Gary Siuzdak

This @RichardZare paper doi.org/10.1021/acsm... shows spray ionization creates new molecules via microdroplet chemistry, which then undergo ISF, together explaining much of the LC–MS signal explosion. Recognizing source-derived ions is essential to keep metabolomics grounded in biology.

[ASAP] In-Source Fragmentation Annotation in Sterol Mass Spectrometry Imaging Analytical ChemistryDOI: 10.1021/acs.analchem.5c05199

(ACS Anal Chem) [ASAP] In-Source Fragmentation Annotation in Sterol Mass Spectrometry Imaging: Analytical ChemistryDOI: 10.1021/acs.analchem.5c05199 #MassSpecRSS #ACSAChem

glad it worked out as well as it has Johannes!
It will be interesting to see what you think of our next venture

xcms in Peak Form: Now Anchoring a Complete Metabolomics Data Preprocessing and Analysis Software Ecosystem High-quality data preprocessing is essential for untargeted metabolomics experiments, where increasing data set scale and complexity demand adaptable, robust, and reproducible software solutions. Mode...

xcms in Peak Form: Now Anchoring a Complete Metabolomics Data Preprocessing and Analysis Software Ecosystem #AC pubs.acs.org/doi/10.1021/...

Congratulations Steffen!

xcms in Peak Form: Now Anchoring a Complete Metabolomics Data Preprocessing and Analysis Software Ecosystem High-quality data preprocessing is essential for untargeted metabolomics experiments, where increasing data set scale and complexity demand adaptable, robust, and reproducible software solutions. Modern preprocessing tools must evolve to integrate seamlessly with downstream analysis platforms, ensuring efficient and streamlined workflows. Since its introduction in 2005, the xcms R package has become one of the most widely used tools for LC-MS data preprocessing. Developed through an open-source, community-driven approach, xcms maintains long-term stability while continuously expanding its capabilities and accessibility. We present recent advancements that position xcms as a central component of a modular and interoperable software ecosystem for metabolomics data analysis. Key improvements include enhanced scalability, enabling the processing of large-scale experiments with thousands of samples on standard computing hardware. These developments empower users to build comprehensive, customizable, and reproducible workflows tailored to diverse experimental designs and analytical needs. An expanding collection of tutorials, documentation, and teaching materials further supports both new and experienced users in leveraging broader R and Bioconductor ecosystems. These resources facilitate the integration of statistical modeling, visualization tools, and domain-specific packages, extending the reach and impact of xcms workflows. Together, these enhancements solidify xcms as a cornerstone of modern metabolomics research.

Out now! xcms in Peak Form: Now Anchoring a Complete Metabolomics Data Preprocessing and Analysis Software Ecosystem doi.org/10.1021/acs....
with Phillipine and @jorainer.bsky.social (EURAC), @metabomichael.bsky.social, Hendrik and Norman from @ipbhalle.bsky.social, @janstanstrup.bsky.social, et al.

Congratulations Johannes, nicely done!

Great work from @philouail.bsky.social 🙌

#xcms now fully integrated into @bioconductor.bsky.social 💪

👉 #metabolomics #MassSpectrometry #rstats

Quantitative Systems Pharmacology (QSP)
Clear, authoritative overview from PK/PD & mechanistic models to AI and regulatory use. A landmark resource for QSP, PK/PD, and translational modeling Erica Bradshaw & @Mary_Spilker

Amazon: a.co/d/fZfZBSW
link.springer.com/book/10.1007...

A new concept in MRM generation — adaptive modeling of tandem MS data using spline fitting of absolute intensities.

Now in Analytical Chemistry (open access article): doi.org/10.1021/acs....

Empirical MRM transitions created for 960K compounds → METLIN 960K MRM.
#MassSpec #METLIN #AIinScience

MRM generation using adaptive modeling of tandem MS data. A simple concept that allows for MRM analysis without the need for standards.
• Especially useful for preclinical metabolites, that have no standards.
Analytical Chemistry (open access article)
pubs.acs.org/doi/10.1021/...

In response to the multiple requests on how MRM generation works (without standards) from the MS/MS data, here it is step by step.
Analytical Chemistry (open access article)
doi.org/10.1021/acs....

In response to the multiple requests on how MRM generation works (without standards) from the MS/MS data, here it is step by step.
Analytical Chemistry (open access article)
doi.org/10.1021/acs....

