Daniel Petras

Thanks! And yes, depending on the reagent and pH, you will have some ion suppression and the sensitive will drop. To bypass that, I would run the initial runs without infusion/pH modulation.

Thanks so much to everybody who made this interdisciplinary project possible. And epically the editor and the three reviewers at @natcomms.nature.com for their throughout positive feedback.

Implementing the MCheM setup is pretty easy, and all reagents and hardware components are commercially available and relatively cheap.
MCheM data analysis is supported in @mzmine.bsky.social @gnps2.bsky.social and SIRIUS (@brightgiant.bsky.social) and free for academic researchers.

Enhancing tandem mass spectrometry-based metabolite annotation with online chemical labeling - Nature Communications To improve annotation in non-targeted metabolomics studies, authors develop a Multiplexed Chemical Metabolomics (MCheM) platform, combining post-column derivatization with integrated data processing. ...

New paper from the group. Together with Chambers Hughes, Giovanni Vitale and our amazing collaborators, we developed a multiplexed chemical metabolomics workflow to assign functional groups in non-targeted LC-MS/MS data:

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

Behind the paper story:
go.nature.com/45ljV4d

Thanks Gabriel :)

Thanks Don! Will post about the new work here and on our webpage www.functional-metabolomics.com/publication

Thanks a lot Tri :)

Thanks a lot Manuel!

Super excited that I’ve been selected as a Simons Early Career Investigator in Aquatic Microbial Ecology and Evolution. We will explore how marine microbes shape the production, transformation, and fate of dissolved organic matter.
Thanks so much @simonsfoundation.org
We can’t wait to get started!

www.grainger.com/product/SMC-...

I looked into it for a long time, happy to chat about details. I was close to buying one, but acilities finally increased the pressure to 110 psi. Was definitely worth the fight. Passive N2 generator works like a charm.

#mzmine 4.7 is now available!

This release brings our most significant improvement in memory efficiency to date, unlocking new capabilities for analyzing large-scale datasets.

Join us for a live software demo at our booth today and tomorrow at 12:00/noon during #ASMS2025

We are pretty stoked that our paper on chemical shifts in kelp forests in the Gulf of Maine made it onto the front cover of ‪@science.org
Big congratulations to Shane Farrell and everybody involved! ✌️✌️✌️

🎉 Fantastic News 🎉

Our CMFI Cluster of Excellence @unituebingen.bsky.social receives funding extension for the next seven years.

Spokesperson Andreas Peschel @andreaspeschel.bsky.social: "We can now advance our research into resistance mechanisms and new antimicrobial agents!"

shorturl.at/rcK1A

AutoMLST2: a web server for phylogeny and microbial taxonomy Abstract. Accurate and accessible phylogenetic analysis is essential for understanding microbial taxonomy and evolution, which are integral to microbiology

Happy to announce that our „newest old tool“ autoMLST2.0 is out and published. You need an accurate and easy to use tool to build #phylogenetictrees from #bacterialgenomes: academic.oup.com/nar/advance-...

Thanks @ucriverside.bsky.social for featuring our work!

news.ucr.edu/articles/202...

I am thrilled to share after years of work/procrastination that the MassQL manuscript is finally published in @natmethods.nature.com - "A universal language for finding mass spectrometry data patterns". This was an team effort from all co-authors that helped shape MassQL and how it could be used.

YouTube video by Michael T Marty IsoDec Tutorial 1: Analysis of Individual Spectra

Check out the latest tutorial video, from Marty Lab postdoc John Pavek, on how to analyze individual spectra with IsoDec, our new neural network for isotopic deconvolution: youtu.be/aOR37-j28NI

Another year, another @mzmine.bsky.social workshop at
@iocbprague.bsky.social! Both new and advanced users are learning about the latest mzmine features from our amazing instructors @ansgarkorf.bsky.social, Josh Smith,
@titodamiani.bsky.social, and @roman-bushuiev.bsky.social.

Big Congrats!!!

