Markus Hartl
@hartl.bsky.social
Biologist and proteomics specialist at Max Perutz Labs Vienna.
Reposted by Markus Hartl
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.
1/
You’ve got RNA-seq.
Methylation.
Proteomics.
Time to “integrate” the data.
But how? And why?
Let’s break it down.
November 17, 2025 at 2:15 PM
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.
1/
You’ve got RNA-seq.
Methylation.
Proteomics.
Time to “integrate” the data.
But how? And why?
Let’s break it down.
Reposted by Markus Hartl
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...
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...
www.cell.com
February 26, 2025 at 6:14 PM
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...
Reposted by Markus Hartl
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".
July 22, 2025 at 2:13 PM
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".
Reposted by Markus Hartl
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...
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...
doi.org
September 9, 2025 at 11:46 AM
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...
Reposted by Markus Hartl
"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...
1/n
www.project-syndicate.org/commentary/a...
October 25, 2025 at 6:08 AM
"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...
1/n
www.project-syndicate.org/commentary/a...
Reposted by Markus Hartl
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...
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...
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. ...
doi.org
October 20, 2025 at 7:07 AM
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...
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...
Reposted by Markus Hartl
🎉 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
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
September 23, 2025 at 9:10 AM
🎉 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
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
Reposted by Markus Hartl
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!
📢 Open Call! The Max Perutz Labs invite applications for a Tenure-Track Professorship in Mechanistic Cell and Developmental Biology. More details ➡️ tinyurl.com/3fbkp89c
September 10, 2025 at 5:32 PM
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!
Reposted by Markus Hartl
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
September 7, 2025 at 12:48 PM
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
Reposted by Markus Hartl
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!
September 6, 2025 at 5:11 PM
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!
Reposted by Markus Hartl
Academic authors, here's a peek into the black box of journal publishing from an journal editor if you can bear it:
September 6, 2025 at 11:09 PM
Academic authors, here's a peek into the black box of journal publishing from an journal editor if you can bear it:
Reposted by Markus Hartl
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...
Original publication on vPro-MS here:
www.nature.com/articles/s41...
August 26, 2025 at 9:01 PM
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...
Original publication on vPro-MS here:
www.nature.com/articles/s41...
Reposted by Markus Hartl
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 quick intro from @kmechtler.bsky.social and we kick off two days of exciting science starting with SCP of neutrophils in glioblastoma
August 26, 2025 at 6:59 AM
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 quick intro from @kmechtler.bsky.social and we kick off two days of exciting science starting with SCP of neutrophils in glioblastoma
Reposted by Markus Hartl
A really nice example on how to visually communicate the text contents of a paper on mobile phones
A must-read, must-share piece - clearly deconstructing the shoddy science of the Geiers (who are inexplicably in charge of studies at HHS).
Consider this an early warning for what lies ahead. 🛟🩺🧪
www.nytimes.com/interactive/...
Consider this an early warning for what lies ahead. 🛟🩺🧪
www.nytimes.com/interactive/...
Opinion | The Playbook Used to ‘Prove’ Vaccines Cause Autism (Gift Article)
Data can easily be manipulated to show a causation that doesn’t exist.
www.nytimes.com
August 19, 2025 at 2:07 PM
A really nice example on how to visually communicate the text contents of a paper on mobile phones
Reposted by Markus Hartl
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
The position provides the opportunity to closely interact with experimentalists and develop own research projects.
Please RT.
Details 👇:
shorturl.at/iiiOv
116 FB 5 Research Assistant (m/f/d) field of Theoretical Ecology and Evolution or Computational Biology: Uni Osnabrück
shorturl.at
August 8, 2025 at 10:09 AM
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
The position provides the opportunity to closely interact with experimentalists and develop own research projects.
Please RT.
Details 👇:
shorturl.at/iiiOv
Reposted by Markus Hartl
▶️▶️ 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
Thanks @diegofgar.bsky.social for sharing!
#teammassspec
#AcademicSky
#ChemSky
For more information, I've attached the call in German and translated to English.
Feel free to contact me or @sinzandrea.bsky.social
#Postdoc #MassSpec #Proteomics #Hiring
Feel free to contact me or @sinzandrea.bsky.social
#Postdoc #MassSpec #Proteomics #Hiring
July 15, 2025 at 1:37 PM
▶️▶️ 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
Thanks @diegofgar.bsky.social for sharing!
#teammassspec
#AcademicSky
#ChemSky
Reposted by Markus Hartl
‼️ 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
www.verwaltung.uni-halle.de/dezern3/Auss...
#Academicsky
#Chemsky
#teammassspec
www.verwaltung.uni-halle.de
June 25, 2025 at 12:44 PM
‼️ 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
www.verwaltung.uni-halle.de/dezern3/Auss...
#Academicsky
#Chemsky
#teammassspec
Reposted by Markus Hartl
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 .
This is, of course, a horrible idea. Here’s my response with @jbakcoleman.bsky.social .
