Thilo Muth

Results from a multi-laboratory ocean metaproteomic intercomparison: effects of LC-MS acquisition and data analysis procedures Abstract. Metaproteomics is an increasingly popular methodology that provides information regarding the metabolic functions of specific microbial taxa and has potential for contributing to ocean ecolo...

Ocean Metaproteomics intercomparison study out. Really fun project working together with colleagues to examine this method. And Intercomparisons are really valuable to connect between dstasets across time and space in the environment bg.copernicus.org/articles/21/...

Precise Discovery of Novel N-Terminal Proteoforms beyond the Limitations of Proteogenomics and De Novo Sequencing Alternative splicing-mediated protein N-terminal sequence variation is closely associated with diseases, but its identification by mass spectrometry faces technical bottlenecks. Traditional proteogeno...

Precise Discovery of Novel N-Terminal Proteoforms beyond the Limitations of Proteogenomics and De Novo Sequencing | Analytical Chemistry pubs.acs.org/doi/abs/10.1...

AlphaFold - A practical guide AlphaFold - A practical guide

Recently I learnt that EMBL-EBI has a free online course about AlphaFold — how it works, strengths and limitations, how to use it — and it's very good!

There are also little quizzes and interactives.
www.ebi.ac.uk/training/onl...

GitHub - hoelzer/dfg: A LaTeX template for a basic DFG (Deutsche Forschungsgemeinschaft, German Research Foundation) grant proposal. A LaTeX template for a basic DFG (Deutsche Forschungsgemeinschaft, German Research Foundation) grant proposal. - hoelzer/dfg

Happy that the LaTeX template I created for DFG proposals is being used! 🎉

Just heard from someone in data engineering who got funded using it (🎯 content matters most, but hey, layout helps too 😄)

See: github.com/hoelzer/dfg

Also loving the community input via PRs & issues! 💙

Homo-Tag-Assembler Assay for Full-Length Antibody Sequencing Antibodies are proteins produced by the immune system in response to antigens. Determining the sequence of purified unknown antibodies remains difficult due to factors like incomplete sequence coverage, ambiguous isobaric residues (I/L), and unstable assembly processes. To overcome these issues, we developed the Homo-Tag-Assembler, a software tool using a homology tag fuzzy string matching algorithm. By analyzing amino acid distributions from many similar antibody variable region sequences, we created a probability table specific to these regions. This helped evaluate peptide similarity during de novo sequencing, distinguish peptides from light and heavy chains, and differentiate leucine from isoleucine. Testing with the Herceptin antibody showed full-length sequence coverage with accuracy of 99.1% for the light chain and 100% for the heavy chain variable regions. This method uses conserved regional features and homology based information to enable accurate full-length antibody sequence reconstruction.

Homo-Tag-Assembler Assay for Full-Length Antibody Sequencing | Analytical Chemistry pubs.acs.org/doi/abs/10.1...

New work from great collaboration partners of mine: Biological Function Assignment across Taxonomic Levels in Mass-Spectrometry-Based Metaproteomics via a Modified Expectation Maximization Algorithm | Journal of Proteome Research pubs.acs.org/doi/10.1021/...

Perspectives in Computational Mass Spectrometry: Recent Developments and Key Challenges chemrxiv.org/engage/...

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#proteomics #prot-preprint

a group of people are dancing in a forest and a man is holding a woman 's hand . ALT: a group of people are dancing in a forest and a man is holding a woman 's hand .

Just realised that my institute is on Bluesky @bamresearch.bsky.social ! YAY!
Let the party begin.

This paper represents a great effort by @roman-bushuiev.bsky.social and his brother @anton-bushuiev.bsky.social. The DreaMS foundation model for mass spectra of small molecules now opens lots of avenues for possible downstream applications. It might be a game changer for computational metabolomics.

Improvements to Casanovo, a deep learning de novo peptide sequencer Casanovo is a state-of-the-art deep learning model for de novo peptide sequencing from mass spectrometry proteomics data. Here we report on a series of enhancements to Casanovo, aimed at improving the...

🚀 Preprint out by the Noble Lab: Casanovo v5.0 is here! Usability, speed & interoperability all improved — with better-calibrated scores, faster performance, and smoother integration into proteomics workflows. De novo sequencing just got more practical, check it out:
dx.doi.org/10.1101/2025...

CoVerage: SARS-CoV-2 lineage, S-protein mutation, antigenic variation dynamics Impressum (DE) / Imprint (EN) Datenschutz (DE) / Data protection (EN)

🚨 New in Nature Communications!

