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Yasset Perez-Riverol @ypriverol.bsky.social · 25d

If you need more than 3k is not done for desktop;😃

Yasset Perez-Riverol @ypriverol.bsky.social · 25d

I was in that position last week. I just got a gaming laptop this week. I will let you know if Casanovo and other GPU-based algorithms work. For spectrum prediction tools like MS2PIP, you can use CPU, I have never tried de novo

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Yasset Perez-Riverol @ypriverol.bsky.social · 26d

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...

Release v0.0.34 - DIANN and MaxDIA support · bigbio/pmultiqc

What's Changed fix bugs and add plots for mzid by @yueqixuan in #295 Multiple fix in mzidentml by @ypriverol in #296 MaxQuant: Fix NaN intensity errors by @cbielow in #304 Fix bug in proteobench_u...

github.com

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Yasset Perez-Riverol @ypriverol.bsky.social · 28d

Asking here for others, does anyone have the same issue in USA?, please share to know if that is the case, just to know how many are in the same case. @nesvilab.bsky.social I will give priority to this. For you the entire database in block, even searching?

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Yasset Perez-Riverol @ypriverol.bsky.social · 28d

@nesvilab.bsky.social I can bring the topic to proteomeXchange and implement a system, a mechanism is PRIDE to replicate the data from iProx into PRIDE for the users, then you will be downloading from PRIDE. Let me know if that could be useful? It would be good to know the reason why it is blocked.

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Reposted by Yasset Perez-Riverol

Lindsay K Pino @lindsaykpino.com · 28d

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

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Yasset Perez-Riverol @ypriverol.bsky.social · 28d

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

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Reposted by Yasset Perez-Riverol

Magnus Palmblad @magnuspalmblad.bsky.social · 29d

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).

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Yasset Perez-Riverol @ypriverol.bsky.social · Sep 5

We recommend zipping each independent .d folder in its own zip file, and the tool should enable them to annotate them as RAW. Not all together in one zip, but one zip per .d. This is better for downloading, statistics etc.

Yasset Perez-Riverol @ypriverol.bsky.social · Sep 5

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...

Release v2.10.4 · PRIDE-Archive/px-submission-tool

🚀 PX Submission Tool v2.10.4 📦 Downloads Versioned: px-submission-tool-v2.10.4.zip Latest: px-submission-tool-latest.zip (always points to current version) 🔗 Universal Links Latest Release: http...

github.com

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Yasset Perez-Riverol @ypriverol.bsky.social · Sep 1

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 .

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Yasset Perez-Riverol @ypriverol.bsky.social · Aug 30

#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.

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...

www.biorxiv.org

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Yasset Perez-Riverol @ypriverol.bsky.social · Aug 17

Honestly is also about the metadata, and the title selected originally by the users I guess. I was using a tiny model before, I will dedicate sometime to see if a better CPU model is available

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Yasset Perez-Riverol @ypriverol.bsky.social · Aug 17

Im updating the model this week. Btw, I notice that the model mistakes increase interactions 😉

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Yasset Perez-Riverol @ypriverol.bsky.social · Aug 15

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.

Ben Neely @benneely.com · Aug 15

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!

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Yasset Perez-Riverol @ypriverol.bsky.social · Aug 11

Do you take holidays? @benneely.com @proteomicsnews.bsky.social, and I, don't. 😎

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Reposted by Yasset Perez-Riverol

ProteomicsNews (Ben Orsburn) @proteomicsnews.bsky.social · Aug 11

Sneakpeak at this week's episode!

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Yasset Perez-Riverol @ypriverol.bsky.social · Aug 11

This is an early release, go easy on it, but happy to take issues here: github.com/bigbio/pmult...

GitHub - bigbio/pmultiqc: A library for QC report based on MultiQC framework

A library for QC report based on MultiQC framework - bigbio/pmultiqc

github.com

Yasset Perez-Riverol @ypriverol.bsky.social · Aug 11

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.

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Yasset Perez-Riverol @ypriverol.bsky.social · Aug 11

🚀 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

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Yasset Perez-Riverol @ypriverol.bsky.social · Aug 5

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.

Reposted by Yasset Perez-Riverol

Steffen Neumann @sneumann.bsky.social · Jul 16

🚀 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...

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Reposted by Yasset Perez-Riverol

Fengchao @fcyucn.bsky.social · Jul 15

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!

Yasset Perez-Riverol @ypriverol.bsky.social · Jul 15

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/...

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Yasset Perez-Riverol @ypriverol.bsky.social · Jul 15

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/...

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Yasset Perez-Riverol @ypriverol.bsky.social · Jul 12

Well, someone has to do the job 😉