Johannes Zimmermann
@johannes-uni-wue.bsky.social
4. year, 1. Gen PhD student #UniWürzburg in the Warscheid lab. Phospho-/Proteomics, python, mechanical stress, #TeamMassSpec.
Pinned
Who is messing with your favorite protein Filamin C in stressed muscle cells? 🧩🔬 We tackled this riddle in our latest paper in Scientific Reports. A huge shoutout to former lab mate Anja and Thomas from the @mkoehn.bsky.social lab - this was a true team effort! 👏🎉! A short thread: 🧵(1/5)
Reposted by Johannes Zimmermann
Solving the computational challenge of phosphoproteomics with 𝐏𝐡𝐨-𝐓𝐢𝐩: dephosphorylation on-tip identifies the sequences of phosphorylated peptides.
This serves as a basis for predicted spectral libraries, reducing the search space 10x-20x. www.biorxiv.org/content/10.1...
This serves as a basis for predicted spectral libraries, reducing the search space 10x-20x. www.biorxiv.org/content/10.1...
November 19, 2025 at 10:07 AM
Solving the computational challenge of phosphoproteomics with 𝐏𝐡𝐨-𝐓𝐢𝐩: dephosphorylation on-tip identifies the sequences of phosphorylated peptides.
This serves as a basis for predicted spectral libraries, reducing the search space 10x-20x. www.biorxiv.org/content/10.1...
This serves as a basis for predicted spectral libraries, reducing the search space 10x-20x. www.biorxiv.org/content/10.1...
Reposted by Johannes Zimmermann
I have been using SAINT for #interactome/ #apms analysis forever but always found it cumbersome to pipe into workflows especially on macOS/unix env. But no mas! We made a full Python port of SAINTexpress (spc only for now)
github.com/FossatiLab/s...
github.com/FossatiLab/s...
GitHub - FossatiLab/saintPy: Python port of SAINT algorithm for scoring AP-MS datasets
Python port of SAINT algorithm for scoring AP-MS datasets - FossatiLab/saintPy
github.com
November 4, 2025 at 5:30 PM
I have been using SAINT for #interactome/ #apms analysis forever but always found it cumbersome to pipe into workflows especially on macOS/unix env. But no mas! We made a full Python port of SAINTexpress (spc only for now)
github.com/FossatiLab/s...
github.com/FossatiLab/s...
Reposted by Johannes Zimmermann
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 Johannes Zimmermann
The big picture:
Tracing the arc of conceptual milestones in life sciences over the past century, centered around major discoveries driven by evolving technologies.
We are excited about the progress & the research enabled by tech from @ParallelSqTech.
youtu.be/SrzoLGBVTsY?...
Tracing the arc of conceptual milestones in life sciences over the past century, centered around major discoveries driven by evolving technologies.
We are excited about the progress & the research enabled by tech from @ParallelSqTech.
youtu.be/SrzoLGBVTsY?...
Proteomics: The arc of progress in life sciences | Research Fest by PTI
YouTube video by Nikolai Slavov
youtu.be
October 24, 2025 at 7:38 PM
The big picture:
Tracing the arc of conceptual milestones in life sciences over the past century, centered around major discoveries driven by evolving technologies.
We are excited about the progress & the research enabled by tech from @ParallelSqTech.
youtu.be/SrzoLGBVTsY?...
Tracing the arc of conceptual milestones in life sciences over the past century, centered around major discoveries driven by evolving technologies.
We are excited about the progress & the research enabled by tech from @ParallelSqTech.
youtu.be/SrzoLGBVTsY?...
What an excellent opportunity with so many great labs and interesting projects. Planed lab rotations inside the network to connect and learn from others. And you can go "all in on AI" as Mr. Mann called for in last years HUPO.
🌟Ready to apply?
16 fully funded PhD positions are open in ProtAIomics Doctoral Network!
Join 16 labs across Europe to advance AI-powered proteomics and drive discoveries in health & biotechnology.
👉 Apply here: www.protaiomics.eu
#Proteomics #ArtificialIntelligence #MSCA #PhDOpportunities
16 fully funded PhD positions are open in ProtAIomics Doctoral Network!
Join 16 labs across Europe to advance AI-powered proteomics and drive discoveries in health & biotechnology.
👉 Apply here: www.protaiomics.eu
#Proteomics #ArtificialIntelligence #MSCA #PhDOpportunities
October 11, 2025 at 1:37 PM
What an excellent opportunity with so many great labs and interesting projects. Planed lab rotations inside the network to connect and learn from others. And you can go "all in on AI" as Mr. Mann called for in last years HUPO.
