Daniel Wendscheck

What's more irritating in talks?

A) Speakers saying "I'm going to switch gears" when they mean "I'm going to change direction and talk about something else"?

B) A metaphorical collaboration slide that shows 3 or more gear cogs in a configuration that could not possible work.

Thinking about putting this sign outside my facilities door . 🤔

Having a PhD means you can find the word “unfortunately” in an email faster that the search function

A Universal Spectrum Annotator for Complex Peptidoforms in Mass Spectrometry-Based Proteomics Accurate and comprehensive peptide spectrum annotation is a crucial step to interpreting mass spectrometry-based proteomics data. While peak assignment in peptide fragmentation spectra is central to a broad range of proteomics applications, current tools tend to be specialized to a specific task. Here, we present a more comprehensive interactive graphical tool (Annotator), along with the underlying codebase written in Rust (rustyms). Annotator enables unified spectrum annotation for bottom-up, middle-down, top-down, cross-linked, and glycopeptide fragmentation mass spectra from all fragmentation methods, including all ion types: a/b/c, x/y/z, d/v/w, and immonium ions. The Annotator integrates all known post-translational modifications from common databases and additionally allows for the definition of custom fragmentation models and modifications. Modifications allow for diagnostic fragment ions, site-specific neutral losses, and multiple breakage sites for cross-linkers. The underlying library used for the theoretical fragmentation and matching is based on the unified peptidoform notation ProForma 2.0 and is made available as a Rust library with Python bindings. This enables spectrum annotation in an interactive, graphical interface of diverse and complex peptidoforms across the broad range of mass spectrometry-based proteomics applications.

Our universal peptide spectrum Annotator (and codebase rustyms) is now published in Analytical Chemistry, check it out!
pubs.acs.org/doi/10.1021/...
github.com/snijderlab/a...
github.com/jspaezp/rust...

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...

"That's one small step for [a] man, one giant leap for #peroxisome research" Yesterday I finally submitted my PhD thesis @uni-wuerzburg.de ! Thanks to everyone involved from the @warscheidlab.bsky.social and others and very much looking forward to the defense 🛡⚔️ #proteomics #TeamMassSpec #PhDlife

Peroxisomal metabolism of branched fatty acids regulates energy homeostasis - Nature A UCP1-independent mechanism of thermogenesis involving ATP-consuming metabolism of monomethyl branched-chain fatty acids in peroxisomes is described and a previously unrecognized role for peroxisomes...

Peroxisomal metabolism of branched fatty acids regulates energy homeostasis

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

10 Rules for a Structural Bioinformatic Analysis The Protein Data Bank (PDB) is one of the richest open‑source repositories in biology, housing over 277,000 macromolecular structural models alongside much of the experimental data that underpins thes...

Structural bioinformatics is incredibly powerful on its own or when paired with theory or experiment. One of the PDB's superpowers isn’t from one structure, but comparing many to uncover folds, binding sites, and subtle conformational shifts. chemrxiv.org/engage/chemr...

Ensemble model of the full length Pex5 receptor (different blue color) in complex with Pex8 (green colors). Key Findings: Pex8 binds to a novel site on the mostly unfolded N-terminal region of the Pex5 receptor. This interaction is essential for peroxisomal protein import. Computational modelling reveals the formation of an assembly with the trimeric peroxisomal E3-ubiquitin ligase. We propose that this action positions the Pex5 receptor for its recycling, a step essential for the entire protein import process. Why this matters: Peroxisomes rely entirely on the import of folded proteins to function. Impaired peroxisome function is linked to severe disorders, and recent data show their crucial roles in carcinogenesis and the immune response. Our work elevates Pex8 from an enigma to a central player in this critical biological process. Read the full story and see the structures here: https://www.biorxiv.org/content/10.1101/2025.08.30.673231v1 #CellBiology #StructuralBiology #Peroxisome #ProteinImport #bioRxiv #Biochemistry

We are excited to share our latest work, where we unravel the structural and functional secrets of the once-mysterious protein Pex8 revealing how it controls the peroxisomal cargo import receptor Pex5.

Read more here: www.biorxiv.org/content/10.1101/2025.08.30.673231v1

Thanks "loading" Lorenz! 🙏

Thank you Ralph for your warm words and this fantastic wrap-up of our work. As an ECR I can only guess that such productive and regardful colabs are an exception rather than the rule 🙏

Thank you Walter for your generous words🙏
The project was really fun and fueled my interest for basic research🤩

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

🧬🧶

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

CryoEM-enabled visual proteomics reveals de novo structures of oligomeric protein complexes www.cell.com/structu...

