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ometa-labs.bsky.social

@ometa-labs.bsky.social
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Uncovering the dark matter of the metabolome | Empowering researchers to measure, connect, visualize, and understand the hidden chemical world within untargeted tandem mass spectrometry data | www.ometalabs.net

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ometa-labs.bsky.social @ometa-labs.bsky.social · 08/09/2025
MASST searches billions of spectra in seconds, answering the question, "Where have I seen this molecule before?" in the same time it takes to ask it. Custom MASST databases tailor searches to your research questions. Want to try it out? Check out our new tutorial: www.youtube.com/watch?v=9mga....
youtube.com
Tutorial: Building Custom MASST Databases
YouTube video by Ometa Labs
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ometa-labs.bsky.social @ometa-labs.bsky.social · 19/08/2025
Love metabolite annotation? Check out this new paper on reverse spectral search, a simple idea that can dramatically improve annotation of chimeric spectra. Full text here: pubmed.ncbi.nlm.nih.gov/40815677/. Congrats to all the authors, especially @shipei-xing.bsky.social!
pubmed.ncbi.nlm.nih.gov
Reverse Spectral Search Reimagined: A Simple but Overlooked Solution for Chimeric Spectral Annotation - PubMed
The exponential growth of untargeted metabolomics data, now reaching billions of mass spectra in public repositories, benefits from reannotation strategies for data reuse. While tandem mass spectromet...
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ometa-labs.bsky.social @ometa-labs.bsky.social · 07/08/2025
Cool new paper alert! 𝗜𝗻𝘁𝗲𝗴𝗿𝗮𝘁𝗶𝗻𝗴 𝗠𝗮𝘀𝘀𝗤𝗟 𝗮𝗻𝗱 𝗠𝗼𝗹𝗲𝗰𝘂𝗹𝗮𝗿 𝗡𝗲𝘁𝘄𝗼𝗿𝗸𝗶𝗻𝗴 𝘁𝗼 𝗜𝗱𝗲𝗻𝘁𝗶𝗳𝘆 𝗕𝗶𝗼𝗮𝗰𝘁𝗶𝘃𝗲 𝗖𝗼𝗺𝗽𝗼𝘂𝗻𝗱𝘀 𝗶𝗻 𝙄𝙙𝙚𝙨𝙞𝙖 𝙥𝙤𝙡𝙮𝙘𝙖𝙧𝙥𝙖 𝗠𝗮𝘅𝗶𝗺 is a great example of how combining MassQL with molecular networking can cut through the noise and reveal bioactive compounds. Read more here: pubs.acs.org/doi/10.1021/....
pubs.acs.org
Integrating MassQL and Molecular Networking to Identify Bioactive Compounds in Idesia polycarpa Maxim
Idesia polycarpa Maxim (Salicaceae) is a well-studied plant producing various hydroxycyclohexenone (HCH) ester derivatives, which constitute most of its secondary metabolites. However, these major metabolites have been reported as unrelated to the alpha-melanocyte stimulating hormone (α-MSH) induced microphthalmia-associated transcription factor (MITF) expression observed in B16F10 melanoma cells, suggesting they may not be responsible for the antimelanogenic effect previously seen with the crude extract. To resolve this discrepancy and identify the bioactive metabolites in the crude extracts, the chemical diversity of I. polycarpa was reanalyzed using Mass Spec Query Language (MassQL)-enhanced molecular networking analysis, which indicated the presence of molecular families of phenolic glycosides without HCH esters. Following the MassQL-guided strategy to uncover the compounds responsible for the bioactivity, a targeted isolation study yielded five previously undescribed compounds and three known compounds, consistent with the MassQL annotations. Notably, one of the isolated non-HCH ester compounds, compound 1, demonstrated significant inhibition of α-MSH-induced melanogenesis via tyrosinase inhibition and MITF downregulation. This finding provides a potential explanation for the previously observed antimelanogenic activity of the crude extract, addressing the inconsistency associated with the major metabolites.
