Shabaz Lab

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...

New chemical strategy boosts accuracy in proteomics Researchers develop a methylamine-based method that nearly eliminates peptide overlabeling in proteomics, improving accuracy in protein identification and quantitation.

Saw this amazing write up and just had to share 😉 (also is that an lcq?)

www.asbmb.org/asbmb-today/...

Didn't realise until now that 'gift' from my partner were @biognosys.bsky.social socks. Cheapo.

Carafe enables high quality in silico spectral library generation for data-independent acquisition proteomics - Nature Communications Accurate spectral libraries are essential for analyzing data-independent acquisition (DIA) proteomics data. Here, the authors present Carafe, which trains on DIA data to build experiment-specific spec...

Fantastic project led by @bo-wen.bsky.social. Excited to see the future uses of AI and transfer learning in proteomics. #massspec #proteomics
www.nature.com/articles/s41...

Music and modern languages courses suspended at University of Nottingham In a statement the institution also says it is

Very sad to see the major university in the East Midlands 'suspending' (i.e. planning to close) key courses like Modern Languages and Music and scaling back Nursing. It's a scandal that top universities are just being left to go to the wall after years of underfunding.
www.bbc.co.uk/news/article...

Wellcome Discovery Award secured for ground-breaking malaria research The Wellcome Trust gives Discovery Award to Professor Matt Higgins to support his "Molecular mechanisms of erythrocyte invasion in malaria" research

The Wellcome Trust has awarded a prestigious Discovery Award to Professor Matt Higgins to support his research on “Molecular mechanisms of erythrocyte invasion in malaria”. 👏👏👏 Read the full story: ⬇️

Knowledge! Oxford Blackwell's Norrington room

Profiling the proteome-wide selectivity of diverse electrophiles - Nature Chemistry Covalent inhibitors are powerful entities in drug discovery. Now the amino acid selectivity and reactivity of a diverse electrophile library have been assessed proteome-wide using an unbiased workflow...

How can we study target engagement and selectivity of covalent inhibitors? Which electrophilic probes are best suited to study a certain amino acid?

Our study on "Profiling the proteome-wide selectivity of diverse electrophiles" is published in Nature Chemistry.(1/7)

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

High-throughput discovery of a [4+3] dearomative cycloaddition enables dual photochemical-photophysical perturbative probing of protein function Proteins exist in multiple conformations or states, often associated with different functional capacities. The ability to selectively identify and study these states is crucial for under-standing the ...

www.biorxiv.org/content/10.1...

Fall Workshop Homepage Help us promote the workshop:

Join us Nov. 3–4 for the #ASMSFallWorkshop on Fundamentals of Instrumentation. This 2-day program offers an in-depth look at the essential technologies that drive modern mass spectrometry from ion sources to analyzers and detectors.
This is an IN-PERSON event. Register here: https://bit.ly/4okbr41

🧵(4/7)

🔬 We have put together a fascinating #Keynote #Speakers team:
• Prof. Albert Heck - @hecklab.bsky.social
• Dr. Hamish Stewart - @hamishs.bsky.social
• Prof. Olga Vitek - @olgavitek.bsky.social l
• Prof. Ron M.A. Heeren

My latest story on the multitude of reference genomes.
www.nature.com/articles/s41...

Biomolecular tracking by FIRESCAPE reveals distinct modes of clearance, damage induction and cellular uptake for extracellular histone H3 In attempting to observe the behaviour of a protein of interest in vivo, akin to other observer effects, current techniques require modifications or interventions that inherently alter the protein or ...

www.biorxiv.org/content/10.1...

Independent research fellowships leading to tenured positions at the John Innes Centre.

Repost = nice. Thank you very much!!!

Good to see better integration of (low bias) industry employees within publishing and scientific societies.

There is a point during the creation of a manuscript that I stop caring about typos, perfect language and figures. I just want it gone. Definitely not a perfectionist.

