Markus Hartl

Acquisition news for bottom up and top down proteomics with Thermo acquiring Proteinaceous and MSAID.

Proteinaceous was founded in 2016 (possibly earlier) as a spin out from Neil Kelleher’s lab at Northwestern.

MSAID was spun out from Mathias Wilhelm and Bernhardt Kuster’s labs in 2019.

A problem is that some search engines do not allow to specify that the C-terminal Lys must not be acetylated, which leads to a nice collection of artifacts if you do not remove them manually.

The one science reform we can all agree on, but we're too cowardly to do OR: the long overdue forest fire

Wonderful (and fun!) read from @mastroianni.bsky.social which finishes with a clear answer on how to solve the collective action problem of dismantling scientific publishing

Awesome name and logo! 👏

Really happy to see this one out: www.sciencedirect.com/science/arti... Alibek's drive & great coll w/ friends @gekaragoz.bsky.social & E. Hallacli resulted in a cool story that starts with our beloved #Marchantia and ends with iPSC-derived neurons 🤩🤪 A short 🧵

So 2025 turned out to be a big year for de novo antibody design! Here are thoughts and predictions on the state of de novo antibody design heading into 2026 🧵

Thread: Multi-omics sounds cool—until you actually try it. Here's are the nuances.
1/
You’ve got RNA-seq.
Methylation.
Proteomics.
Time to “integrate” the data.
But how? And why?
Let’s break it down.

Predictomes, a classifier-curated database of AlphaFold-modeled protein-protein interactions Schmid and Walter train a classifier that discerns functionally relevant structure predictions in proteome-wide protein-protein interaction (PPI) screens using AlphaFold-Multimer, and they use this co...

Very excited to share that my thesis work is out in Molecular Cell! We trained a Structure and Omics informed Classifier (SPOC) to score binary AlphaFold multimer (AF-M) predictions by structural quality and consistency with experimental omics datasets. www.cell.com/molecular-ce...

Unexpectedly, @jurgjn.bsky.social found that running Alphafold3 predictions for protein interactions can yield ipTM scores that are more predictive of true interactions when run in pools of proteins instead of pairwise predictions. Presumably, this reflects some sort of "competition effect".

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. However, current isolat...

New preprint: We isolate peptide–RNA photo-crosslinks with tunable RNA chains from living cells for mass spec. This maps over 4,700 crosslinking sites across 744 proteins and offers the first glimpse into the RNA sequences in crosslinks by MS. Read here: doi.org/10.1101/2025...

"Many scholars, including us, have highlighted the threat posed by techno-solutionism in education: Rather than expanding our intellectual horizons, these technologies undermine the very conditions that allow us to think for ourselves."

1/n

www.project-syndicate.org/commentary/a...

Computational Approaches for Pathway‐Centric Analysis of Protein Post‐Translational Modifications Protein function is dynamically modulated by post-translational modifications (PTMs). Many different types of PTMs can nowadays be identified and quantified at a large scale using mass spectrometry. ...

Our new review paper about Pathway-Centric PTM Data Analysis is out this week in #Proteomics!
We cover databases, enrichment tools, software for pathway reconstruction, and full-fledged platforms that help to interpret high-throughput PTM datasets.
Check it out here: doi.org/10.1002/pmic...

🎉 Exciting opportunity for students in proteomics! 🎉
The Student Proteomics Fund (SPF) is back!

📅 Key dates:
Call opens: October 1, 2025
Submission deadline: November 30, 2025
Don’t miss your chance to bring your research idea to life!
New boost
#SPF #YPIC #Proteomics

Just one more week left to get an application in! Starting my lab at the Perutz and the @viennabiocenter.bsky.social has been a fantastic opportunity that shaped me as a scientist!

The Vienna BioCenter PhD program in Molecular BioSciences will offer 20+ fully-funded positions in the Autumn Call which is now open. Have a look at what our campus has to offer: www.vbcphd.at

Do you or your lab use the Skyline software for #MassSpectrometry #proteomics? I'm looking for instructors to help with this year's Skyline Online, a virtual workshop/crash-course for all things Skyline! I'm especially looking for early career researchers for this opportunity. Please DM!

Academic authors, here's a peek into the black box of journal publishing from an journal editor if you can bear it:

Impressive work from great colleagues at RKI. Ultra-fast virus 🦠 diagnostics with mass spec.

Original publication on vPro-MS here:
www.nature.com/articles/s41...

And what a fantastic first speaker! Thanks for the excellent talk Alejandro!

After the DVP symposium now begins the start of the European Symposium on Single Cell Proteomics #ECSP25

A quick intro from @kmechtler.bsky.social and we kick off two days of exciting science starting with SCP of neutrophils in glioblastoma

A really nice example on how to visually communicate the text contents of a paper on mobile phones

I am excited to announce that the position of a senior postdoc (3 +3 years) in the field of theoretical biology is available in my group.

The position provides the opportunity to closely interact with experimentalists and develop own research projects.

Please RT.

Details 👇:
shorturl.at/iiiOv

Manche ziehen deshalb entsprechende Konsequenzen. Hier geht es zwar um Dissertationen, aber die Diskussion werden wir wohl allgemein an Bildungseinrichtungen führen müssen. bsky.app/profile/stat...

▶️▶️ To all mass spec enthusiasts: A postdoc position (three years) is available in our international group. Please apply if you are interested in structural MS and in developing novel cross-link ing MS workflows!🧪
Thanks @diegofgar.bsky.social for sharing!
#teammassspec
#AcademicSky
#ChemSky

‼️ Job alert 🚨: I have an open 3-year postdoc position in my lab to develop novel crosslinking mass spectrometry workflows. 🧪🧪 So if you want to do cool stuff in protein MS, please apply ! ⬇️ Please RT
www.verwaltung.uni-halle.de/dezern3/Auss...

#Academicsky
#Chemsky
#teammassspec

AI, peer review and the human activity of science When researchers cede their scientific judgement to machines, we lose something important.

A few months ago, Nature published how-to guide for using ChatGPT to write your peer reviews in 30 minutes.

This is, of course, a horrible idea. Here’s my response with @jbakcoleman.bsky.social .

I agree, this is a real problem. It's great to see people work on it. I am just wondering how much of the "carry-over" is actually noise being interpreted as signal. DIA also has less missing values because it is often "imputing" with noise, leading to false positives and ratio compression.

Excited to see this published! It is a good step in the process for people to assess their FDR control in proteomics experiments. Great work from @bo-wen.bsky.social and @urikeich.bsky.social in particular who drove this.

12/
Bioinformatics isn't just code.
It's skepticism.
It’s pattern recognition.
It’s noticing when something feels off.
Your instincts matter.
Listen to them.
Then verify with data.

BEFORE THE BATHROOM SCALE WAS INVENTED, THE ONLY WAY TO WEIGH PEOPLE WAS MASS SPECTROMETRY.

Love today’s #xkcd comic on
#MassSpec
🤣