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ometa-labs.bsky.social @ometa-labs.bsky.social · 14/07/2025
Cool paper alert! 𝗔𝗻 𝗲𝘃𝗮𝗹𝘂𝗮𝘁𝗶𝗼𝗻 𝗺𝗲𝘁𝗵𝗼𝗱𝗼𝗹𝗼𝗴𝘆 𝗳𝗼𝗿 𝗺𝗮𝗰𝗵𝗶𝗻𝗲 𝗹𝗲𝗮𝗿𝗻𝗶𝗻𝗴-𝗯𝗮𝘀𝗲𝗱 𝘁𝗮𝗻𝗱𝗲𝗺 𝗺𝗮𝘀𝘀 𝘀𝗽𝗲𝗰𝘁𝗿𝗮 𝘀𝗶𝗺𝗶𝗹𝗮𝗿𝗶𝘁𝘆 𝗽𝗿𝗲𝗱𝗶𝗰𝘁𝗶𝗼𝗻 introduces a reproducible method for evaluating ML models that predict spectral similarity. Read more here: bmcbioinformatics.biomedcentral.com/articles/10.... Congrats to the authors!
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ometa-labs.bsky.social @ometa-labs.bsky.social · 07/07/2025
Love natural products? We do too! In our new video tutorial, we show you how to go from MS/MS data to a novel bioactive natural product produced across the tree of life - all in under 5 minutes. Watch here: www.youtube.com/watch?v=hg79....
youtube.com
Discovering Natural Products in Ometa Flow
YouTube video by Ometa Labs
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ometa-labs.bsky.social @ometa-labs.bsky.social · 19/06/2025
How do microbes shape host biology - and how can we measure it? This excellent new review offers a comprehensive look at how to tackle this question. Read the full text here: pubs.rsc.org/en/content/a... Congrats to all the authors!
pubs.rsc.org
Mass spectrometry-based metabolomics approaches to interrogate host–microbiome interactions in mammalian systems
Covering: 2015 to 2025Chemical crosstalk is universal to all life, niche-specific, and essential to thrive. This crosstalk is mediated by a large diversity of molecules, including metal ions, small mo...
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ometa-labs.bsky.social @ometa-labs.bsky.social · 18/06/2025
Check out our new blog post on peak integration! www.ometalabs.net/resources/pe...
ometalabs.net
Peak Integration — Ometa Labs
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ometa-labs.bsky.social @ometa-labs.bsky.social · 17/06/2025
The cool papers just keep coming! 𝘌𝘹 𝘝𝘪𝘷𝘰 Interaction Between Human Gut Microbiota and Artemisinin: A Multi-Omics Perspective explores how the antimalarial drug artemisinin is metabolized by the human gut microbiota. Read more here: pmc.ncbi.nlm.nih.gov/articles/PMC... Congrats to the authors!
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ometa-labs.bsky.social @ometa-labs.bsky.social · 16/06/2025
Cool new paper alert! 𝘛𝘩𝘦 𝘮𝘪𝘤𝘳𝘰𝘣𝘪𝘰𝘮𝘦 𝘥𝘪𝘷𝘦𝘳𝘴𝘪𝘧𝘪𝘦𝘴 𝘭𝘰𝘯𝘨- 𝘵𝘰 𝘴𝘩𝘰𝘳𝘵-𝘤𝘩𝘢𝘪𝘯 𝘧𝘢𝘵𝘵𝘺 𝘢𝘤𝘪𝘥-𝘥𝘦𝘳𝘪𝘷𝘦𝘥 𝘕-𝘢𝘤𝘺𝘭 𝘭𝘪𝘱𝘪𝘥𝘴 uses MassQL to identify over 750 new 𝘕-acyl lipids. Read the full text here: www.cell.com/cell/fulltex... Congrats to all the authors!
cell.com
The microbiome diversifies long- to short-chain fatty acid-derived N-acyl lipids
Mass spectrometry data mining tools enabled the creation of an MS/MS spectral library containing hundreds of N-acyl lipids, including conjugates with short-chain fatty acids. This resource enabled the...
