Harrison Specht

Exciting new #Zebrafish research from the #WeinsteinLab, led by Jong Park!
“Specialized gas-exchange endothelium of the zebrafish gill” —

www.biorxiv.org/content/10.6...

Amazing to see red blood cells moving through the gills! Don’t forget to check out the supplemental movies ;-)

The 2026 Chemistry Faculty Jobs List

The 2026 Chemistry Faculty Jobs List has 330 tenure-track positions and 47 teaching-only positions: docs.google.com/spreadsheets... #facultychemjobs #chemsky #chemchat ⚗️🧪

one of the coolest things about ChatGPT is how you can actually just never use it. you can fill your whole entire life with simply not once using it. it's incredible.

So which AI peer review tool can tell me authors gave all the Code to make their Figures? 🧪

✅ Code uses right functions for plot type in Figure?

✅ Is there a 1:1 correspondence between Code and Figures?

❌ Automated reanalysis --> IMO this requires expert knowledge to know the data wasn't hacked

Proteomics + an elegant mechanism! I cannot wait to read in full! #proteomics #TeamMassSpec 🧪

No one is immune to aging but what exactly happens to our immune system as it ages? @thibaultcolombani.bsky.social takes a molecular dive into the immune system and talks about understanding age-induced immune altercations through single-cell proteomics.

www.youtube.com/watch?v=WUU1...

Barcodes and the future of measuring proteins - PTI - Parallel Squared Technology Institute Increasing the rate at which we measure proteins increases the rate at which we can discover new biology and solve disease.

Check out our new blog post on barcodes and the future of quickly measuring proteins for biomedical research! 🧪

www.parallelsq.org/blog/barcode...

Koina: Democratizing machine learning for proteomics research - Nature Communications Koina is an open-source, online platform that simplifies access to machine learning models in proteomics, enabling easier integration into analysis tools and helping researchers adopt and reuse ML mod...

Exited to share our latest work! Out now in @natcomms.nature.com

Koina aims to transform how #proteomics uses machine learning. You no longer need to be a tech wizard to use ML and now can easily run #ML models. Integrated with FragPipe, Skyline and EncyclopeDIA!

www.nature.com/articles/s41...

May Institute on Computation & Statistics for MS and Proteomics is taking great shape. Fantastic new and repeat instructors and lots of new content. We are grateful to our sponsors Fragmatics and Biognosys. Keep an eye on the website computationalproteomics.khoury.northeastern.edu

🧪 Two of my favorite sci-things!

Already run q.e.d on my latest bioRxiv submissions :)

R/Bioconductor for Mass Spectrometry and Proteomics Dates 17-19 November 2025 To foster international participation, this course will be held online

🎓 Upcoming Online Course: R/Bioconductor for Mass Spectrometry & Proteomics

📅 November 17–19, 2025

Join Dr Laurent Gatto for a hands-on course on mass spectrometry–based proteomics analysis using R and Bioconductor.

👉 Register & learn more: www.physalia-courses.org/courses-work...

Thanks!

Not yet, but I wouldn't expect huge benefits over the default LF models unless you are trying some exotic chromatography, collision energies or additives.

Fantastic Proteins and Where to Find Them - PTI - Parallel Squared Technology Institute Here, we will offer a tutorial for how to build instrument-specific spectral library predictions for PSMtag modified peptides using DIA-NN 2.3.0. This will allow users to do more accurate proteome-wid...

#Proteomics Tutorial drop!

Had fun writing this, ping me if interested in other search engines. #TeamMassSpec

www.parallelsq.org/blog/fantast...

How to design 1000-plex mass tags using the differential mass defect Multiplexing samples in mass spectrometry-based proteomics has long been accomplished by isotopologues of small molecules. These chemically-identical "mass tags" conjugate to peptides to encode sample...

A bit dense, but the important message is dead simple:

We got to cite the E = mc² paper!

Kidding :)

The important part is that combinations of isotopes unlock 100-1000x gains in protein measurement speed.

Here's how: www.biorxiv.org/content/10.1...

#TeamMassSpec #Proteomics 🧪

🧪🔥🔥🔥

AlphaDIA enables DIA transfer learning for feature-free proteomics - Nature Biotechnology An open-source platform for data-independent acquisition proteomics adapts predicted libraries to experimental settings.