CoVerage (sarscoverage.org) enables early in silico detection of emerging SARS-CoV-2 variants.

Led by Helmholtz Centre for Infection Research, driving innovation in genomic surveillance.

🔗 www.nature.com/articles/s41...

#GenomicSurveillance

UniScore, a unified and universal measure for peptide identification by multiple search engines t.co/oh4mLgHXWc --- #proteomics #prot-preprint t.co/lqDUaJRqua

To Fly, or Not to Fly, That Is the Question: A Deep Learning Model for Peptide Detectability Prediction in Mass Spectrometry Identifying detectable peptides, known as flyers, is key in mass spectrometry-based proteomics. Peptide detectability is strongly related to peptide sequences and their resulting physicochemical prope...

To Fly, or Not to Fly, That Is the Question: A Deep Learning Model for Peptide Detectability Prediction in Mass Spectrometry | Journal of Proteome Research pubs.acs.org/doi/10.1021/...

🎉 2026 marks a double milestone for Metaproteomics: 20 years of #metaproteomics and 10 years since the first MP symposium!
Join June 21–24, 2026 in Dessau, Germany for the 7th Metaproteomics Symposium - a unique opportunity to meet, exchange ideas, and explore latest developments:
lnkd.in/eBCXTbT9

Ultra-sensitive metaproteomics redefines the dark metaproteome, uncovering host-microbiome interactions and drug targets in intestinal diseases - Nature Communications The gut microbiome is key to health, yet its protein functions remain largely unexplored. Here, the authors present uMetaP, ultra-sensitive metaproteomics workflow that combines the timsTOF Ultra and ...

Exciting times ahead. Revolutionary study in #Metaproteomics out! Using de novo sequencing and latest LC/MS technology to redefine the „dark metaproteome“:
dx.doi.org/10.1038/s414...

ganon2: up-to-date and scalable metagenomics analysis Abstract. The fast growth of public genomic sequence repositories greatly contributes to the success of metagenomics. However, they are growing at a faster

ganon2: up-to-date and scalable metagenomics analysis url: academic.oup.com/nargab/artic...

Integrative systems biology approaches for analyzing microbiome dysbiosis and species interactions Abstract. Microbiomes are crucial for human health and well-being, with microbial dysbiosis being linked to various complex diseases. Therefore, understand

Sounds like something for a read in between. New review: Integrative systems biology approaches for analyzing microbiome dysbiosis and species interactions academic.oup.com/bib/article/...

A transformer model for de novo sequencing of data-independent acquisition mass spectrometry data - Nature Methods Cascadia is a mass spectrometry-based de novo sequencing model that uses a transformer architecture to handle data-independent acquisition data and achieves substantially improved performance across a...

If you asked me 5 years ago if it would be possible to use a de novo tool on DIA data, I would have thought it would only exist in science fiction. Love being proved wrong. Great work from Justin Sanders. #proteomics #massspectrometry
www.nature.com/articles/s41...

An ELIXIR scoping review on domain-specific evaluation metrics for synthetic data in life sciences Synthetic data has emerged as a powerful resource in life sciences, offering solutions for data scarcity, privacy protection and accessibility constraints. By creating artificial datasets that mirror ...

arxiv.org/abs/2506.14508

MLMarker is live! This ML-tool predicts tissue similarity and uncovers biomarkers from your proteomics data. It was trained on public data of healthy human tissues.
Preprint & app: www.biorxiv.org/content/10.1...
Let's chat at #EuPA2025 - Award session (Wednesday) & poster session (Thursday)!

Correct FDR control in proteomics is tricky, and this @natmethods.nature.com study by Wen et. al is a great example highlighting the specific challenges. It provides a formal framework to evaluate entrapment estimation methods. Fantastic read!

Pairwise Attention: Leveraging Mass Differences to Enhance De Novo Sequencing of Mass Spectra A fundamental challenge in mass spectrometry-based proteomics is determining which peptide generated a given MS2 spectrum. Peptide sequencing typically relies on matching spectra against a known seque...

pubs.acs.org/doi/10.1021/...
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Inspired by AlphaFold2’s pair representations of protein sequences, researchers feed antisymmetric pairwise matrix into their transformer blocks as an attention bias.