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ometa-labs.bsky.social @ometa-labs.bsky.social · 10/06/2025
Ometa MASST is coming - and we want your feedback! We’re opening beta registration for the new Ometa Labs MASST server, purpose-built to bring high-throughput mass spectrometry search to the forefront of your research. Register here: ometa-labs.neetoform.com/febd96405b1f...
Banner announcing registration for beta testing of Ometa Lab's new MASST server.
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ometa-labs.bsky.social @ometa-labs.bsky.social · 05/06/2025
Did you use GNPS during your academic career? Ometa Labs adapts the cutting-edge workflows of GNPS for industry. This means one-on-one support and troubleshooting, enhanced data privacy, and custom development to fit your analysis needs. Contact us to learn more: www.ometalabs.net/contact
Banner image with text Ometa Labs: the cutting edge features of GNPS, designed for industry.
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ometa-labs.bsky.social @ometa-labs.bsky.social · 04/06/2025
Beta test our new MASST server! MASST is a revolutionary algorithm that can search billions of mass spectra in seconds. By beta testing, you'll get two weeks of unlimited searches free! Register here: ometa-labs.neetoform.com/febd96405b1f... New to MASST? Learn more here: youtu.be/jAOj4XBFQEM?...
Banner announcing registration for beta testing of Ometa Lab's new MASST server.
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ometa-labs.bsky.social @ometa-labs.bsky.social · 03/06/2025
Potential activity for next year's #ASMS? m.xkcd.com/3094/
Mass spec comic from xkcd: https://m.xkcd.com/3094/
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ometa-labs.bsky.social @ometa-labs.bsky.social · 29/05/2025
What's the difference between Ometa Labs and GNPS/GNPS2? TL;DR: GNPS2 is great, but is only available for non-commercial use. Ometa Flow provides GNPS2 workflows to businesses, with analysis solutions, security, and support tailored to industry needs.
Comparison of GNPS/GNPS2 and Ometa Labs. Ometa Labs provides GNPS2 workflows to businesses.
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ometa-labs.bsky.social @ometa-labs.bsky.social · 28/05/2025
What is MASST? At Ometa Labs, we're tackling one of metabolomic's biggest challenges: the fact that over 80% of small molecules go unannotated using traditional library searches. MASST changes the game. Learn more here: youtu.be/jAOj4XBFQEM?... Don't miss the exciting announcement at the end!
youtu.be
What is MASST? Uncovering the Unknown in Mass Spectrometry
YouTube video by Ometa Labs
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ometa-labs.bsky.social @ometa-labs.bsky.social · 21/05/2025
Natural products have shaped modern medicine, but their discovery is still challeneging. Our newest application note highlights how Ometa Flow can accelerate natural products discovery by going from raw data to lead compounds in less than 15 minutes. Read more here: www.ometalabs.net/application-...
ometalabs.net
Accelerating Natural Products Research with Ometa Flow — Ometa Labs
Natural products and their derivatives make up the majority of FDA-approved small molecule drugs, yet natural products discovery still plays a small role in pharmaceutical R&D. Learn how Ometa Flo...
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ometa-labs.bsky.social @ometa-labs.bsky.social · 15/05/2025
Ever looked at a compound and wondered: where have I seen this before? Domain-specific MASST can answer that question in seconds, and show where your compound is detected across microbes, plants, tissues, and more. Learn more here: www.ometalabs.net/resources/do...
ometalabs.net
Domain-Specific MASST — Ometa Labs
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ometa-labs.bsky.social @ometa-labs.bsky.social · 12/05/2025
So exited to see this paper out! MassQL is game changing for compound identification (plus it's really fun to use!). You can read more about MassQL here: www.ometalabs.net/resources/ma.... Congrats to the authors!
ometalabs.net
MassQL — Ometa Labs
What is the Mass Spec Query Language and how can it help you analyze your mass spectrometry data?