Reposted by Johannes Zimmermann
How much hands-on lab expertise gets lost? We developed a multimodal AI agent that turns videos into protocols and detects procedural errors. Making science accessible. Great collaboration with #Google.
Preprint: www.biorxiv.org/content/10.1...
@patiskowronek.bsky.social explains👇
Preprint: www.biorxiv.org/content/10.1...
@patiskowronek.bsky.social explains👇
In labs, hands-on expertise is often lost because it's not written down. We leverage multimodal AI agents to capture & share expertise by analyzing video and speech to generate protocols, detect errors, and guide researchers. #AI #TeamMassSpec
📄 Preprint: doi.org/10.1101/2025... 1/🧵
📄 Preprint: doi.org/10.1101/2025... 1/🧵
Multimodal AI agents for capturing and sharing laboratory practice
We present a multimodal AI laboratory agent that captures and shares tacit experimental practice by linking written instructions with hands-on laboratory work through the analysis of video, speech, an...
doi.org
October 9, 2025 at 10:54 AM
How much hands-on lab expertise gets lost? We developed a multimodal AI agent that turns videos into protocols and detects procedural errors. Making science accessible. Great collaboration with #Google.
Preprint: www.biorxiv.org/content/10.1...
@patiskowronek.bsky.social explains👇
Preprint: www.biorxiv.org/content/10.1...
@patiskowronek.bsky.social explains👇
Reposted by Johannes Zimmermann
🚀 Excited to share our new preprint: msBayesImpute - A Versatile Framework for Addressing Missing Values in Biomedical Mass Spectrometry Proteomics Data
👉 Improves imputation accuracy, normalization, and differential expression detection
📝https://www.biorxiv.org/content/10.1101/2025.10.02.679746v1
👉 Improves imputation accuracy, normalization, and differential expression detection
📝https://www.biorxiv.org/content/10.1101/2025.10.02.679746v1
October 7, 2025 at 8:47 AM
🚀 Excited to share our new preprint: msBayesImpute - A Versatile Framework for Addressing Missing Values in Biomedical Mass Spectrometry Proteomics Data
👉 Improves imputation accuracy, normalization, and differential expression detection
📝https://www.biorxiv.org/content/10.1101/2025.10.02.679746v1
👉 Improves imputation accuracy, normalization, and differential expression detection
📝https://www.biorxiv.org/content/10.1101/2025.10.02.679746v1
Reposted by Johannes Zimmermann
Predicting protein-protein interactions.
They '...systematically screened 200 million human protein pairs and predicted 17,849 interactions with anexpected precision of 90%, of which 3,631 interactions were not identified in previous experimental screens.'
www.science.org/doi/epdf/10....
They '...systematically screened 200 million human protein pairs and predicted 17,849 interactions with anexpected precision of 90%, of which 3,631 interactions were not identified in previous experimental screens.'
www.science.org/doi/epdf/10....
Predicting protein-protein interactions in the human proteome
Protein-protein interactions (PPI) are essential for biological function. Coevolutionary analysis and deep learning (DL) based protein structure prediction have enabled comprehensive PPI identificatio...
www.science.org
September 30, 2025 at 2:45 PM
Predicting protein-protein interactions.
They '...systematically screened 200 million human protein pairs and predicted 17,849 interactions with anexpected precision of 90%, of which 3,631 interactions were not identified in previous experimental screens.'
www.science.org/doi/epdf/10....
They '...systematically screened 200 million human protein pairs and predicted 17,849 interactions with anexpected precision of 90%, of which 3,631 interactions were not identified in previous experimental screens.'
www.science.org/doi/epdf/10....
Reposted by Johannes Zimmermann
🥁 Check out our new preprint on OmniPath, the prior knowledge resource for #SystemsBiology, and its brand-new OmniPath Explorer web app! 🥳
📖 Preprint: www.biorxiv.org/content/10.1...
🔍 Explorer: explore.omnipathdb.org
OmniPath integrates 160+ resources for multi-omics analysis & modeling.
🧶⬇️
📖 Preprint: www.biorxiv.org/content/10.1...
🔍 Explorer: explore.omnipathdb.org
OmniPath integrates 160+ resources for multi-omics analysis & modeling.
🧶⬇️
September 17, 2025 at 1:10 PM
🥁 Check out our new preprint on OmniPath, the prior knowledge resource for #SystemsBiology, and its brand-new OmniPath Explorer web app! 🥳
📖 Preprint: www.biorxiv.org/content/10.1...
🔍 Explorer: explore.omnipathdb.org
OmniPath integrates 160+ resources for multi-omics analysis & modeling.
