iiinova — where your digital self keeps evolving

Yasset Perez-Riverol @ypriverol.bsky.social · 24/09/2026

On my way to #HUPO2026, more releases are coming this week from @pride-ebi.bsky.social team, also looking foward to discuss about agentic annotation/reuse of datasets.

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Yasset Perez-Riverol @ypriverol.bsky.social · 21/09/2026

We are in #HUPO2026 mode. Check the new @pride-ebi.bsky.social web: www.ebi.ac.uk/pride/

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Yasset Perez-Riverol @ypriverol.bsky.social · 18/09/2026

We’ve annotated ~9k PRIDE datasets using SDRF Skills + LLMs: github.com/bigbio/sdrf-.... We’ve built a GitHub ecosystem to validate, report errors, and track progress. SDRFs sync directly to PRIDE. It’s also a great way to learn about LLMs and #proteomics. Have spare tokens? Just open a PR! 🚀

github.com

GitHub - bigbio/sdrf-annotated-datasets: A repository of datasets in ProteomeXchange annotated in SDRF, previously part of the specification

A repository of datasets in ProteomeXchange annotated in SDRF, previously part of the specification - bigbio/sdrf-annotated-datasets

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Yasset Perez-Riverol @ypriverol.bsky.social · 13/09/2026

Astral & TimsTOF Ultra are challenging @pride-ebi.bsky.social infrastructure.

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Reposted by Yasset Perez-Riverol

Phil W @pwilmarth.bsky.social · 12/09/2026

The science is in the selection of samples, the experimental design, and the quality of the sample prep. The LC, MS, and software can screw that up, but it has never and will never be able fix the most important parts of proteomics experiments. The "advances" are always in the wrong places.

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Yasset Perez-Riverol @ypriverol.bsky.social · 10/09/2026

The new #GitHub feature Stack is really insane!!!

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Yasset Perez-Riverol @ypriverol.bsky.social · 09/09/2026

We received the first submission today on #PRIDE: 270k raw files! 🎉 We had to squash a couple of bugs along the way (including a few Java Spring ones 😅), but we got it processed. The previous record was ~4k files. What an incredible development & curation team @pride-ebi.bsky.social has! 🚀

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Yasset Perez-Riverol @ypriverol.bsky.social · 05/09/2026

@pride-ebi.bsky.social is adding more features for filtering data; check how nicely you can query all datasets from a given PI: wwwdev.ebi.ac.uk/pride/archiv... example @mannlab.bsky.social

wwwdev.ebi.ac.uk

PRIDE - PRoteomics IDEntifications Database

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Yasset Perez-Riverol @ypriverol.bsky.social · 30/08/2026

16% of @pride-ebi.bsky.social Agentically annotated guided by multiple contributors and a community github.com/bigbio/sdrf-.... If you want to contribute, pick a disease, species, analytical method, or your own dataset and use github.com/bigbio/sdrf-... to give us a PR with annotated datasets.

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Yasset Perez-Riverol @ypriverol.bsky.social · 21/08/2026

I don't know the capabilities of AI for real thinking, but the capabilities for searching and finding data are 🤯.

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Yasset Perez-Riverol @ypriverol.bsky.social · 19/08/2026

Reading a lot about proteoforms and top-down lately. How much could the field gain from bottom-up algorithms that infer partial proteoforms, ranked PTM/variant combinations with confidence; instead of leaving the field only to Top-down for progress?

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Yasset Perez-Riverol @ypriverol.bsky.social · 05/08/2026

We need your contribution 📝; you can take the datasets from your lab or datasets of interest that do not have metadata and try to annotate them here 👇. After the annotations, you can contribute to the sdrf-annotated-datasets, which is an open collection of well-annotated #SDRF #proteomics datasets.

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Yasset Perez-Riverol @ypriverol.bsky.social · 05/08/2026

Transfer speed within China from IPROX is about 10 Mb/s; Downloading from #PRIDE in China is 50-60 Mb/s.