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Reposted by @ometa-labs.bsky.social
Mingxun Wang @mingxunwang.bsky.social · 12/05/2025
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.
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ometa-labs.bsky.social @ometa-labs.bsky.social · 16/04/2025
In small‑molecule mass spec, we often treat spectral differences caused by adducts or collision energies as nuisances. But this new study flips that script and demonstrates a powerful way to predict chemical modifications. Read more here: pubmed.ncbi.nlm.nih.gov/40202176/ Congrats to the authors!
pubmed.ncbi.nlm.nih.gov
Multispectrum ModiFinder Site Localization Performance - PubMed
Tandem mass spectrometry (MS/MS) is a powerful technique for structural identification of small molecules, yet a significant portion of MS/MS spectra from untargeted experiments remain unidentifiable ...
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ometa-labs.bsky.social @ometa-labs.bsky.social · 09/04/2025
Want to learn about Ometa Flow but only have 49 seconds? Here you go! youtu.be/U2aAHK8ysvU?... #discovery #smallmolecules #metabolomics
youtu.be
What is Ometa Flow?
YouTube video by Ometa Labs
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ometa-labs.bsky.social @ometa-labs.bsky.social · 07/04/2025
Great news! We're rolling out a new licensing tier designed for smaller teams. These licenses include all the tools and workflows Ometa has to offer, along with our best-in-class expert support. Learn more on our website: www.ometalabs.net.
Banner announcing new licensing tier that provides Ometa Flow for as low as $15K
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ometa-labs.bsky.social @ometa-labs.bsky.social · 03/04/2025
Really cool paper applying MassQL to system suitability testing: www.authorea.com/doi/full/10..... Congrats to the authors Heather Winter, Dylan Johnson, and Alan K. Jarmusch! Haven't heard of MassQL? Check out our blog post here: www.ometalabs.net/resources/ma...
authorea.com
Open-source System Suitability: Mass Spectrometry Query Language Lab (MassQLab)
Reproducible analytical instrumentation system performance is critical for mass spectrometry, particularly metabolomics, aptly named system suitability testing. We identified a need based on literatur...
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ometa-labs.bsky.social @ometa-labs.bsky.social · 01/04/2025
Guess our job here is done.
Banner image with breaking news that scientists have discovered the final metabolite.
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ometa-labs.bsky.social @ometa-labs.bsky.social · 27/03/2025
Have a burning compound identification question? Drop by our office hours on Tuesdays from 12-1 pm Eastern to discuss with our team. Sign up here: www.ometalabs.net/contact Note: if you're an academic, check out the GNPS2 office hours here: wang-bioinformatics-lab.github.io/GNPS2_Docume...
ometalabs.net
Contact — Ometa Labs
Get in touch! Drop in for office hours or schedule a meet and greet to discuss your small molecule analysis needs with Ometa's expert team.
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ometa-labs.bsky.social @ometa-labs.bsky.social · 25/03/2025
Considering running small molecule analysis through a contract research organization (CRO)? While we're not a CRO, we've helped a lot of people analyze data from CROs. Check out our new blog post on what to consider when using a CRO for metabolomics. www.ometalabs.net/resources/me...
ometalabs.net
What to look for in metabolomics CROs — Ometa Labs
CROs are a great and cost-effective way to run metabolomics experiments, but not every CRO provides the same level of analysis. Learn what questions to ask when considering a metabolomics CRO.
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ometa-labs.bsky.social @ometa-labs.bsky.social · 17/03/2025
Have opinions about mass spectrometry file formats? Check out the new mzPeak white paper and join the discussion on how to make mass spectrometry data formats open, scalable, and interoperable. zenodo.org/records/1492... #massspectrometry #bigdata
zenodo.org
Seeking community input for: mzPeak - a modern, scalable, and interoperable mass spectrometry data format for the future
Abstract Advancements in mass spectrometry (MS) instrumentation—including higher resolution, faster scan speeds, increased throughput, and improved sensitivity—along with the growing adoption of imagi...
