🚀 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.

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...

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.

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...

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

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

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

🚀 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.

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.

Template definitions (required/recommended/optional), with clear validation rules for times, units, and intervals. Fully integrated with ontologies & more important community oriented. If you want to be part of this, create an issue; do a PR.

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-...

Which Ollama model?

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.

In affinity proteomics, SomaScan and Olink, we still have a long way to go toward standardization, but even before that, we need well-defined output files from each technology. This was one of my surprises during the project. Output files vary massively across tools, platforms, etc.

You can contact pride support team. Here, the format description github.com/PRIDE-Archiv.... Facilities some times provide incomplete formats with columns that are not valid.

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...

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...

Jaajaj, I have to update the model. But to be honest we get more engage in this way; @ajbrenes.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...

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#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

I was going more in the direction that you can really review code, AI-guided 😉. Take own data, put it into the package structure, & tested really quickly with not too much effort. At the same time, you can download the paper data & perform analysis with your own tools without too much effort either

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. 🤯🚀😎

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.

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.

#quantms doubles down on #SDRF, eliminating non-standardized input parameters for greater consistency. github.com/bigbio/quant...

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

Sorry to hear that

Thanks to all collaborators and contributors, especially to @vadim-demichev.bsky.social #OpenMS team, @compomics.com team, and all the core contributors of #quantms. We now have more than 23 contributors, including @microsoft-copilot.bsky.social and other LLM tools.

Other improvements:

- Support for TMT16 & TMT18 correction matrices
- New .dia file format support + improved docs
- Continued DIA-NN & PTM workflow improvements
- ThermoRawFileParser migrated to bigbio nf-modules
- More robustness for cloud / HPC infrastructure runs

#bigdata #cloud #HPC

#onsite (onsite.quantms.org) – phosphorylation site scoring

- Multiple algorithms: #PhosphoRS, #AScore, #Luciphor
- Advanced localization & confidence assessment using pAla method from @andrewrobertjones.bsky.social group
- Reliable PTM interpretation at scale

#phosphoproteomics #PTMs #proteomics

#quantms-rescoring received a major upgrade, making it more powerful and adaptable across datasets and acquisition strategies.

- MS2 transfer learning across instruments & setups (AlphaPeptDeep)
- Improved model #DeepLC and #MS2PIP handling & fixed rescoring ranges

#machinelearning #proteomics

🚀 #quantms 1.7.0 released (#Caracas)

MS2 transfer learning, #DeepLC, #MS2PIP, #AlphaPeptDeep, advanced rescoring, and onsite phosphorylation scoring are here! 🧵

> github.com/bigbio/quant...
> docs.quantms.org/en/latest/in...
> quantms.org/home

#quantms #proteomics #massspectrometry