Mauricio Caraballo

The mass spectrometry of microbiome-mediated metabolism of food: challenges and opportunities With the exception of molecules acquired through the lungs, skin absorption, or part of a medication regime, nearly all molecules in our bodies origin…

The interactions between food, microbiome and host that modulate health can be complex. Here, we offer a perspective on how mass spectrometry can be leveraged to address some of these challenges to understand host and microbial metabolism of food. A step closer to personalized health and nutrition.

Nova: A library for rapid development of mass spectrometry software applications Nova is a software library for the reading, writing, and management of mass spectrometry data natively in the C# language. It complements similar software libraries ubiquitously used in application development for C++, Python, and Java. Few software libraries and resources for mass spectrometry data analysis have been developed for C# relative to other languages. C#, however, remains the dominant language of choice for development of real time mass spectrometry (RTMS) analysis and instrument control applications, illustrating the need for native C# libraries when developing RTMS software. Nova provides fast, easy-to-use structures and classes built upon interfaces that support open community standards, and are easily extensible for current or future mass spectrometry software development needs.

(BioRxiv All) Nova: A library for rapid development of mass spectrometry software applications: Nova is a software library for the reading, writing, and management of mass spectrometry data natively in the C# language. It complements similar software libraries ubiquitously… #BioRxiv #MassSpecRSS

Tryptophan metabolism in children with migraine: The role of kynurenine pathway Migraine is a common neurological disorder in children, significantly impacting quality of life and academic performance. The kynurenine pathway, a major metabolic route of tryptophan, plays a critica...

Tryptophan metabolism in children with migraine: The role of kynurenine pathway #BrainDev #MassSpec www.brainanddevelopment.com/article/S038...

Our community letter on #FAIR principles in #moleculardynamics simulations has been published on @naturemethods.bsky.social 🎉

This is figure 1, which shows simulated contrasting precipitation responses to deforestation at different scales (0–1,000 km) over the Amazon region.

Amazonian deforestation is making wet seasons wetter and dry seasons dryer, according to research in Nature. The analysis highlights the local and regional effects of removing trees from the tropical region. https://go.nature.com/41jCClO 🧪

This is figure 3, which shows intercontinental species flow of non-native insects.

Global insect invasions are increasing, driven by advances in globalization and technology. A Review in Nature Reviews Biodiversity discusses the effects of increasing trade and transport on insect invasions worldwide, and strategies for mitigation. https://go.nature.com/3X6QkHk

Enhanced Lipidomics Workflows for Plasma and Extracellular Vesicles through Advanced Liquid Chromatography-Tandem Mass Spectrometry Integrated Lipidomics, a subfield of metabolomics, provides comprehensive analysis of lipids in biological systems and is essential for biomedical research, driv…

Enhanced Lipidomics Workflows for Plasma and Extracellular Vesicles through Advanced Liquid Chromatography-Tandem Mass Spectrometry Integrated #Talanta www.sciencedirect.com/science/arti...

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

Discovery of metabolites prevails amid in-source fragmentation - Nature Metabolism Nature Metabolism - Discovery of metabolites prevails amid in-source fragmentation

Discovery of metabolites prevails amid in-source fragmentation #NatMetab www.nature.com/articles/s42...

MSConnect: Open-Source, End-to-End Platform for Automated Mass Spectrometry Data Management, Analysis, and Visualization The scale of mass spectrometry-based proteomics data sets continues to increase, and the analysis workflows are becoming more complex as various steps are carried out using a multitude of software programs developed by both commercial providers and the research community. Manually shepherding data across multiple programs and in-house-developed scripts can be error prone and labor intensive. It is also difficult for others to follow the same steps, leading to poor repeatability. We have developed an integrated data management and analysis platform termed MSConnect that enables simple and traceable processing workflows across multiple programs, thus improving repeatability and automating common backup and analysis steps from the point of data collection through summarization and visualization. The open nature of the MSConnect platform enables the diverse omics community to seamlessly integrate third-party tools or develop and automate their own unique workflows. With an open license and design architecture, MSConnect has the potential to become a community-driven platform serving a wide range of MS-based omics researchers.

MSConnect: Open-Source, End-to-End Platform for Automated Mass Spectrometry Data Management, Analysis, and Visualization #JProteomeRes pubs.acs.org/doi/10.1021/...

Wow, we have been teaching over 12 years #Metabolomics! Our LCMS course is from 3/24-3/28. A couple seats are left. More info/ registration/ payment are here: metabolomics.ucdavis.edu/hands-lc-ms-.... @msacl-org.bsky.social @jjjvanderhooft.bsky.social @pieterdorrestein.bsky.social

It’s not every day one gets to publish an article with NASA astronauts. This journey started in 2019 and withe the goal to understand the microbial and chemical make-up of the space station. We had lots of experience with analysis from swabs on earth.

To Impute or Not To Impute in Untargeted Metabolomics─That is the Compositional Question Untargeted metabolomics often produce large datasets with missing values. These missing values are derived from biological or technical factors and can undermine statistical analyses and lead to biase...