AI, peer review and the human activity of science
When researchers cede their scientific judgement to machines, we lose something important.
www.nature.com
June 25, 2025 at 1:01 PM
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 .
This is, of course, a horrible idea. Here’s my response with @jbakcoleman.bsky.social .
Reposted by Markus Hartl
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.
Assessing error control is fundamental in mass spectrometry-based proteomics. @bo-wen.bsky.social @maccoss.bsky.social @urikeich.bsky.social et al introduce a theoretical foundation for entrapment along with a method for more accurate evaluation of FDR control.
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Assessment of false discovery rate control in tandem mass spectrometry analysis using entrapment - Nature Methods
A theoretical foundation for entrapment methods is presented, along with a method that enables more accurate evaluation of false discovery rate (FDR) control in proteomics mass spectrometry analysis p...
www.nature.com
June 16, 2025 at 6:52 PM
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.
Reposted by Markus Hartl
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.
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.
May 31, 2025 at 1:15 PM
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.
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.
Reposted by Markus Hartl
May 27, 2025 at 5:54 AM
Reposted by Markus Hartl
🚨Our new paper is online🚨
We use zero-distance⚡photo-crosslinking⚡to reveal direct protein-DNA interactions in living cells, enabling quantitative analysis of the DNA-interacting proteome on a timescale of minutes. #DNA #Chromatin #Proteomics
www.cell.com/cell/fulltex...
We use zero-distance⚡photo-crosslinking⚡to reveal direct protein-DNA interactions in living cells, enabling quantitative analysis of the DNA-interacting proteome on a timescale of minutes. #DNA #Chromatin #Proteomics
www.cell.com/cell/fulltex...
The human proteome with direct physical access to DNA
Zero-distance photo-crosslinking reveals direct protein-DNA interactions in living
cells, enabling quantitative analysis of the DNA-interacting proteome on a timescale
of minutes with single-amino-aci...
www.cell.com
May 22, 2025 at 6:44 PM
🚨Our new paper is online🚨
We use zero-distance⚡photo-crosslinking⚡to reveal direct protein-DNA interactions in living cells, enabling quantitative analysis of the DNA-interacting proteome on a timescale of minutes. #DNA #Chromatin #Proteomics
www.cell.com/cell/fulltex...
We use zero-distance⚡photo-crosslinking⚡to reveal direct protein-DNA interactions in living cells, enabling quantitative analysis of the DNA-interacting proteome on a timescale of minutes. #DNA #Chromatin #Proteomics
www.cell.com/cell/fulltex...
Reposted by Markus Hartl
If there any #Sciex decision makers here on Bluesky - I urge you to reconsider. Skyline/Proteowizard support is not only important for your customers using these tools, but it also benefits other bioinformatics efforts that depend on these tools.
Disappointing to see, across both parties.
Sciex is no longer providing funding for Skyline/Proteowizard as part of the multi-vendor agreement to keep Skyline supported across all major vendors.
I can see the arguments from both sides, just a shame it's resulted in this.
Sciex is no longer providing funding for Skyline/Proteowizard as part of the multi-vendor agreement to keep Skyline supported across all major vendors.
I can see the arguments from both sides, just a shame it's resulted in this.
May 15, 2025 at 1:24 AM
If there any #Sciex decision makers here on Bluesky - I urge you to reconsider. Skyline/Proteowizard support is not only important for your customers using these tools, but it also benefits other bioinformatics efforts that depend on these tools.
Reposted by Markus Hartl
Please apply for this open position for a senior scientist at our faculty. It is the head of the mass spec center and you will be my close colleague! Application Deadline:8.5.2025
jobs.univie.ac.at/job/Senior-S...
jobs.univie.ac.at/job/Senior-S...
Senior Scientist
Senior Scientist
jobs.univie.ac.at
April 30, 2025 at 4:52 PM
Please apply for this open position for a senior scientist at our faculty. It is the head of the mass spec center and you will be my close colleague! Application Deadline:8.5.2025
jobs.univie.ac.at/job/Senior-S...
jobs.univie.ac.at/job/Senior-S...
Reposted by Markus Hartl
DIA-MS and targeted #proteomics workshop
May 19, 2025, Masaryk University, Brno CZ
Organized by CZproteo
keynote by Alexey Nesvizhskii @nesvilab.bsky.social
Program & Registration:
czproteo.cz/workshop-cur...
May 19, 2025, Masaryk University, Brno CZ
Organized by CZproteo
keynote by Alexey Nesvizhskii @nesvilab.bsky.social
Program & Registration:
czproteo.cz/workshop-cur...
April 22, 2025 at 11:16 AM
DIA-MS and targeted #proteomics workshop
May 19, 2025, Masaryk University, Brno CZ
Organized by CZproteo
keynote by Alexey Nesvizhskii @nesvilab.bsky.social
Program & Registration:
czproteo.cz/workshop-cur...
May 19, 2025, Masaryk University, Brno CZ
Organized by CZproteo
keynote by Alexey Nesvizhskii @nesvilab.bsky.social
Program & Registration:
czproteo.cz/workshop-cur...