AlphaDIA enables DIA transfer learning for feature-free proteomics - @mannlab.bsky.social @jalew188.bsky.social go.nature.com/4qmEQMM

🧪 I tried it and I'm happily surprised!

As long as it doesn't boil the oceans, I would run it on all new papers I read for:

🌎 Mapping the interrelatedness of claims -- papers are so complex now!

🔬 Calling out potential gaps -- so that I can know the experiments were properly controlled.

YouTube video by Parallel Squared Technology Institute Jmod: Joint modeling of mass spectra for empowering mulitplexed DIA proteomics | Kevin McDonnell

And, we are back with another presentation from this year's Research Fest. PTI's Senior Computational Scientist, Kevin McDonnell, talks about developing joint modeling (aka JMod) of mass spectra for empowering multiplexed DIA proteomics.

www.youtube.com/watch?v=plK4...

Yes! This 100x over.

Well color me curious... and perfect choice of portrait 😂

Good read, I learned a few new facts!

Where's the paragraph explaining WHY AI will not replace scientists ? 🧪

The general audience would benefit from this.

🧪

a teddy bear is standing in front of a blue door ALT: a teddy bear is standing in front of a blue door

Increasingly in favour of the Marie Kondo approach to collaborations in science. Does your collaborator spark joy? If not ➡️♻️🗑️

No one's skills or knowledge are so unique or indispensable that they get to make your day miserable with every interaction. 🧪🔭

Parquet fans unite!

mzPeak: Designing a Scalable, Interoperable, and Future-Ready Mass Spectrometry Data Format Advances in mass spectrometry (MS) instrumentation, including higher resolution, faster scan speeds, and improved sensitivity, have dramatically increased the data volume and complexity. The adoption of imaging and ion mobility further amplifies these challenges in proteomics, metabolomics, and lipidomics. Current open formats such as mzML and imzML struggle to keep pace due to large file sizes, slow data access, and limited metadata support. Vendor-specific formats offer faster access but lack interoperability and long-term archival guarantees. We here lay the groundwork for mzPeak, a next-generation community data format designed to address these challenges and support high-throughput, multidimensional MS workflows. By adopting a hybrid model that combines efficient binary storage for numerical data and both human- and machine-readable metadata storage, mzPeak will reduce file sizes, accelerate data access, and offer a scalable, adaptable solution for evolving MS technologies. For researchers, mzPeak will support complex workflows and regulatory compliance through faster access, improved metadata, and interoperability. For vendors, it offers a streamlined, open alternative to proprietary formats. mzPeak aims to become a cornerstone of MS data management, enabling sustainable, high-performance solutions for future data types and fostering collaboration across the mass spectrometry community.

I'm a huge fan of this proposal!

If we can get vendor buy-in to an open, common format, it could bring more computational folks into the field. How can these folks be excited about #proteomics when its hard to even read the already complicated data?

pubs.acs.org/doi/10.1021/...

YouTube video by Parallel Squared Technology Institute Tags for improving peptide sequencing and throughput in sensitive proteomics | Maddy Yeh, Mark Adamo

Throwback Thursday continues with a presentation by Maddy Yeh and Mark Adamo from Research Fest: "Tags for improving peptide sequencing and throughput in sensitive proteomics".

Watch on YouTube: www.youtube.com/watch?v=jA2I...

The functional landscape of the human ubiquitinome Protein ubiquitination regulates cell biology through diverse avenues, from quality control-linked protein degradation to signaling functions such as modulating protein-protein interactions and enzyme...

new preprint: Ubiquitin is a protein modification linked with degradation but known to regulate other functions. Over 100k ubiquitination sites have been discovered and here we (@julianvangerwen.bsky.social + others) try to prioritize those most critical to the cell www.biorxiv.org/content/10.1...

Today my @nytimes.com colleagues and I are launching a new series called Lost Science. We interview US scientists who can no longer discover something new about our world, thanks to this year‘s cuts. Here is my first interview with a scientist who studied bees and fires. Gift link: nyti.ms/3IWXbiE

When that mass spectrometry data gives Patrick vibes ...

(so sorry in advance, couldn't resist)

@jasonderks.bsky.social is presenting at iSCMS! Come by this Saturday afternoon around 2pm to hear his talk: "Increasing proteomics throughput by multiplexing in the mass and time domains".

singlecellms.org?page_id=442