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Yasset Perez-Riverol @ypriverol.bsky.social · 05/08/2026

Agentic #SDRF curation is here! Use sdrf-skills (github.com/bigbio/sdrf-...) with #Claude, #Cursor, #Gemini, or #Codex to annotate and validate proteomics datasets and contribute to sdrf-annotated-datasets (github.com/bigbio/sdrf-...) Community contributions welcome! 🧬🚀

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Yasset Perez-Riverol @ypriverol.bsky.social · 16/07/2026

Don't get jealous, my dear MS friends, but now the bot is also picking #olink datasets.

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Yasset Perez-Riverol @ypriverol.bsky.social · 15/07/2026

In football, leadership and management can matter more than the players. How do you expect to protect a 1-0 lead against Argentina and Messi by putting seven defenders on the pitch for the last 30 minutes? That's asking to lose.

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Yasset Perez-Riverol @ypriverol.bsky.social · 13/07/2026

Does anyone know why: gpmdb.thegpm.org is not working?

gpmdb.thegpm.org

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Yasset Perez-Riverol @ypriverol.bsky.social · 23/06/2026

The most underrated feature of LLMs isn't productivity; it's curiosity. They let you explore ideas, ask questions, test assumptions, and draft experiments endlessly. I'm infinitely curious, and I feel like I spend all day learning.

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Yasset Perez-Riverol @ypriverol.bsky.social · 30/05/2026

Submitting an uncompressed TimsTOFF .d to an archive and doing it with 200 raw files is one of the worst ideas ever. WE are trying to formalize the file structures more: github.com/PRIDE-Archiv.... If you want to give feedback let us know

github.com

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Yasset Perez-Riverol @ypriverol.bsky.social · 18/05/2026

I love how #claude with SDRF-Skills can now pick up wrong annotations from existing datasets and cell lines: github.com/bigbio/sdrf-... #SDRF. Really powerful to annotate large-scale datasets from the public domain.

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Yasset Perez-Riverol @ypriverol.bsky.social · 12/05/2026

The single cell template for SDRF dev version is out there sdrf.quantms.org/templates/si.... If you are interested in contributing, let us know. We are trying to make single-cell proteomics data #SCP FAIR and easy to annotate.

sdrf.quantms.org

single-cell - SDRF Template

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Yasset Perez-Riverol @ypriverol.bsky.social · 04/05/2026

If you are annotating SDRFs from public proteomics data or your own submission, and you have access to #Claude; #gemini #OpenAI #Codex or ClaudeCode, you can use #SDRF-skills; really simple github.com/bigbio/sdrf-...

github.com

GitHub - bigbio/sdrf-skills: Agentic plugins to annotate SDRF using Claude; Codex; Cursor; Gemini

Agentic plugins to annotate SDRF using Claude; Codex; Cursor; Gemini - bigbio/sdrf-skills

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Yasset Perez-Riverol @ypriverol.bsky.social · 30/04/2026

🚀 SDRF Validator is LIVE! Check it out 👉 www.ebi.ac.uk/pride/servic... With #SDRF v1.1.0, we’ve rolled out tailored templates for different experiment types - from Single Cell proteomics #SCP to Crosslinking, & more. The new validator + web interface makes it easy to catch issues before submission.

ebi.ac.uk

SDRF Validator

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Yasset Perez-Riverol @ypriverol.bsky.social · 30/04/2026

Question: If the manuscript has only one author, why still use sentences like: "In this manuscript; We ..." For me, that sentence should be constructed differently or just use In this manuscript, I ....

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Yasset Perez-Riverol @ypriverol.bsky.social · 20/04/2026

🚀 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.

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Yasset Perez-Riverol @ypriverol.bsky.social · 03/04/2026

I like it when Copilot says, "Looks like humans are talking."

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Reposted by Yasset Perez-Riverol

Vadim Demichev @vadim-demichev.bsky.social · 12/03/2026

A Ground-truth validation of FDR & false localisation control in proteomics – a must-read from Stefan Tenzer’s lab! The benchmarks are quite enlightening. We are pleased to see our DIA-NN 2.0 excelling in sensitivity - often by a wide margin - while controlling FDR and false localisation rates.

