Yun Chiang

Excited to share the new Steering Committee of PAASTA 🎉
An ECR-driven community working to foster an open, inclusive, and collaborative space for palaeoproteomics researchers worldwide.
Looking forward to building and growing this community together 🧬

Have fun Zandra 🥳

Foundation model for mass spectrometry proteomics Mass spectrometry is the dominant technology in the field of proteomics, enabling high-throughput analysis of the protein content of complex biological samples. Due to the complexity of the instrument...

Interested in prediction tasks involving peptide mass spectra? Our foundation model uses pre-trained spectrum representations learned by a de novo sequencing model to solve many tasks better and with less data, from recognizing chimeras to separating N- and O-glycopeptides. arxiv.org/abs/2505.10848

SHARK: web server for alignment-free homology assessment for intrinsically disordered and unalignable protein regions academic.oup.com/nar...

---
#proteomics #prot-paper

Exciting news: We have released #FragPipe 23, and it's one of our biggest updates ever. Windows installer, support for TMT on Astral and timsTOF, TMT35, PTM site reports for DIA, improved Astral data handling in #MSFragger, improved diaTracer for diaPASEF data, better Skyline integration, and more!

I'm so happy to see this paper out, as it has a special place in my heart! A weird, silly idea that worked out brilliantly. If you want a serious thread about the results, read the one by @welkergroup.bsky.social. I will instead provide you with a thread about involving your dog in your research:

MSFragger-DDA+ enhances peptide identification sensitivity with full isolation window search - Nature Communications Proteomics often misses co-fragmented peptides in DDA data. Here, the authors introduce MSFragger-DDA+, a database search tool that enhances peptide identification by searching the full isolation wind...

DDA is still great for many applications, and #MSFragger-DDA+ improves peptide identification sensitivity via full isolation window search. Huge boosts in IDs, including Astral DDA! Fully integrated in #FragPipe, simply annotate your DDA files as DDA+ and RUN. www.nature.com/articles/s41...

Fast and memory efficient searching of large-scale mass spectrometry data using Tide www.biorxiv.org/cont...

---
#proteomics #prot-preprint

Laboratory Manager Codicum Project

1 of 4 We're hiring a Laboratory Manager for the CODICUM project at @UniCopenhagen to help explore medieval manuscript fragments using cutting-edge biomolecular methods!
Apply by April 13, 2025!
Link: employment.ku.dk/staff?show=1...
#LabJobs #BiomolecularScience #AncientDNA
👇

Google colab has free GPUs (T4). Instanovo now has a Hugging Face space for online predictions! CPUs still work for Casa & Insta (just slower🐢)

In following suit with @isbarchaeology.bsky.social, we have moved from our former chat platform home of Slack over to Element. More details *and* how to make the switch can be found here: www.isbarch.org/chat and from the ISBA space, you can readily find us (paasta:archaeo.social)!

InstaNovo enables diffusion-powered de novo peptide sequencing in large-scale proteomics experiments - Nature Machine Intelligence InstaNovo, a transformer-based model, and InstaNovo+, a multinomial diffusion model, enhance de novo peptide sequencing, enabling discovery of novel peptides, improved therapeutics sequencing coverage...

🎉 Big news! Our paper is out in Nature Machine Intelligence!
"InstaNovo enables diffusion-powered de novo peptide sequencing in large-scale proteomics experiments"
🔗 www.nature.com/articles/s42...
👇 Thread 🧵

Im teaching here about DIANN (DIA analysis), OpenMS and quantms analysis for DDA. We have lectures about MaxQuant, PeptideShaker, ProteomeXchange, data reuse, standards, @pride-ebi.bsky.social One week fully packed with lectures about the fundamentals of computational proteomics.

“We confirmed the workflow its exceptional stability through analysis of 1,500 quality control samples systematically interspersed among 36,000 plasma samples measured continuously over 311 days.” 🤯 🫠

Release DIA-NN 2.0 · vdemichev/DiaNN We are excited to announce DIA-NN 2.0, the most significant milestone in the history of DIA-NN development. Key Breakthroughs Proteoform Confidence mode: DIA-NN 2.0 solves the long-standing chall...