🧶⬇️
📖 Preprint: www.biorxiv.org/content/10.1...
🔍 Explorer: explore.omnipathdb.org
OmniPath integrates 160+ resources for multi-omics analysis & modeling.
🧶⬇️
Abuse of power at universities is a problem in many countries. Unfortunately, the open to read book is just available in German language.
" #Machtmissbrauch an Hochschulen ist zu 1 drängenden Problem geworden.[…] Es wurde lange Zeit verschwiegen[...], aber es wird zunehmend sichtbar und ist mittlerweile [...] in der Öffentlichkeit angelangt. Das ist längst überfällig." 1/2
#IchBinHanna #IchBinReyhan
library.oapen.org/bitstream/ha...
#IchBinHanna #IchBinReyhan
library.oapen.org/bitstream/ha...
library.oapen.org
September 10, 2025 at 1:59 PM
Abuse of power at universities is a problem in many countries. Unfortunately, the open to read book is just available in German language.
Reposted by Johannes Zimmermann
If you are a #PhD candidate or #student in the fields of #Biochemistry or #ChemBio and would like to go to the #Biochemistry2026 conference in Würzburg, consider applying for the brand new @gdchbiochem.bsky.social Meeting #Award!
en.gdch.de/network-stru...
#ChemSky #ECR #EarlyCareerResearcher
en.gdch.de/network-stru...
#ChemSky #ECR #EarlyCareerResearcher
📢 New Award for #ECRs in #Biochemistry!
Apply for our Meeting Award to get:
✅ 500 € grant for #Biochemistry2026
✅ 1 year of free @gdchbiochem.bsky.social membership
Apply now: en.gdch.de/network-s...
Share with a #ECR who needs to see this! 👇
#ChemSky #ChemBio #AcademicTwitter #PhD @gdch.de
Apply for our Meeting Award to get:
✅ 500 € grant for #Biochemistry2026
✅ 1 year of free @gdchbiochem.bsky.social membership
Apply now: en.gdch.de/network-s...
Share with a #ECR who needs to see this! 👇
#ChemSky #ChemBio #AcademicTwitter #PhD @gdch.de
August 21, 2025 at 5:12 AM
If you are a #PhD candidate or #student in the fields of #Biochemistry or #ChemBio and would like to go to the #Biochemistry2026 conference in Würzburg, consider applying for the brand new @gdchbiochem.bsky.social Meeting #Award!
en.gdch.de/network-stru...
#ChemSky #ECR #EarlyCareerResearcher
en.gdch.de/network-stru...
#ChemSky #ECR #EarlyCareerResearcher
Reposted by Johannes Zimmermann
Major part of my PhD thesis is finally online! Thanks to everyone involved 🙏 @walterwchen.bsky.social @rjdlab.bsky.social @tmoeckli.bsky.social @hirakdas.bsky.social and the entire @warscheidlab.bsky.social #peroxisomes #Massspec #proteomics
#Biochemistry: #PEX39, a newly discovered #peroxin protein, transports enzymes into #peroxisomes like a relay racer. New paper @natcellbio.nature.com – congratulations to @dwendscheck.bsky.social @warscheidlab.bsky.social et al!
➡️ www.uni-wuerzburg.de/en/news-and-...
➡️ www.uni-wuerzburg.de/en/news-and-...
July 30, 2025 at 10:13 AM
Major part of my PhD thesis is finally online! Thanks to everyone involved 🙏 @walterwchen.bsky.social @rjdlab.bsky.social @tmoeckli.bsky.social @hirakdas.bsky.social and the entire @warscheidlab.bsky.social #peroxisomes #Massspec #proteomics
Reposted by Johannes Zimmermann
Excited to share our latest work published in #ScienceSignaling! 🚀
www.science.org/doi/10.1126/...
(1/4)
www.science.org/doi/10.1126/...
(1/4)
Proteomic analyses identify targets, pathways, and cellular consequences of oncogenic KRAS signaling
Proteomic analyses offer insights into how KRAS inhibitors affect oncogenic KRAS signaling.
www.science.org
July 31, 2025 at 8:10 AM
Excited to share our latest work published in #ScienceSignaling! 🚀
www.science.org/doi/10.1126/...
(1/4)
www.science.org/doi/10.1126/...