New reprint from the team: Lead by @nike-wagner.bsky.social, we used our native metabolomics setup to shed new light onto the function of the CutA protein.
www.biorxiv.org/content/10.1...

Looks amazing!

MS-RT: A Method for Evaluating MS/MS Clustering Performance for Metabolomics Data The clustering of tandem mass spectra (MS/MS) is a crucial computational step to deduplicate repeated acquisitions in data-dependent experiments. This technique is essential in untargeted metabolomics, particularly with high-throughput mass spectrometers capable of generating hundreds of MS/MS spectra per second. Despite advancements in MS/MS clustering algorithms in proteomics, their performance in metabolomics has not been extensively evaluated due to the lack of database search tools with false discovery rate control for molecule identification. To bridge this gap, this study introduces the MS1-retention time (MS-RT) method to assess MS/MS clustering performance in metabolomics data sets. Here, we validate MS-RT by comparing MS-RT to established proteomics clustering evaluation approaches that utilize database search identifications. Additionally, we evaluate the performance of several MS/MS clustering tools on metabolomics data sets, highlighting their advantages and drawbacks. This MS-RT method and the MS/MS clustering tool benchmarking will provide valuable real world practical recommendations for tools and set the stage for future advancements in metabolomics MS/MS clustering.

I am excited to share this new paper out in JPR - "MS-RT: A Method for Evaluating MS/MS Clustering Performance for Metabolomics Data." This work introduces the MS-RT method to assess MS/MS clustering accuracy on metabolomics data.

doi.org/10.1021/acs....

Very important read about the discussion on in-source fragments in LC-MS/MS based metabolomics.
By reanalyzing data from 30,000 authentic standards @yelabiead.bsky.social @adafede.bsky.social @pieterdorrestein.bsky.social et al. show that ISFs are substantially less that what Giera et al. reported 👌

I can’t think of a better group to learn metabolomics data science from.

Phosphorylated glycosphingolipids are commonly detected in Caenorhabditis elegans lipidomes - Metabolomics Introduction The identification of lipids is a cornerstone of lipidomics, and due to the specific characteristics of lipids, it requires dedicated analysis workflows. Identifying novel lipids and lipi...

I'm happy to share my latest article published today. A nice collaboration with Aiko and Sven from Bruker Daltonics. #metabolomics #lipidomics #celegans
doi.org/10.1007/s113...

🚨 Webinar Reminder! 🚨

Don’t forget to join us for our first webinar of the year:
“Learning From Repository-Scale Untargeted Metabolomics Data”
📅 Date: 22 January
🕒 Time: 3 PM UTC

#MetabolomicsSociety #MetSoc #Metabolomics #ECR #TeamMassSpec #EMNMetSoc

Such a wonderful SIMB workshop on @gnps2.bsky.social covering classical mol networking, FBMN, ion identity based mol networking, FBMN-STATS, gnps-dashboard, CMMC-kb, Modifinder, MicrobeMASST, MassQL, and limited ReDU - many were covered at a workshop for the first time. 1/4

Release UniDec Version 8.0.0 · michaelmarty/UniDec Version 8.0.0 UniDec. Please cite Marty et al. Anal. Chem. 2015. DOI: 10.1021/acs.analchem.5b00140 if you use UniDec in publications. Check out a video tutorial: https://www.youtube.com/watch?v=e33...

Really excited to release a beta version of UniDec 8.0!

The coolest feature is a new AI-based charge assignment for isotopic resolution data. It's performing a little better than Thrash/Xtract but way faster. Try out IsoDec if you are doing top-down!

github.com/michaelmarty...

Assistant Professor in Fungal Biology University of California, Riverside is hiring. Apply now!

My department is hiring a fungal biologist! aprecruit.ucr.edu/JPF01990

👨‍🔬👩‍🔬Grants announcement !!!
A limited number of supporting grants will be given to early career researchers and #ICTC13 participants from lower income countries.
Don't miss the opportunity to submit an abstract and apply for an #ICTC13 grant !
Deadline: 20 December
More: ictc13.gr/grants/