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#proteomics #prot-paper

Antonov - The World's Largest Aircraft - Watch the full documentary | ARTE in English The Antonov AN-225 Mriya, the world's largest cargo plane and the pride of Ukraine, was destroyed in a Russian attack on Hostomel airport near Kyiv at the beginning of the invasion in 2022. With exclu...

www.arte.tv/en/videos/11...

Highly recommended ☝️ so far undisclosed video material embedded in insightful interviews!

Organelles share the load Peroxisome-mitochondria contact sites manage mitochondrial oxidative stress

Organelles share the load | Science www.science.org/doi/10.1126/...

Excited to receive an NIH K08 Clinical Investigator Award to support my research on #mitochondria #peroxisomes 😀 The $775K will be critical in helping me transition to independence as I begin looking for a place to start my lab 🙏🏻 @the-asci.bsky.social

Dallas researchers find cancer’s secret weapon to defeat death Cancers use lipids to build a shield with vitamin E. Stripping that shield could lead to new treatments.

Today in @dallasnews.com by @sodendritic.bsky.social: "Dallas researchers find cancer’s secret weapon to defeat death" ⬇️ read more www.dallasnews.com/news/2025/06...
🧪 #relentlessdiscovery @rjdlab.bsky.social

‼️ 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

ACAD10 and ACAD11 enable mammalian 4-hydroxy acid lipid catabolism - Nature Structural & Molecular Biology Rashan, Bartlett and colleagues show that mammalian 4-hydroxy fatty acids are primarily catabolized by ACAD10 and ACAD11 (atypical mitochondrial and peroxisomal acyl-CoA dehydrogenases, respectively) ...

AND IT'S DONE! A 🧵 on our recent article now out in @natsmb.nature.com! Co-led with @abbybartlett.bsky.social, Pagliarini Lab, @judisimcox.bsky.social, we find ACAD10/11 are NOT like other acyl-CoA dehydrogenases and instead catabolize atypical lipids called 4-hydroxy acids 🤯 doi.org/10.1038/s415...

I am already excited for my talk later, where I have the honor to present my PhD Thesis. Are you at #EuPA2025? Then join the award session and refresh your knowledge about #muscle #proteomics!

Spitzenforschung wird immer mehr mit einem Leistungssport gleichgesetzt, keinem Mannschaftssport, keine Teamveranstaltung
Der Spitzenforscher wird glorifiziert, die notwendige Vorarbeit die von Dutzenden anderen Forschenden geleistet wird, wird ausgeblendet und herabgewürdigt

📺 #IchBinHanna​-Community: Ihr werdet gesucht für 1 TV-Format! Die Anfrage:

„Für eine Dokumentation für den Öffentlich-rechtlichen Rundfunk suchen wir Wissenschaftler*innen ohne Lebenszeitprofessur, die bereit wären, mit uns über ihre Erfahrungen mit dem dt. Wissenschaftssystem zu sprechen:

(1/3)

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.

MS Word suggests to use more consice language by abrreviating RING with "interesting new gene" instead of "really interesting new gene"

I like your humor #microsoft Word! Preparing the list of abbreviations for my #PhD thesis #PhDlife #proteomics

Nikolai Yezhov - Wikipedia

en.m.wikipedia.org/wiki/Nikolai...

Evaluation of an Orbitrap Astral Zoom mass spectrometer prototype for quantitative proteomics - beyond identification lists Mass spectrometry instrumentation continues to evolve rapidly, yet quantifying these advances beyond conventional peptide and protein detections remains challenging. Here, we evaluate a modified Orbit...

New Preprint ... This was a bit different of a project than what we normally do for hardware comparisons. I think there is a lot of potential in the methods mentioned here for calibrating the instrument response to a common scale. Nice work by @chrhsu.bsky.social!

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

hu.MAP3.0: atlas of human protein complexes by integration of >25,000 proteomic experiments | Molecular Systems Biology imageimagehu.MAP3.0 integrates mass spectrometry experiments to identify human protein complexes. Using this resource, this study characterizes covariation of complexes, identifies mutually exclusive ...

Very excited that our work describing hu.MAP3.0 is published in @molsystbiol.org. Here we use machine learning to integrate >25k mass spectrometry experiments to place ~70% of human proteins into 15k protein complexes.

www.embopress.org/doi/full/10....