(1/4)
Reposted by Johannes Zimmermann
When analysing peptides from in-gel digests by LC-MS/MS, has anyone noticed a 1+ ion of m/z 1342.93 after washing the column with 80% ACN? We are leaving the pump at 80% ACN at 1uL/min for 5 mins after our usual 0-40% ACN gradient. Doesn't correspond to any contaminants. #massspechelp
July 31, 2025 at 7:05 AM
When analysing peptides from in-gel digests by LC-MS/MS, has anyone noticed a 1+ ion of m/z 1342.93 after washing the column with 80% ACN? We are leaving the pump at 80% ACN at 1uL/min for 5 mins after our usual 0-40% ACN gradient. Doesn't correspond to any contaminants. #massspechelp
Reposted by Johannes Zimmermann
PepMapViz: A Versatile Toolkit for Peptide Mapping, Visualization, and Comparative Exploration academic.oup.com/bio...
---
#proteomics #prot-paper
---
#proteomics #prot-paper
July 17, 2025 at 2:40 PM
PepMapViz: A Versatile Toolkit for Peptide Mapping, Visualization, and Comparative Exploration academic.oup.com/bio...
---
#proteomics #prot-paper
---
#proteomics #prot-paper
Reposted by Johannes Zimmermann
Jesper Olsen Lab (Guzman et al) independently reproduces MAP-MS (eDR) proteome depth and compares Astral Zoom MS to the older model.
"...yielding ~15,000 and ~30,000 additional precursors..."
eDR: www.biorxiv.org/content/10.1...
MAP-MS: www.biorxiv.org/content/10.1...
"...yielding ~15,000 and ~30,000 additional precursors..."
eDR: www.biorxiv.org/content/10.1...
MAP-MS: www.biorxiv.org/content/10.1...
July 19, 2025 at 9:58 AM
Jesper Olsen Lab (Guzman et al) independently reproduces MAP-MS (eDR) proteome depth and compares Astral Zoom MS to the older model.
"...yielding ~15,000 and ~30,000 additional precursors..."
eDR: www.biorxiv.org/content/10.1...
MAP-MS: www.biorxiv.org/content/10.1...
"...yielding ~15,000 and ~30,000 additional precursors..."
eDR: www.biorxiv.org/content/10.1...
MAP-MS: www.biorxiv.org/content/10.1...
Reposted by Johannes Zimmermann
As Requested - A Starter Pack of PIs in Biology (or adjacent) fields who are recruiting POSTDOCS! Please don't hesitate to reach out if you wish to be added! go.bsky.app/4gbXXR3
July 18, 2025 at 6:33 PM
As Requested - A Starter Pack of PIs in Biology (or adjacent) fields who are recruiting POSTDOCS! Please don't hesitate to reach out if you wish to be added! go.bsky.app/4gbXXR3
Reposted by Johannes Zimmermann
▶️▶️ 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 Johannes Zimmermann
Check out our newest paper (tinyurl.com/scp-ms) straight from the lab of @erwinschoof.bsky.social. If you are considering to FAIMS or not to FAIMS and whether wide or narrow window DIA is better, you might find some answers you are looking for. #proteomics
July 11, 2025 at 1:45 PM
Check out our newest paper (tinyurl.com/scp-ms) straight from the lab of @erwinschoof.bsky.social. If you are considering to FAIMS or not to FAIMS and whether wide or narrow window DIA is better, you might find some answers you are looking for. #proteomics
Reposted by Johannes Zimmermann
🚀 Attention DIA/DDA proteomics users! Whether you're using #DIA-NN, #MaxQuant, #quantms, or any tool that outputs mzIdentML and mzML, the NEW pmultiqc v0.0.29 is here!
💡 Create stunning, shareable HTML reports for your collaborators in seconds.
✨ Try pmultiqc.quantms.org Examples👇
#Proteomics #QC
💡 Create stunning, shareable HTML reports for your collaborators in seconds.
✨ Try pmultiqc.quantms.org Examples👇
#Proteomics #QC
July 11, 2025 at 8:43 AM
🚀 Attention DIA/DDA proteomics users! Whether you're using #DIA-NN, #MaxQuant, #quantms, or any tool that outputs mzIdentML and mzML, the NEW pmultiqc v0.0.29 is here!
💡 Create stunning, shareable HTML reports for your collaborators in seconds.
✨ Try pmultiqc.quantms.org Examples👇
#Proteomics #QC
💡 Create stunning, shareable HTML reports for your collaborators in seconds.
✨ Try pmultiqc.quantms.org Examples👇
#Proteomics #QC
Reposted by Johannes Zimmermann
📣📣It is great to finally welcome @cnicproteomics.bsky.social to Bluesky 🎊 Follow them if you want to learn about the latest development in PTM research applied to cardiovascular diseases! 🫀🧪🧫🖥️🛠️
July 4, 2025 at 5:38 PM
📣📣It is great to finally welcome @cnicproteomics.bsky.social to Bluesky 🎊 Follow them if you want to learn about the latest development in PTM research applied to cardiovascular diseases! 🫀🧪🧫🖥️🛠️
Reposted by Johannes Zimmermann
DIA, DOA, DUI, DDA, etc. Here is a comparisons of some quantitative proteomics methods from a POV you might not have seen before:
github.com/pwilmart/qua...
github.com/pwilmart/qua...
