsky.social. Full LIMS 🤩. An Android app allow you to do even term search and selection. Really nice.

Had a chat with @ajbrenes.com at #BSPR2025 about data reuse, and how some datasets, once combined and reused for a new biological question, are absolute gold. It's always worth depositing your data. 💿 Here are the statistics of his #HipSci dataset, which has remained at 2% after 6 years. 📈

I had a great chat with a PhD student from @mtrost.bsky.social lab, Mengchun Li, about Bayesian approaches to tackle missing values in #proteomics; challenges with Limma, Perseus, KKN, and other packages are clear in proteomics; we should pay more attention to this topic. Poster 3 at #BSPR2025.

@slavov-n.bsky.social starting his talk on #SCP. Full house.

Andy talking about PTMeXchange at #BSPR2025. A collaboration between multiple teams PRIDE, Andy's Group, Uniprot and PeptideAtlas.

Running at Liverpool was fun yesterday. Git some nice pictures. #BSPR2025

On my way to #BSPR2025, is difficult to get me out of office, but BSPR is a great conference. Moving from Cambridge to Liverpool has been a 5h journey by train 😅. At least I manage to debug some of our new services at @pride-ebi.bsky.social

Best read for the weekend.

Proteomics + LaTeX lovers: does anyone have LaTeX templates for JPR, JOP, or MCP submissions? Would appreciate it!

@pride-ebi.bsky.social A resource serving the world. #OpenAccess #DataFair #Proteomics

Excited about this manuscript: Facilitating Analysis and Dissemination of Proteomics Data through Metadata Integration in MaxQuant! SDRF family keeps growing 💪 Huge shoutout to Jürgen’s team for their unwavering support of #OpenData & standards🙌 #FAIRdata #Proteomics www.biorxiv.org/content/10.1...

Hey Team Proteomics. New release of MetaMorpheus now natively supports Bruker .d files for DDA PASEF. Also now supporting .msalign as inputs. get your copy free now while they last: github.com/smith-chem-w...

🚨 Has PRIDE helped your research? Take 15 mins to tell funders why open data matters! 📊 Fill out the EMBL-EBI 2025 survey 👉 www.surveymonkey.com/r/QGFMBH8?ch... Your feedback helps keep PRIDE open, FAIR & impactful. 🙏 Please share! #FAIR #OpenData #Proteomics #MassSpectrometry #PRIDE

🚨 Has PRIDE helped your research? Take 15 mins to tell funders why open data matters! 📊 Fill out the EMBL-EBI 2025 survey 👉 www.surveymonkey.com/r/QGFMBH8?ch... Your feedback helps keep PRIDE open, FAIR & impactful. 🙏 Please share! #FAIR #OpenData #Proteomics #MassSpectrometry #PRIDE

Join us in Saint-Malo for the #EuBIC-MS session at #EuPA2025! After a short introduction, we have three exciting talks lined up, as well as an interactive discussion on open issues in computational proteomics. @eupaproteomics.bsky.social @uszkoreitju.bsky.social @harirmds.bsky.social

🚀 We’ve teamed up with #NVIDIA to help bioinformatics teams scale faster, analyze more efficiently, and simplify cloud operations 🧵 📖 Read now: hubs.la/Q03rQZx-0

Everyone talks about LLMs and AI in bioinformatics in terms of big breakthroughs. But the real impact I see is in the small things—data formatting, ID conversions, reproducibility. These tools free us up to focus on the science that truly matters.

"AI models, once feared as inscrutable black boxes threatening science’s reproducibility, have revealed themselves paradoxically as instruments of greater openness, rigor, and FAIR principles — advancing knowledge through transparency rather than obscurity." #AI #Science #FAIR #Reproducibility

1 in 100 would be amazing, specifically for those 5+ years old. Anything from 2023-2025 probably have been downloaded every year since there's so many of those AI proteomics companies popping up.

How many datasets in @pride-ebi.bsky.social do you think are actively & consistently downloaded (e.g. every year) by the community? 📦📥 - 1 in 4? - 1 in 10? - 1 in 100? And what do you think would be a good ratio for a healthy reuse ecosystem? I'm curious to hear what you think. #proteomics #FAIRdata

The PRIDE Dataset Bot 🤖 doesn’t sleep. It formats. It renders. It posts. If it sparked joy (or just didn’t break anything), smash that ❤️. Feedback fuels its ego. The PRIDE team wants to get feedback on each service we put out there. Now is the time for the Dataset Bot. 🤖

Thank you to everyone who submitted abstracts for @ukbspr.bsky.social 2025 annual conference. We had many excellent abstracts submitted, and you should have received poster/talk outcomes in the last few minutes. Reminder: registration closes NEXT FRIDAY payments.liv.ac.uk/conferences-...

We recently released a tool to help you with this. 🚀 Say hello to pridepy — your Python for grabbing data from the @pride-ebi.bsky.social! To search metadata or download files via FTP, Aspera, Globus, or S3, and is perfect for bioinfo workflows. Check it out 👉 github.com/PRIDE-Archiv...

August must be PRIDE @pride-ebi.bsky.social month for proteomics researchers 📊🧬 Why else would download rates spike like it’s a secret mass spectrometry ritual? 🧙 Im preparing the team for next August. 🧑‍💻🏝️

PXD058255 🚨 Plasma proteome profiling of 37 individual samples before and after exercise. 🚨 New dataset alert! 🚨

People tend to learn syntax, but not structure. They'll write software to scratch their own itch, but not really create it in a way that makes it easy to extend. Here's where a knowledge of patterns would make it easier to "play well with others".

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

🎉 Big news from the @pride-ebi.bsky.social Team! 🎉 We’re officially in #ASMS2025 mode and kicking things off with a major milestone: 🚀 Introducing PRIDE-AP – the first Affinity Proteomics archive! 🔗 www.ebi.ac.uk/pride/archiv... A new home for your #Olink and #SomaScan and other non-MS data.👇

In bioinformatics, having an idea is easy. Implementing it is harder. But putting it into production, reproducible, and usable by other people? That’s where 99% of projects vanish.

@magnuspalmblad.bsky.social taking accession number 9 for the PRIDE affinity proteomics archive. Early adopter of #OpenData in Affinity Proteomics; leading by example. www.ebi.ac.uk/pride/archiv...

New Preprint ... This was a bit different of a project than what we normally do for hardware comparisons. I think there is a lot of potential in the methods mentioned here for calibrating the instrument response to a common scale. Nice work by @chrhsu.bsky.social! www.biorxiv.org/content/10.1...

🚀 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

Happy to announce that the development version of DIA-NN has preliminary support for multi-column setups that allow acquiring multiple samples in the same run, in collaboration with @coonlab.bsky.social. See SynchroSep-MS poster by Noah Lancaster for the concept.

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).