We have released DIA-NN 2.1.0, download link github.com/vdemichev/Di..., release notes github.com/vdemichev/Di....
It is a minor update, main highlights are:
- Built-in support for Thermo .raw (Windows + Linux)
- New QC metrics in PDF report & visualising trends across the experiment

Dino!!! Yay time to go to colab🙈

GitHub - smith-chem-wisc/MetaMorpheus: Proteomics search software with integrated calibration, PTM discovery, bottom-up, top-down and LFQ capabilities Proteomics search software with integrated calibration, PTM discovery, bottom-up, top-down and LFQ capabilities - smith-chem-wisc/MetaMorpheus

Free copies of MetaMorpheus available for an unlimited time. Get yours now before they are all gone!

github.com/smith-chem-w...

These are some examples of #tidyplots built-in color schemes 🌈

Feel free to create your own!

#rstats #dataviz #phd

Cheers @matthewcollins.bsky.social 🎉 It’s been fun and thanks for the custom Lego mini with an Orthrus script jumper 🐾

Limelight: An Open, Web-Based Tool for Visualizing, Sharing, and Analyzing Mass Spectrometry Data from DDA Pipelines Liquid chromatography-tandem mass spectrometry employing data-dependent acquisition (DDA) is a mature, widely used proteomics technique routinely applied to proteome profiling, protein–protein interac...

If you want a free way to organize, filter, share, QC, and visualize proteomics DDA search results you should check out Limelight. A fantastic tool spearheaded by @mriffle.bsky.social
pubs.acs.org/doi/10.1021/...

FIORA: Local neighborhood-based prediction of compound mass spectra from single fragmentation events - Nature Communications FIORA, an advanced graph neural network, enhances the simulation of tandem mass spectra by learning molecular bond-breaking patterns. The open-source algorithm generates high-quality reference spectra...

Our paper on FIORA is now officially published in @naturecomms.bsky.social! 🔓Peer-reviewed and ready to shake up mass spec predictions. ⚗️🔨💻📈

Github: github.com/BAMeScience/...
Paper: www.nature.com/articles/s41...

Many thanks to everyone involved 🙌 #MachineLearning #MassSpec #Metabolomics #FIORA

Thread 5/5: 🧬 Amber's preservation capabilities for proteins remain debated.

While promising, paleoproteomics requires exceptional methodology to distinguish genuine ancient proteins from contamination. Let's wait for peer review and independent verification. #paleoproteomics #scienceskepticism 🙂

If you're about to order an Exploris 480, Astral, or even an EasySpray source, I would either:
A) Wait for the clearance deals in the coming 6 weeks and take advantage of the deals
B) Wait until after ASMS and then update the order

One of the most significant and challenging projects of my career so far. PepCentric: a scalable computational platform utilizing novel 2-D fragment indexing for rapid peptide-centric searches, enabling proteogenomics searches against billions of spectra in seconds. www.biorxiv.org/content/10.1...

New #tidyplots cheatsheet 🤩

tidyplots.org/cheatsheet

#rstats #dataviz #phd

Entering the era of deep single-cell proteomics - Nature Methods Advances in single-cell proteomics allow quantification of half of the expressed proteome in an individual cell.

Our News & Views on the recent advances in high-coverage single-cell proteomics (on Orbitrap Astral) www.nature.com/articles/s41...

Mass-spectrometry-based proteomics: from single cells to clinical applications - Nature This Review summarizes advances in mass-spectrometry-based proteomics and explores the potential applications of these technologies in the clinic.

In our latest @Nature review with Tiannan Guo & Judith Steen, we explore how technological breakthroughs are revolutionizing MS-based proteomics: From enhanced sensitivity enabling single-cell analysis to high-throughput plasma proteomics & AI-based data interpretation
www.nature.com/articles/s41...

It’s Pokémon Day! And your terminal can evolve … into a Pokédex with some of these magical repos!
github.com/klaudiosinan...
github.com/LazoCoder/Po...

Protein degradation and growth dependent dilution substantially shape mammalian proteomes Cellular protein concentrations are maintained through a balance of synthesis and clearance. Clearance occurs through both protein degradation and growth-dependent dilution. At slow growth, clearance ...

Our study reconfigures our understanding of the mechanism cells use regulate gene expression.

What was previously reported to have little global impact now is reported to explain up to half of the variation in how protein levels are controlled. Protein degradation matters!

shorturl.at/5wPiS

Yeah have been banging my head against the wall trying to ID some ancient complex mixtures with limited peps and bad ion coverage…maybe time to go back to the drawing board and write more codes 🙈💻☠️