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.

Yasset Perez-Riverol@ypriverol.bsky.social · 12h ago

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! 🧬🚀

So easy to download data from @pride-ebi.bsky.social & #ProteomeXchange using pridepy github.com/PRIDE-Archiv.... Here is a short introduction for students youtube.com/watch?v=TiuG... generated with #GeminiNotebook #NotebookLM #OpenData

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.

github.com

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

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! 🧬🚀

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

PRIDE Database@pride-ebi.bsky.social · 3w ago

PAD000044 🚨 The Olink® Target 48 Cytokine panel is derived from human circulating MAIT cells that were exposed to a combination of different stimuli, including IL-33 and IL-12p70. 🚨 New dataset alert! 🚨

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.

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

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.

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

OK, for those that reanalyze data in proteomics #pridepy now can download not only from PRIDE but from other ProteomeXchange Partners. github.com/PRIDE-Archiv.... Really easy to configure and have control for FTP, HTTPS fallback, etc.

Release v0.0.16 - MassIVE, iProX; jPOST and ProteomeXchange · PRIDE-Archive/pridepy

What's Changed Add --version flag to CLI by @jonasscheid in #96 Minor change to have the version of the tool. by @ypriverol in #97 Add direct download support for MassIVE accessions by @ypriverol...

github.com

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.

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.

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 - 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

github.com

🚀 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.

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 ....

🚀 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.

Another nice paper using #quantms DDA and DIA link.springer.com/article/10.1.... Happy to support the community, and that our tools are used by others.

Extensive peripheral immunoglobulin repertoire analyses in people with multiple sclerosis reveal disease-specific signatures and distinct treatment effects of disease modifying drugs - Journal of Neur...

Journal of Neuroinflammation - B cells are crucial players in the pathogenesis of multiple sclerosis (MS), however, limited information is available on peripheral immunoglobulin (Ig) repertoires of...

link.springer.com

For #quantms users: github.com/bigbio/quant...

quantmsdiann a new complete pipeline for DIA analysis. · Issue #697 · bigbio/quantms

Dear quantms community, The quantms team has been working hard to build a fully independent pipeline for DIA-NN and DIA analysis. This effort is driven by two main reasons: 1. Keeping pace with DIA...

github.com

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

🚀 Introducing pyprideap — one unified Python API for #SomaScan & #Olink QC and analysis (finally!). Normalisation, LOD, DE, interactive HTML reports. Open source and community-oriented as part of the @pride-ebi.bsky.social Affinity Archive. github.com/PRIDE-Archiv... #Proteomics #OpenScience.

GitHub - PRIDE-Archive/pyprideap: pyprideap is a library to handle affinity proteomics files from PRIDE database; including reading; parsing validating and other algorithms

pyprideap is a library to handle affinity proteomics files from PRIDE database; including reading; parsing validating and other algorithms - PRIDE-Archive/pyprideap

github.com

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.

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-...

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

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.

Big PR to modify and standardize all channels in Proteomics for all quant methods; working towards more standardization in SDRF and PRIDE at the label of the samples. Feedback more than welcome: github.com/PRIDE-Archiv...

Major updates in Labels for plexDIA and TMTpro by ypriverol · Pull Request #164 · PRIDE-Archive/pride-ontology

Quantification Labeling Terms — Ontology Restructuring Summary This PR restructures all quantification labeling terms in the PRIDE CV ontology to follow a consistent pattern: is_a for taxonomy (ch...

github.com

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.

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

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

Brett Phinney@ucdproteomics.bsky.social · 6mo ago

Want to make your DIA-NN QC reports in a web browser and then go back in time to the 80's and 90's? Now you can with my completely AI vibe coded streamline app! dia-nn-qc.streamlit.app You're welcome 😜

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.

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. 🤯🚀😎