Wow, a record breaking number of the Nesvizhskii lab members attending #ASMS2025! 9 posters, 3 evening workshops, and one Bioinformatics Hub on #FragPipe. Plus multiple collaborative posters with other groups. See you in Baltimore! PS. Below is our recent group photo, including all those attending

Microbiome

A study published in Microbiome discusses how Mix7, a consortium of seven commensal bacteria, has a barrier effect against vancomycin-resistant enterococci and promotes overall restoration of microbiota functions.
bit.ly/3Hfumgc

#MedSky

"𝘉𝘦𝘭𝘭 𝘓𝘢𝘣𝘴 𝘸𝘢𝘴 𝘢 𝘳𝘦𝘴𝘦𝘢𝘳𝘤𝘩𝘦𝘳’𝘴 𝘱𝘢𝘳𝘢𝘥𝘪𝘴𝘦. 𝘖𝘶𝘳 𝘮𝘢𝘯𝘢𝘨𝘦𝘮𝘦𝘯𝘵 𝘴𝘶𝘱𝘱𝘭𝘪𝘦𝘥 𝘶𝘴 𝘸𝘪𝘵𝘩 𝘧𝘶𝘯𝘥𝘪𝘯𝘨, 𝘴𝘩𝘪𝘦𝘭𝘥𝘦𝘥 𝘶𝘴 𝘧𝘳𝘰𝘮 𝘣𝘶𝘳𝘦𝘢𝘶𝘤𝘳𝘢𝘤𝘺, 𝘢𝘯𝘥 𝘶𝘳𝘨𝘦𝘥 𝘶𝘴 𝘵𝘰 𝘥𝘰 𝘵𝘩𝘦 𝘣𝘦𝘴𝘵 𝘴𝘤𝘪𝘦𝘯𝘤𝘦 𝘱𝘰𝘴𝘴𝘪𝘣𝘭𝘦."

-- Steven Chu, Nobel Lecture 1997

Deep Coverage and Extended Sequence Reads Obtained with a Single Archaeal Protease Expedite de novo Protein Sequencing by Mass Spectrometry www.biorxiv.org/cont...

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#proteomics #prot-preprint

We are excited to have it out: a combination of archaeal proteases and hybrid fragmentation for antibody de novo sequencing. Poster TP-005 #asms2025 #teammassspec
It was a true team effort @lperezpaneda.bsky.social @tkadava.bsky.social @joostsnijder.bsky.social and @hecklab.bsky.social

Investigating the Use of Novel Blood Processing Methods to Boost the Identification of Biomarkers for Non-Small Cell Lung Cancer: A Proof of Concept Diagnosis of non-small cell lung cancer (NSCLC) currently relies on imaging; however, these methods are not effective for detecting early stage disease. Investigating blood-based protein biomarkers aims to simplify the diagnostic process and identify disease-associated changes before they can be seen by using imaging techniques. In this study, plasma and frozen whole blood cell pellets from NSCLC patients and healthy controls were processed using both classical and novel techniques to produce a unique set of four sample types from a single blood draw. These samples were analyzed using 12 immunoassays and liquid chromatography–mass spectrometry to collectively screen 3974 proteins. Analysis of all fractions produced a set of 522 differentially expressed proteins, with conventional blood analysis (proteomic analysis of plasma) accounting for only 7 of the total. Boosted regression tree analysis of the differentially expressed proteins produced a panel of 13 proteins that were able to discriminate between controls and NSCLC patients, with an area under the ROC curve (AUC) of 0.864 for the set. Our rapid and reproducible (<10% CV for technical replicates) blood preparation and analysis methods enabled the production of high-quality data from only 30 μL of complex samples that typically require significant fractionation prior to proteomic analysis. With our methods, almost 4000 proteins were identified from a single fraction over a 62.5 min gradient by LC-MS/MS.

Our proof of concept paper has just been published in the Journal of Proteome Research. Demonstrates our capabilities for blood proteomics, using both immunoassay and mass spec for fractionated blood and VAMS (dried blood spot) devices. #massspec #proteomics

pubs.acs.org/doi/10.1021/...

Recent Advances in Mass Spectrometry-Based Bottom-Up Proteomics Mass spectrometry-based proteomics is about 35 years old, and recent progress appears to be speeding up across all subfields. In this review, we focus on advances over the last two years in select are...

Check out our new review on recent advances in proteomics in collaboration with these PIs: Jie Sun, Devin Schweppe, and Stacy Malaker pubs.acs.org/doi/10.1021/...

A Vaccine For Pancreatic Cancer Continues To Show Promise In a small trial, nearly half of pancreatic cancer patients who received an mRNA vaccine for the disease had no relapse three years later.

90% of people diagnosed with pancreatic cancer die from the disease. That's why the medical community is excited about the results of a small trial in which nearly half of the pancreatic cancer patients who received an mRNA vaccine for the disease remained relapse-free three years later.