Yasset Perez-Riverol
@ypriverol
Team Coordinator Proteomics Services, EMBL-EBI. omics, data science, and coding Lead of bigbio projects
🚀 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.
SDRF 1.1 is almost here 🎉 Big format & tooling updates ahead. Thanks to the community! We’ll keep refining together. One key question just opened: should we remove prefixes for samples, data files & factor values? Join the discussion 👉 github.com/bigbio/prote... or let me know here.
Check the Examples, one for each platform #DIANN @maxquant.bsky.social and @pride-ebi.bsky.social complete submission. So nice!!! When you run a public #PRIDE project, go for a coffee ☕️, and you can see the plugin working.
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/...
🚀 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. 📈
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
@pride-ebi.bsky.social A resource serving the world. #OpenAccess #DataFair #Proteomics
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. 🧑💻🏝️
Want to combine MS and Olink data, and submit everything to PRIDE. Check out this benchmark study by Joshua Coon’s lab where MS and Olink data were integrated in a single analysis: pubs.acs.org/doi/10.1021/... see cross-references in @pride-ebi.bsky.social
🚨 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
Releasing crosslinks datasets from @pride-ebi.bsky.social to other #omics archives—a big step for #multiomics integration and making proteomics data more #FAIR. You can now find links from PRIDE to @egaarchive.bsky.social, #GEO, & #BioStudies via #identifiers.org & with the help of @europepmc.org
A dataset > 5 years old, that continues to be relevant every year in @pride-ebi.bsky.social. From @kusterlab.bsky.social PXD010154 (www.ebi.ac.uk/pride/archiv...). Nice to see our component for data download now in production. Thanks to Bernard for the discussion at HUPO about tracing downloads
Gilberto Domont once said something that stuck with me: 'One of the greatest privileges of being a scientist is working with friends all over the world.' 12+ years of friendship and science with Oliver and Timo, and proud to be part of the OpenMS family. Last week’s OpenMS Dev meeting, Legendary! 🚀🎉
Our chatbot is so good and not biased, If you ask where to submit the data to @pride-ebi.bsky.social or MassIVE or #ProteomeXchange, it says any of them, all are members of ProteomeXchange.
This is so bad. You can try to use #EuropePMC europepmc.org or @ebi.embl.org. I can't imagine the number of services failing because Pubmed is out. Since a long time ago, all our literature pipelines at @pride-ebi.bsky.social run against @europepmc.org
Someone was having fun with @pride-ebi.bsky.social in August 2022.
Most of this 👇 data is not public, @pride-ebi.bsky.social is trying to change that. Led by @deeptijkundu.bsky.social & our development team, we are building an Affinity Proteomics (AP) Archive. If you have AP data that you can make public, please get in contact. #FAIR #OpenData #proteomics
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.
This tweet from Andrej Karpathy is so true. When I started Software engineering, I remember the geometry of every small component in the image/figure. LLMs are not encoding all of that into one universal model.
This is where we see it in quantms.org quantms.org/baseline/tis...
hi @maccoss.bsky.social, we are trying to reanalyze datasets for different human tissues, cell lines / etc, and release some kind of expression profiles for each protein (similar to proteomicsDB). The idea is that researchers can check the expression range of a given protein in those conditions.
Highly recommended! 🎥 An inspiring tale of groundbreaking science and the journey that led to the birth of IVF. Beautifully shot with stunning views of #Cambridge. Don't miss it! 🌟 #Science