Having a great time at msandm2025.org with a great bunch of people interesting in visualizing biomolecules, together with my co-chairs @joostsnijder.bsky.social @vixklen.bsky.social & Kyle Fort. Learning so much from all posters & lectures. We thanks all participants for joining us in Utrecht.

Check out this thread from @haopengxiao.bsky.social on his recent paper! I’m happy I was able to help out on what has turned out to be a really cool story.

Does the NYT Wordle follow the zeitgeist? Some of the word choices (such as today, no 1547) seem pertinent.

Improvement of Recovery and Repeatability in Liquid Chromatography−Mass Spectrometry Analysis of Peptides Poor repeatability of peak areas is a problem frequently encountered in peptide analysis with nanoLiquid Chromatography coupled on-line with Mass Spectrometry (nanoLC−MS). As a result, quantitative an...

For larger scale (more sample or volume) we prefer 5% DMSO. Bonus it cleans system at the same time.

pubs.acs.org/doi/abs/10.1...

Found it:Peptide samples resuspended in 5% FA
or 5% FA/0.015% n-Dodecyl-β-D-maltoside (DDM) solutions were loaded on Evotip pure (samples were a few uLs)

Similiar levels to Ryan (and Jesper Olsen) i.e. very low levels (it's in the paper somewhere). We were less fussed about accumulation since we used evosep for both first and second dimension. Nevertheless, we were worried about compromising the column but at these low levels not an issue.

Also we use DDM but we don't have a nice figure but but it's cheaper!

Repurposed 3D Printer Allows Economical and Programmable Fraction Collection for Proteomics of Nanogram Scale Samples In this work, we describe the construction and application of a repurposed 3D-printer as a fraction collector. We utilize a nano-LC to ensure minimal volumes and surfaces although any LC can be coupled. The setup operates as a high-pH fractionation system capable of effectively working with nanogram scales of lysate digests. The 2D RP–RP system demonstrated superior proteome coverage over single-shot data-dependent acquisition (DDA) analysis using only 5 ng of human cell lysate digest with performance increasing with increasing amounts of material. We found that the fractionation system allowed over 60% signal recovery at the peptide level and, more importantly, we observed improved protein level intensity coverage, which indicates the complexity reduction afforded by the system outweighs the sample losses endured. The application of data-independent acquisition (DIA) and wide window acquisition (WWA) to fractionated samples allowed nearly 8000 proteins to be identified from 50 ng of the material. The utility of the 2D system was further investigated for phosphoproteomics (>21 000 phosphosites from 50 μg starting material) and pull-down type experiments and showed substantial improvements over single-shot experiments. We show that the 2D RP–RP system is a highly versatile and powerful tool for many proteomics workflows.

Can I suggest a slightly crappier but much cheaper alternative? Also a little more painful to set up BUT it's cheaper!

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

@cnicproteomics.bsky.social is finally in Bluesky!!

Follow us to learn about our quest to advance proteomics research with a special focus on open search strategies and the study of post-translational modifications (PTMs).

@dakshatt.bsky.social
@shabazlab.bsky.social
@zjayres.bsky.social
@darraghobrien.bsky.social

You're also our 1st UK followers & win yourself a bag or a mug! DM us your choice, colour & full UK address & we'll ship them to you!
15 more still to be won...🧪🎉

Kevin Pagel giving a fantastic talk on IMS and gas phase IR for sugar analysis. I for one am convinced of the power. #BMSS2025

Illustration of a DIA MS/MS spectrum with unidentified peaks (top) and labelled peaks for two identified peptides (middle and bottom).

Probabilistic scoring of DIA matches without spectral deconvolution? Not only is it possible, we're working on implementing it in Mascot DIA.

www.matrixscience.com/blog/probabi...

#proteomics #massspec

(BioRxiv All) Peptide-RNA photo-crosslinks with tunable RNA chain map protein-RNA interfaces: Photo-crosslinking mass spectrometry enables the identification of protein-RNA interactions in living cells, pinpointing interaction interfaces at single-amino acid resolution.… #BioRxiv #MassSpecRSS