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ometa-labs.bsky.social @ometa-labs.bsky.social · 12/03/2025
Great protocol on reverse metabolomics. An incredible technique if you are generating lead compounds or optimizing production or purification of natural products. Congrats to the wonderful team of authors! www.nature.com/articles/s41... #reversemetabolomics #massspectrometry #discovery #bigdata
nature.com
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 these search results enabl...
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ometa-labs.bsky.social @ometa-labs.bsky.social · 10/03/2025
Incredibly interesting paper on metabolite discovery and in-source fragmentation. Congrats to all the authors! Check it out here: www.nature.com/articles/s42... #discovery #metabolites #massspectrometry
nature.com
Discovery of metabolites prevails amid in-source fragmentation - Nature Metabolism
Nature Metabolism - Discovery of metabolites prevails amid in-source fragmentation
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ometa-labs.bsky.social @ometa-labs.bsky.social · 07/03/2025
Another fascinating paper evaluating MS/MS clustering performance in metabolomics data: pubs.acs.org/doi/10.1021/... Spoiler alert: if you'd like to try Falcon clustering, let us know! Congrats to @mingxunwang.bsky.social, the team at @corteva.bsky.social, and all the other authors!
pubs.acs.org
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...
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ometa-labs.bsky.social @ometa-labs.bsky.social · 06/03/2025
Congrats to all the people who put in tremendous effort to make this study possible. Such a fun project! www.cell.com/cell/fulltex... #space #metabolomics #microbes
cell.com
The International Space Station has a unique and extreme microbial and chemical environment driven by use patterns
With long-term space travel and extraterrestrial habitation becoming feasible, understanding how space environmental exposures, microbial communities, and molecular profiles differ from Earth is cruci...
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ometa-labs.bsky.social @ometa-labs.bsky.social · 04/03/2025
Detecting PFAS requires a new approach to environmental analysis that goes beyond traditional targeted methods. Learn how Ometa Flow can detect both known and unknown PFAS in minutes. www.ometalabs.net/application-... #PFAS #MassQL #Environment #Exposome #MassSpectrometry
ometalabs.net
PFAS identification with MassQL — Ometa Labs
The environmental persistence of per- and polyfluoroalkyl substances (PFAS) creates unique challenges for detection and regulation of this large class of synthetic chemicals. Learn how MassQL and mole...
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ometa-labs.bsky.social @ometa-labs.bsky.social · 25/02/2025
Do you have a new printer and want a nice overview of Ometa Flow? You're welcome. #massspectrometry #metabolomics #compoundidentification
Overview of Ometa Labs tools and services. Ometa Labs provides software for compound identification, molecular networking, library management, search tools, and statistical analysis of mass spectrometry data.
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ometa-labs.bsky.social @ometa-labs.bsky.social · 19/02/2025
Curious about Ometa but not sure where to begin? We've got you covered! youtu.be/bv46lZJMZgY?... #metabolomics #massspectrometry #dataanalysis #smallmolecules
youtu.be
What can Ometa Labs do for you?
YouTube video by Ometa Labs
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ometa-labs.bsky.social @ometa-labs.bsky.social · 12/02/2025
Looking to improve your quality control processes? Check out our newest application note on metabolomics for quality control! www.ometalabs.net/application-... #qualityassurance #qualitycontrol #massspectrometry #metabolomics #qc
ometalabs.net
Untargeted Metabolomics for Quality Control — Ometa Labs
Discover how untargeted metabolomics can rapidly identify novel contaminants in manufacturing and pinpoint sources of contamination.
