Yasset Perez-Riverol
@ypriverol.bsky.social
Team Coordinator Proteomics Services, EMBL-EBI.
omics, data science, and coding
Lead of bigbio projects
omics, data science, and coding
Lead of bigbio projects
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.
August 11, 2025 at 1:28 PM
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/...
July 15, 2025 at 6:12 AM
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
💡 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
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.
July 8, 2025 at 2:39 PM
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. 📈
Here are the statistics of his #HipSci dataset, which has remained at 2% after 6 years. 📈
July 8, 2025 at 8:37 AM
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. 📈
Here are the statistics of his #HipSci dataset, which has remained at 2% after 6 years. 📈
@slavov-n.bsky.social starting his talk on #SCP. Full house.
July 7, 2025 at 11:09 AM
@slavov-n.bsky.social starting his talk on #SCP. Full house.
June 26, 2025 at 5:46 PM
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. 🧑💻🏝️
Why else would download rates spike like it’s a secret mass spectrometry ritual? 🧙
Im preparing the team for next August. 🧑💻🏝️
June 6, 2025 at 5:35 AM
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. 🧑💻🏝️
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
June 4, 2025 at 1:45 PM
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
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
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
May 14, 2025 at 1:32 PM
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
April 23, 2025 at 6:46 PM
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! 🚀🎉
March 27, 2025 at 7:16 PM
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.
March 12, 2025 at 10:25 PM
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
March 2, 2025 at 8:48 AM
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
Beautiful day to 🏃♂️ in Cambridge.
January 25, 2025 at 12:13 PM
Beautiful day to 🏃♂️ in Cambridge.
Someone was having fun with @pride-ebi.bsky.social in August 2022.
January 14, 2025 at 2:16 PM
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
January 11, 2025 at 8:21 AM
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.
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.
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.
December 17, 2024 at 3:02 PM
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...
December 15, 2024 at 6:27 PM
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.
December 5, 2024 at 1:56 PM
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.