Yun Chiang
@yc386.bsky.social
Proteomics data analysis 💻 + levelling up in RimWorld/BG3/coding🤖🙈
Postdoc @Cambridge ➡️ERC Pepinsure
Postdoc @Cambridge ➡️ERC Pepinsure
Reposted by Yun Chiang
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
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...
arxiv.org
May 22, 2025 at 11:49 AM
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
Reposted by Yun Chiang
SHARK: web server for alignment-free homology assessment for intrinsically disordered and unalignable protein regions academic.oup.com/nar...
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#proteomics #prot-paper
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#proteomics #prot-paper
May 21, 2025 at 7:20 PM
SHARK: web server for alignment-free homology assessment for intrinsically disordered and unalignable protein regions academic.oup.com/nar...
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#proteomics #prot-paper
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#proteomics #prot-paper
Reposted by Yun Chiang
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!
May 5, 2025 at 4:06 AM
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!
Reposted by Yun Chiang
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:
New publication! 🎉 Here you can read all about dog drool, bleach, and a probable Central Asian Neanderthal child:
doi.org/10.1016/j.ja...
doi.org/10.1016/j.ja...
April 24, 2025 at 1:16 PM
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:
Reposted by Yun Chiang
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...
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...
www.nature.com
April 9, 2025 at 1:27 PM
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...
Reposted by Yun Chiang
Fast and memory efficient searching of large-scale mass spectrometry data using Tide www.biorxiv.org/cont...
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#proteomics #prot-preprint
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#proteomics #prot-preprint
April 7, 2025 at 4:01 PM
Fast and memory efficient searching of large-scale mass spectrometry data using Tide www.biorxiv.org/cont...
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#proteomics #prot-preprint
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#proteomics #prot-preprint
Reposted by Yun Chiang
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
👇
Apply by April 13, 2025!
Link: employment.ku.dk/staff?show=1...
#LabJobs #BiomolecularScience #AncientDNA
👇
Laboratory Manager Codicum Project
employment.ku.dk
April 6, 2025 at 8:38 PM
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
👇
Apply by April 13, 2025!
Link: employment.ku.dk/staff?show=1...
#LabJobs #BiomolecularScience #AncientDNA
👇
Reposted by Yun Chiang
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)!
Chat platform · ISBA
www.isbarch.org
April 1, 2025 at 1:14 PM
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)!
Reposted by Yun Chiang
🎉 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 🧵
"InstaNovo enables diffusion-powered de novo peptide sequencing in large-scale proteomics experiments"
🔗 www.nature.com/articles/s42...
👇 Thread 🧵
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...
www.nature.com
April 1, 2025 at 7:30 AM
🎉 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 🧵
"InstaNovo enables diffusion-powered de novo peptide sequencing in large-scale proteomics experiments"
🔗 www.nature.com/articles/s42...
👇 Thread 🧵
Reposted by Yun Chiang
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.
If you’re looking to gain hands-on training in the basics of mass spectrometry and proteomics bioinformatics, then this course is for you! Make sure you’ve submitted your application by 6 April: www.ebi.ac.uk/training/eve...
Some financial assistance is available - see the course website.
🧪🧶🧬🖥️
Some financial assistance is available - see the course website.
🧪🧶🧬🖥️
March 27, 2025 at 12:57 PM
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.
Reposted by Yun Chiang
“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.” 🤯 🫠
Our PCA-N workflow featuring a neutralization step allows direct enzymatic digestion, doubles proteome depth from 5µL neat plasma, and handles 10K+ sample-preps daily. Democratizing plasma proteomics with 50K sample validation. Check it out on bioRxiv!
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
A simplified perchloric acid workflow with neutralization (PCA-N) for democratizing deep plasma proteomics at population scale
Large scale plasma proteomics studies offer tremendous potential for biomarker discovery but face significant challenges in balancing analytical depth, throughput and cost effectiveness. We present an...
www.biorxiv.org
March 27, 2025 at 9:20 AM
“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.” 🤯 🫠
Reposted by Yun Chiang
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
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
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...
github.com
March 25, 2025 at 12:04 PM
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
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
Reposted by Yun Chiang
Free copies of MetaMorpheus available for an unlimited time. Get yours now before they are all gone!
github.com/smith-chem-w...
github.com/smith-chem-w...
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
github.com
March 20, 2025 at 7:45 PM
Free copies of MetaMorpheus available for an unlimited time. Get yours now before they are all gone!
github.com/smith-chem-w...
github.com/smith-chem-w...
Reposted by Yun Chiang
These are some examples of #tidyplots built-in color schemes 🌈
Feel free to create your own!
#rstats #dataviz #phd
Feel free to create your own!
#rstats #dataviz #phd
March 17, 2025 at 8:29 PM
These are some examples of #tidyplots built-in color schemes 🌈
Feel free to create your own!
#rstats #dataviz #phd
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 🐾
March 16, 2025 at 7:56 PM
Cheers @matthewcollins.bsky.social 🎉 It’s been fun and thanks for the custom Lego mini with an Orthrus script jumper 🐾
Reposted by Yun Chiang
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/...
pubs.acs.org/doi/10.1021/...
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...
pubs.acs.org
March 12, 2025 at 12:59 AM
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/...
pubs.acs.org/doi/10.1021/...
Reposted by Yun Chiang
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
Github: github.com/BAMeScience/...
Paper: www.nature.com/articles/s41...
Many thanks to everyone involved 🙌 #MachineLearning #MassSpec #Metabolomics #FIORA
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...
www.nature.com
March 11, 2025 at 9:35 AM
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
Github: github.com/BAMeScience/...
Paper: www.nature.com/articles/s41...
Many thanks to everyone involved 🙌 #MachineLearning #MassSpec #Metabolomics #FIORA
Reposted by Yun Chiang
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 🙂
While promising, paleoproteomics requires exceptional methodology to distinguish genuine ancient proteins from contamination. Let's wait for peer review and independent verification. #paleoproteomics #scienceskepticism 🙂
March 7, 2025 at 7:47 AM
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 🙂
While promising, paleoproteomics requires exceptional methodology to distinguish genuine ancient proteins from contamination. Let's wait for peer review and independent verification. #paleoproteomics #scienceskepticism 🙂
Reposted by Yun Chiang
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
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
March 6, 2025 at 8:51 AM
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
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
Reposted by Yun Chiang
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...
March 4, 2025 at 9:09 AM
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...
Reposted by Yun Chiang
March 3, 2025 at 5:30 PM
Reposted by Yun Chiang
Our News & Views on the recent advances in high-coverage single-cell proteomics (on Orbitrap Astral) www.nature.com/articles/s41...
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.
www.nature.com
March 3, 2025 at 10:14 AM
Our News & Views on the recent advances in high-coverage single-cell proteomics (on Orbitrap Astral) www.nature.com/articles/s41...
Reposted by Yun Chiang
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...
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.
www.nature.com
February 26, 2025 at 4:22 PM
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...
www.nature.com/articles/s41...
Reposted by Yun Chiang
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...
github.com/klaudiosinan...
github.com/LazoCoder/Po...
February 27, 2025 at 6:45 PM
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...
github.com/klaudiosinan...
github.com/LazoCoder/Po...
Reposted by Yun Chiang
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
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
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 ...
www.biorxiv.org
February 25, 2025 at 5:44 PM
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
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