GitHub - pwilmart/quantitative_proteomics_comparison: Comparison of DIA to spectral counting and TMT quantitative techniques using animal lens studies
Comparison of DIA to spectral counting and TMT quantitative techniques using animal lens studies - pwilmart/quantitative_proteomics_comparison
github.com
July 4, 2025 at 5:53 PM
DIA, DOA, DUI, DDA, etc. Here is a comparisons of some quantitative proteomics methods from a POV you might not have seen before:
github.com/pwilmart/qua...
github.com/pwilmart/qua...
Reposted by Johannes Zimmermann
Are you interested in #proteomics and #skeletalmuscle? It can be a real pain to get deep reproducible coverage. Check out our review with @adeshmukh.bsky.social We analyse some considerations including current limitations and how to potentially overcome them #myoblue @unimelbcmr.bsky.social
Skeletal muscle proteomics: considerations and opportunities
npj Metabolic Health and Disease - Skeletal muscle proteomics: considerations and opportunities
www.nature.com
July 3, 2025 at 6:18 PM
Are you interested in #proteomics and #skeletalmuscle? It can be a real pain to get deep reproducible coverage. Check out our review with @adeshmukh.bsky.social We analyse some considerations including current limitations and how to potentially overcome them #myoblue @unimelbcmr.bsky.social
Reposted by Johannes Zimmermann
🚀🚀 🚀 Exciting News! 🚀 🚀 🚀
After more than 4.5 fantastic years at @embl.org, I am excited to announce that from 1 August 2025, I’ll be starting my own research group at Physikalisch-Technische Bundesanstalt (PTB) in Braunschweig, Germany — as part of the Biochemistry Department [1/n]
After more than 4.5 fantastic years at @embl.org, I am excited to announce that from 1 August 2025, I’ll be starting my own research group at Physikalisch-Technische Bundesanstalt (PTB) in Braunschweig, Germany — as part of the Biochemistry Department [1/n]
July 3, 2025 at 7:23 AM
🚀🚀 🚀 Exciting News! 🚀 🚀 🚀
After more than 4.5 fantastic years at @embl.org, I am excited to announce that from 1 August 2025, I’ll be starting my own research group at Physikalisch-Technische Bundesanstalt (PTB) in Braunschweig, Germany — as part of the Biochemistry Department [1/n]
After more than 4.5 fantastic years at @embl.org, I am excited to announce that from 1 August 2025, I’ll be starting my own research group at Physikalisch-Technische Bundesanstalt (PTB) in Braunschweig, Germany — as part of the Biochemistry Department [1/n]
Reposted by Johannes Zimmermann
⏳ Just 1 week left to register for MaxQuant Summer School 2025!
📅 Registration closes: July 7
📍 Utrecht, July 21–25
💻 Hands-on training in MaxQuant, Perseus & mass-spectrometry-based proteomics
🔗 Sign up now: eventbrite.de/e/maxquant-s...
🌐 Details: maxquant.org/summer_school/
#TeamMassSpec
📅 Registration closes: July 7
📍 Utrecht, July 21–25
💻 Hands-on training in MaxQuant, Perseus & mass-spectrometry-based proteomics
🔗 Sign up now: eventbrite.de/e/maxquant-s...
🌐 Details: maxquant.org/summer_school/
#TeamMassSpec
MaxQuant Summer School 2025 (Utrecht, Netherlands)
16th International Summer School On Computational Mass Spectrometry-Based Proteomics
eventbrite.de
July 1, 2025 at 8:05 AM
⏳ Just 1 week left to register for MaxQuant Summer School 2025!
📅 Registration closes: July 7
📍 Utrecht, July 21–25
💻 Hands-on training in MaxQuant, Perseus & mass-spectrometry-based proteomics
🔗 Sign up now: eventbrite.de/e/maxquant-s...
🌐 Details: maxquant.org/summer_school/
#TeamMassSpec
📅 Registration closes: July 7
📍 Utrecht, July 21–25
💻 Hands-on training in MaxQuant, Perseus & mass-spectrometry-based proteomics
🔗 Sign up now: eventbrite.de/e/maxquant-s...
🌐 Details: maxquant.org/summer_school/
#TeamMassSpec