Another fun paper that was started by a good and important question by Prajit - an undergrad in the lab - about imputation. We then teamed up with the Kelley lab as they are good at such benchmarking in data science. So fun to work woth them. pubs.acs.org/doi/10.1021/...

A guide to reverse metabolomics—a framework for big data discovery strategy Nature Protocols - In this reverse metabolomics protocol, a tandem mass spectrometry spectrum is used as a search term to probe public metabolomic data. Analysis of the metadata connected with...

Reverse metabolomics made these two papers a reality. www.nature.com/articles/s41... and www.cell.com/cell/fulltex... but hard for others to do similar analysis as the data science is at a high level. So @vincentlamoureux.bsky.social wanted to enable others with this powerful strategy rdcu.be/ebIF2

Untargeted metabolomics reveals biomarkers for the diagnosis of coronary artery plaques as observed by coronary cardiac computed tomography Patients from the north of Israel who underwent cardiac CT were classified into two groups: Patients with coronary artery plaques (CAD group) and patients without artery plaques (control group). Un-t...

Untargeted metabolomics reveals biomarkers for the diagnosis of coronary artery plaques as observed by coronary cardiac computed tomography #BioFactors iubmb.onlinelibrary.wiley.com/doi/10.1002/...

Modulating the human gut microbiome and health markers through kombucha consumption: a controlled clinical study - Scientific Reports Scientific Reports - Modulating the human gut microbiome and health markers through kombucha consumption: a controlled clinical study

"How does kombucha impact the gut microbiome and health? 🧬🍵 Our new study explores this popular fermented tea's subtle effects on gut bacteria and biochemical markers in a Western diet context. Dive into the findings:

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

Pangenome mining of the Streptomyces genus redefines species’ biosynthetic potential - Genome Biology Background Streptomyces is a highly diverse genus known for the production of secondary or specialized metabolites with a wide range of applications in the medical and agricultural industries. Several...

In July, we tripled the number of high-quality Streptomyces genomes in the NCBI. Today, we have published an updated pangenomic analysis of their biosynthetic potential! Very greatful to Omkar for including me in this project!!

🧪🦠 #microbiology

genomebiology.biomedcentral.com/articles/10....

The 2025 Chemistry Faculty Jobs List

The 2025 Chemistry Faculty Jobs List has 462 tenure-track positions and 77 teaching positions: bit.ly/facultychemj... #facultychemjobs chemjobs chemsky

Such amazing talks in the post-SIMB meeting symposium.

I want some jabuticabas 😍 🙌

Proud of my lab for helping with such a worthy effort. 3 grad students, 1 postdoc, 1 staff, and 1 very tired PI from our lab represented here!

t.co/ysDjvNHxkY

Really excited and impressed by Mitja @marnixmedema.bsky.social and everyone for their efforts to coordinate us globally for the latest iteration of MIBiG, and grateful to have had a role in this rollout!

Elevated bile acids induce circadian rhythm sleep disorders in chronic liver diseases Sleep disorders (SDs) are common in chronic liver diseases (CLDs). Some SDs arise from impaired internal clock and are hence circadian rhythm SDs (CRS…

Elevated bile acids induce #circadian rhythm #sleep disorders in chronic #liver diseases

Cholemia is a major risk factor for CRSDs in CLDs and hence promising target in future clinical study.
www.sciencedirect.com/science/arti...

Deadline - this Friday

Call for ISME Society Awards nominations - ISME We encourage our membership to nominate individuals worthy of winning one of our three prestigious awards.

Every two years, ISME celebrates the achievements of scientists who have substantially advanced the field of microbial ecology. If you know of outstanding members of the community worthy of an ISME Society Award, please fill in the nominations ballot by 31 Jan 2025👇🏼
isme-microbes.org/call-for-ism...

Welcome to CMMC!

We are excited to announce our upcoming workshop designed to be interactive and beginner friendly. We will introduce Reverse Metabolomics, a novel approach to identifying microbial metabolites using mass spec. We will show YOU how to identify and categorize microbial metabolites!

The 2025 Chemistry Faculty Jobs List

The 2025 Chemistry Faculty Jobs List (by Andrew Spaeth, me) has 428 tenure-track positions and 65 teaching positions: bit.ly/facultychemj... facultychemjobs chemjobs chemsky 🧪

The CMMC is hosting a reverse metabolomics workshop. The foundation of these papers www.nature.com/articles/s41..., www.cell.com/cell/fulltex... and www.biorxiv.org/content/10.1... - here searched @gnps2.bsky.social only now @metabolights.bsky.social and @metabolomics workbench as well. #metabolome

The Natural Products Atlas 3.0: extending the database of microbially derived natural products Abstract. The Natural Products Atlas is a database of microbially derived natural products that contains structures, producing organism taxonomy, biosynthe

The Natural Products Atlas 3.0: extending the database of microbially derived natural products - thanks to the Linington lab for letting the Duncan lab be part of the curation efforts academic.oup.com/nar/advance-... #NaturalProducts #SpecializedMetabolites #microsky #microbialchemistry

This is only achieved due to the creativity of people that we get to work and collaborate with. Thanks to all.