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Yasset Perez-Riverol @ypriverol.bsky.social · 07/03/2026

What is coming for #SDRF is huge; we have managed in 20 templates most of the relevant experimental design in #proteomics, including non-MS; #crosslinking, #metaproteomics (soil, water, human gut), DIA/DDA; clinical metadata, oncology proteomics; and single cell #SCP github.com/bigbio/sdrf-...

github.com

GitHub - bigbio/sdrf-templates: SDRF templates and validation yaml files from specification proteomics-sample-metadata

SDRF templates and validation yaml files from specification proteomics-sample-metadata - bigbio/sdrf-templates

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Yasset Perez-Riverol @ypriverol.bsky.social · 05/03/2026

Quick question: Do you have Claude (❤️) or ChatGPT-OpenAI (🔃)? I mean, if you pay for them.

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Yasset Perez-Riverol @ypriverol.bsky.social · 03/03/2026

We’re collaborating with analysis tool providers and instrument vendors to standardize file formats for every @pride-ebi.bsky.social submission: github.com/PRIDE-Archiv... Want your voice heard? Share your feedback by opening an issue on the guidelines. github.com/PRIDE-Archiv... or PR.

github.com

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Yasset Perez-Riverol @ypriverol.bsky.social · 05/02/2026

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.

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Reposted by Yasset Perez-Riverol

PastelBio @pastelbio.bsky.social · 03/02/2026

LFQ Benchmark Dataset - Generation Beta: Assessing Modern Proteomics Instruments and Acquisition Workflows with High-Throughput LC Gradients www.biorxiv.org/cont... --- #proteomics #prot-preprint

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Yasset Perez-Riverol @ypriverol.bsky.social · 02/02/2026

We recently developed pmultiqc.quantms.org that does that for multiple tools. But I think this is the future, guys, welcome to the new era of abundance of tools, libraries, and applications, as code is ♾️X cheaper; we can all produce our own ecosystem of tools/libraries/viz components. Love it

pmultiqc.quantms.org

pmultiqc

A library for QC report based on MultiQC framework

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Yasset Perez-Riverol @ypriverol.bsky.social · 01/02/2026

As AI proliferates, expect an explosion of tools, libraries, and papers. 😰 Authors: remember that reviewers will also use AI to reproduce, benchmark, and stress-test your work. If it’s not open, reproducible, and robust, it won’t survive a cup of tea.

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Yasset Perez-Riverol @ypriverol.bsky.social · 01/02/2026

I did Software Engineering in the 20 years ago. I always remember Soft. Eng. teachers always talking about this career is not for coding, is for Soft design, Arch, Orchestration, Requirements gathering. Communication with the client, they always said code writing will be gone at some point. 🤯🚀😎

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Yasset Perez-Riverol @ypriverol.bsky.social · 30/01/2026

Just when the week is finishing, I accepted a PR to create a #bioconda package for pridepy github.com/PRIDE-Archiv.... Looks like #pridepy is now automatically integrated into pipelines. Thanks to Jonas Scheid for the PR.

github.com

GitHub - PRIDE-Archive/pridepy: Python client for PRIDE Archive Rest API.

Python client for PRIDE Archive Rest API. . Contribute to PRIDE-Archive/pridepy development by creating an account on GitHub.

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Yasset Perez-Riverol @ypriverol.bsky.social · 13/01/2026

🚀 Exciting news for PRIDE users! The new @pride-ebi.bsky.social web submission is launching in February!

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Yasset Perez-Riverol @ypriverol.bsky.social · 01/01/2026

Happy New Year! All the best to everyone. For us Cubans, the wish every year is simple: health. 🎉

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Yasset Perez-Riverol @ypriverol.bsky.social · 14/12/2025

Question for the #proteomics community 👇 What should proteomics repositories be doing today (use cases, features, research) that we’re currently missing? Would love your input—RT to reach more voices. #opendata #mass-spectrometry #proteomics

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