MRM generation using adaptive modeling of tandem MS data. A simple concept that allows for MRM analysis without the need for standards.
• Especially useful for preclinical metabolites, that have no standards.
Analytical Chemistry (open access article)
pubs.acs.org/doi/10.1021/...

A new concept in MRM generation — adaptive modeling of tandem MS data using spline fitting of absolute intensities.

Now in Analytical Chemistry (open access article): doi.org/10.1021/acs....

Empirical MRM transitions created for 960K compounds → METLIN 960K MRM.
#MassSpec #METLIN #AIinScience

Lipidomics combined with CRISPR can help decipher the complex biochemistry that allow cancer cells to evade elimination.
www.nature.com/articles/s41...
#Nature fruitful collaboration with @JavierGarcia-Bermudez UT Southwestern #VitaminE

A free version just posted—courtesy of #Nature.
Lipidomics (via #XCMS / #METLIN) reveals α-tocopherol (vitamin E) as a key player in ferroptosis resistance in cancer.

t.co/HMJSLuTAnM

#Lipidomics #CancerResearch #Ferroptosis #VitaminE

Lipidomics (& #METLIN) reveal a metabolic vulnerability in tumors @Nature doi.org/10.1038/s415...

Tumors don’t just synthesize their own lipids—they scavenge antioxidant-rich lipoproteins. @JaviGBermudez with our lab's lipidomics uncover how this can be used to impair tumor growth

An AI BioSync rendition of METLIN 960K as a dot matrix. Celebrating the creation of METLIN with 960,000 molecular standards, and going live in its original classic form - reengineered.

🔗 Sign in for access: metlin.scripps.edu/auth-login.h...

📖 Read more: DOI: 10.1002/ansa.70012

At least a partial explanation for all the unidentifiable peaks we see in LC/MS/MS experiments of small molecules. More details on the experiments and how ISF determinations were made at doi.org/10.1002/ansa... and doi.org/10.1038/s422...

Unexpected growth on the #METLIN front, now reaching 960K molecular standards with MS/MS natural product additions. 960K METLIN currently available online via XCMS-METLIN. xcmsonline.scripps.edu
@Molsystbio doi.org/10.1038/s443...

Toward Real-Time Proteomics: Blood to Biomarker Quantitation in under One Hour Multistep multihour tryptic proteolysis has limited the utility of bottom-up proteomics for cases that require immediate quantitative information. The power of proteomics to quantify biomarkers of hea...

Krakatoa doesn't have to just mean violent destruction. Close to real-time proteeomics was achieved via a combined effort between @CedarsSinai and Cinder with their unique hypothermophile enzyme "Krakatoa"

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

“Because they wouldn’t let me give it away”

my answer when people ask why did I not publish AMMS with a publishing house.

Free PDF at Scripps Research:
masspec.scripps.edu/about/mass-s...

Royalty-free print version at Amazon ($15.08):
a.co/d/8dEWO8a

You are welcome Pawel, hopefully it will save students from using a bit of their income.

AMMS 2025 book is live, the PDF just became available, and you can freely download the entire book here...
masspec.scripps.edu/about/mass-s...
Two new chapters, new sections, and refinements throughout.

The royalty-free print version of #AMMS 2025 will be available on Amazon next week.

The latest version of Activity Metabolomics and Mass Spectrometry (AMMS 2025) is now in the proof stage. AMMS 2025 has two new chapters, lipids, and a lot of polishing. Still free as a PDF, and as royalty-free print version on Amazon.
Coming as soon as we get the proofs (and are happy with them).

Monday morning session on June 2nd at ASMS will include

"Metabolomics & Lipidomics"

Please submit your abstract to this session, as I am looking forward to introducing the latest in metabolomic and lipidomic technology developments, and their applications.
asms.org/conferences/...

The future of untargeted analysis is closer than we think. Could #AI predict metabolites that are not yet known to exist? #ML combined with #metabolomics/#lipidomics is redefining how we #Scripps are performing discovery using #METLIN's massive dataset & AI's power, the possibilities are intriguing

The central message behind our two recent papers in @NatMetabolism @MolSystBiol

•• If you can’t identify it with XCMS-METLIN,
highly likely it is ISF (in-source fragmentation) ••

Both papers are open access
www.nature.com/articles/s42...
www.embopress.org/doi/full/10....

The simplicity of precursor ion filtering combined with MS/MS matching to deconvolve data on XCMS-METLIN's 935K+ molecular standards @MolSystBiol doi.org/10.1038/s443...
XCMS-METLIN local now available at massconsortium.com