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ometa-labs.bsky.social @ometa-labs.bsky.social · 11/02/2025
Are you a fun, single MS2 spectrum looking for a match this Valentine's Day? Then look no further than MASST: speed dating for MS2 spectra. www.ometalabs.net/resources/ma... #msms #science #massspectrometry #metabolomics
ometalabs.net
MASST — Ometa Labs
MASST is a revolutionary spectral search tool that can return matches to billions of MS/MS spectra in seconds. Learn how MASST can accelerate your metabolomics analysis.
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ometa-labs.bsky.social @ometa-labs.bsky.social · 04/02/2025
Ever wondered what's up with all the different types of molecular networking? Well, this won't answer all your questions but it might answer two of them. www.ometalabs.net/resources/cm... #msms #molecularnetworking #metid
ometalabs.net
Classical vs. Feature-Based Molecular Networking — Ometa Labs
What is the difference between Classical Molecular Networking and Feature-Based Molecular Networking?
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ometa-labs.bsky.social @ometa-labs.bsky.social · 03/02/2025
Learn how molecular networking can rapidly identify novel drug metabolites, without knowing all potential biotransformations in advance. www.ometalabs.net/application-... #metaboliteid #drugsafety #msms #metabolomics
ometalabs.net
Molecular Networking for Metabolite Identification (MetID) — Ometa Labs
Understanding how a drug is modified in the human body is crucial for assessing its safety and efficacy. Every new drug candidate must undergo metabolite identification (MetID) studies to determine wh...
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ometa-labs.bsky.social @ometa-labs.bsky.social · 30/01/2025
Is this you? www.ometalabs.net/molecular-ne...
ometalabs.net
What is molecular networking? — Ometa Labs
So you ran an untargeted metabolomics experiment, now what?Molecular networking is an incredibly powerful tool that can rapidly identify known compounds and discover novel metabolites in tandem mass s...
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ometa-labs.bsky.social @ometa-labs.bsky.social · 29/01/2025
Having trouble finding your perfect match? Maybe you should try cosine scores. www.ometalabs.net/resources/ms... #massspectrometry #msms #compoundID #metID #metabolomics
ometalabs.net
Library Matching — Ometa Labs
I have a mass spectrum - now how do I figure out which metabolite it represents?
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ometa-labs.bsky.social @ometa-labs.bsky.social · 28/01/2025
Did you know we have a youtube channel? The place for all your hot new mass spectrometry tutorial content. youtube.com/@ometalabs?s... #tutorials #massspectrometry #metabolomics
youtube.com
Ometa Labs
Ometa Labs empowers scientists to measure, connect, visualize, and understand the hidden chemical world within untargeted tandem mass spectrometry data. We provide a fully customizable and secure soft...
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ometa-labs.bsky.social @ometa-labs.bsky.social · 27/01/2025
MS or MS/MS? www.ometalabs.net/resources/ms... #massspectrometry #metabolomics #msms
ometalabs.net
MS1 vs. MS2 (or both!) — Ometa Labs
What is MS1 vs. MS2 and why does it matter?
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ometa-labs.bsky.social @ometa-labs.bsky.social · 23/01/2025
Well, while we're all waiting to see what happens to grant reviews, maybe read about targeted vs. untargeted metabolomics? It always makes me feel better. www.ometalabs.net/resources/un...
ometalabs.net
Targeted vs. Untargeted Metabolomics — Ometa Labs
What is the difference between targeted and untargeted metabolomics and why does it matter?
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ometa-labs.bsky.social @ometa-labs.bsky.social · 22/01/2025
We scientists love our acronyms, but if you've ever encountered GC/LC-MS/MS in the wild and want to know what it means, here is your chance to find out: www.ometalabs.net/resources/wh... #massspectrometry #metabolomics #LCMS #GCMS
ometalabs.net
What is mass spectrometry? — Ometa Labs
What is mass spectrometry-based metabolomics?
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ometa-labs.bsky.social @ometa-labs.bsky.social · 21/01/2025
So what is metabolomics? www.ometalabs.net/resources/wh... #metabolomics #massspectrometry
ometalabs.net
What is metabolomics? — Ometa Labs
What is metabolomics?
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