Daniel Wendscheck
@dwendscheck.bsky.social
PhD student (close to finish!) at the University Würzburg. Likes to play with structure prediction tools, Crosslinking-MS, Native MS and bicycles. Proud of DOI:10.1073/pnas.2009502117 and DOI:10.1101/2024.04.30.591961 #TeamMassSpec #phdlife #peroxisomes
Hi #TeamMassSpec ! I'm looking for a new stereo microscope for the MassSpec Lab (for troubleshooting tiny parts and so on) Any suggestions? Mid-budget, no digital camera options would be best. Thanks for recommendations and sharing experiences! #massspechelp #proteomics
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
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...
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.
pubs.acs.org
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...
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...
biorxiv.org
"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 www.nature.com/articles/s41...
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...
nature.com
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...
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...
chemrxiv.org
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
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
Julius-Maximilians-Universität Würzburg@uni-wuerzburg.de · last yr.#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-...
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... --- #proteomics #prot-paper
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
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
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.
dallasnews.com
‼️ 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
verwaltung.uni-halle.de
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...
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) ...
doi.org
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
Amrei Bahr@amreibahr.bsky.social · last yr.Sie ist überall: die Rede vom #Spitzenforscher. Nur: Was soll das überhaupt sein? Über einen Begriff, der das Gros der Wissenschaftler_innen als zweitklassig degradiert & einem Geniekult zuarbeitet, der der Arbeitsrealität in der Wissenschaft weder angemessen noch zuträglich ist. ⬇️ #ArbeitInDerWiss
📺 #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.
Nature Methods@natmethods.nature.com · last yr.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...
I like your humor #microsoft Word! Preparing the list of abbreviations for my #PhD thesis #PhDlife #proteomics
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...
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...
biorxiv.org
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....
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 ...
embopress.org
A new dimension for multiplexing mass spec analysis -- time -- is enabling scaling up throughput at new levels. We demonstrate 27-plex DIA enabling over 500 samples / day. We project that timePlex will enable throughputs exceeding 1,000 samples / day. www.biorxiv.org/content/10.1...
Increasing mass spectrometry throughput using time-encoded sample multiplexing
Liquid chromatography-mass spectrometry (LC-MS) can enable precise and accurate quantification of analytes at high-sensitivity, but the rate at which samples can be analyzed remains limiting. Throughp...
biorxiv.org
Jason Derks@jasonderks.bsky.social · last yr.We are excited to introduce ‘time’ as a new domain for proteomics multiplexing! It enables: -Label-free multiplexing -Combinatorial multiplexing with plexDIA Using combined 9-plexDIA and 3-timePlex we demonstrate 27-plex DIA 🚀
Almost intentionally, looks like all of the new Thermo instrument pages are up (Astral Zoom, Excedion Pro, Optispray). Overall vibes? Excedion is the bigger upgrade, almost 2x faster and can now do ETD. Astral Zoom improvements are more incremental. No change to instrument sensitivity specs.
Now published! Big congrats to first author @gginell.bsky.social We are actively working improving/updating various aspects of FINCHES; don't hesitate to reach out if you run into issues, have questions. www.science.org/doi/10.1126/...
Sequence-based prediction of intermolecular interactions driven by disordered regions
Intrinsically disordered regions (IDRs) in proteins play essential roles in cellular function. A growing body of work has shown that IDRs often interact with partners in a manner that does not depend ...
science.org
Alex Holehouse@alexholehouse.bsky.social · 2y agoExcited to share new work from Garrett Ginell et al where we present an approach for predicting intermolecular interaction driven by disordered regions. We focus on how chemical complementarity can contribute to and even dictate intermolecular interactions www.biorxiv.org/content/10.1...
