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#TipTuesday Do you struggle with false #lipid annotations?   An ongoing concern in lipid analysis is the potential for misidentification of lipid biomarkers due to the misannotation of lipid mass spectra. This issue arises from the similar spectra generated during lipid fragmentation, which often contain only a few signals, such as side chain and headgroup ions. Relying solely on library matching can lead to over annotation of lipid structures.   To address this issue, tools like rule-based lipid annotation in #mzmine offer a solution by annotating lipids at varying levels of confidence based on the data. This tool can annotate features at the species level (sum composition) or molecular species level (side chain length and saturation) automatically in mzmine. Additionally, the use of equivalent carbon number and Kendrick mass defect plots serves as quality control measures, enhancing the reliability of your data interpretation.   For cases involving uncommon or non-biological lipids, users have the flexibility to define their own lipid classes and fragmentation rules, further increasing confidence in lipid annotation and making #lipidomics accessible to both specialists and novices alike.

mzio GmbH Enters Strategic Collaboration with Functional Genomics Center Zurich to Advance Development of Metabolomics and Lipidomics Tools We will kick off our collaboration by hosting a hands-on workshop in Zurich: Register here (https://lnkd.in/dr39urwx) Bring your laptop for the full experience—or just join the live demo! Where: FGCZ, UZH Irchel Campus, Y59 G30, Zurich When: Wednesday, 7 May 2025 | 13:00–17:00 Alaa Othman Christian Panse #metabolomics #lipidomics #mzmine #FGCZ

mzio GmbH Enters Strategic Collaboration with Functional Genomics Center Zurich to Advance Development of Metabolomics and Lipidomics Tools We will kick off our collaboration by hosting a hands-on workshop in Zurich: Register here (https://lnkd.in/dr39urwx) Bring your laptop for the full experience—or just join the live demo! Where: FGCZ, UZH Irchel Campus, Y59 G30, Zurich When: Wednesday, 7 May 2025 | 13:00–17:00 Alaa Othman Christian Panse #metabolomics #lipidomics #mzmine #FGCZ

We are very excited about our new strategic collaboration with Functional Genomics Center Zurich (FGCZ). Stay tuned for more updates coming shortly!

New paper alert! We’re proud to present this latest study tackling one of the biggest challenges in #Microbiology by introducing a rapid, high-confidence profiling of Lipid A.   #LipidA is a key component of the outer membrane of Gram-negative bacteria and a major contributor to bacterial #toxicity. It is highly structurally diverse, stemming from variations to its acyl chains and phosphorylation, resulting in thousands of possible species even within a single bacterial strain.   Bacteria can chemically modify lipid A headgroups, disrupting the ability of the bacterial outer membrane to bind certain antibiotics, reducing their effectiveness and leading to increasing #antibiotic #resistance.   A rapid and automated #bacterialprofiling assay of lipid A species is introduced, in which Trapped Ion Mobility Spectrometry (#TIMS) is utilized to enhance sensitivity and reduce background noise. Selectivity is further improved using the novel SIMSEF data dependent fragmentation mode, unique to mzmine.   #SIMSEF is an automated MALDI-MS/MS data-dependent acquisition strategy, derived from #prm-#PASEF, that selects and fragments precursors based on their ion mobility and m/z values. In this work, SIMSEF has been enhanced to run on MALDI target plates, enabling large-scale assays with rapid fragmentation and minimal manual intervention.   mzmine was subsequently used to annotate the fragmented Lipid A analogues by applying custom fragmentation rules to confirm annotation with high confidence, enabling the characterization of regioisomers C1P vs. C4′P MPLA using diagnostic fragments and differences in CCS values. Using this set of custom rules, up to 2832 lipid A species can be annotated.   This study also introduces the first collision cross section (CCS) values for lipid A, paving the way for future in-silico databases and confident lipidomics at scale.   Congratulations to the authors for this innovative work! Edward Rudt Matti Froning, Steffen Heuckeroth, Lucas Ortmann, Julia Diemand, Linus Hörnschemeyer, Alexander Pleger, Max V.., Robin Schmid, Tomáš Pluskal, Ulrich Dobrindt, Heiko Hayen, Ansgar Korf   Read this open-access paper here https://lnkd.in/gZk8rdh7

Congratulations on the success of the NPLinker workshop, demonstrating how #mzmine facilitates natural product discovery! Biosynthetic gene clusters (#BGCs) are physically clustered groups of genes within a genome that encode a biosynthetic pathway for producing specialized metabolites, often secondary metabolites. These clusters are responsible for producing a wide variety of natural products, including #antibiotics, #toxins, and other bioactive compounds. There are advanced genomic mining tools that identify biosynthetic gene clusters and group them into genetically and functionally similar gene cluster families (GCFs). GCFs likely produce chemically related metabolites, such as analogs or structural variants of a core compound. It is thus adventageous to correlate #genomic data with with large-scale datasets containing #metabolomics data from mass spectrometry. By linking a GCF to an MS/MS feature (or family of features), you gain insight into the function and product class of that gene cluster family. #NPLinker creates a unified workflow that connects genomic and metabolomic datasets, enabling systematic and data-driven discovery, and thus, paving the way for faster, more reliable identification of novel natural products with therapeutic potential by: 🔍 Accelerating discovery by prioritizing novel GCFs linked to unique or interesting metabolite profiles. 🧬 Enabling functional annotation of unknown BGCs based on shared profiles within a GCF. 🔁 Supporting dereplication, helping avoid rediscovery of known compounds by linking GCFs to familiar metabolites. 🧪 Revealing biosynthetic logic and evolutionary relationships between gene clusters and their chemical products. 🔗 Bridging genes and chemistry, enabling genetic manipulation or synthetic biology applications for specific metabolites. Find out more and view the online materials from the last workshop here https://lnkd.in/gUDkxwnG

Spotlight on Ansgar Korf at the upcoming Startup Brain Gain discussion forum Join us on April 1, 2025, as Ansgar Korf, CEO and founding member of mzio, takes the stage with a compelling startup challenge. Ansgar will bring an exciting question to the table, and your insights could help shape the next chapter of innovation. This is your chance to collaborate, brainstorm, and contribute to real-world startup problem-solving. 📍 Where? KUKOON, Bremen 📅 When? April 1, 2025 – Doors open at 5:30 p.m., event starts at 6:00 p.m Hope to see you there! #startup #Bremen #mzio

#TipTuesday Does your lab have multiple platforms? Are you looking to invest in new technology? It can be tedious and time consuming to adopt a processing method across different software packages. This is especially challenging, as vendor software is often exclusively built for a single vendor or platform. This can also hinder the development of your lab, as it discourages the adoption of new technologies. mzmine PRO saves time and money on training users by supporting multiple vendors and technologies on a single platform. This enables you to streamline and scale your workflows, without worrying about locking out new tech. And it’s supported by experts to help you on your journey. #mzmine #newtech #massspectrometry

New paper alert! A recent study introduces deep characterization of bile acids, overcoming the limitations of traditional MS/MS spectral library matching. #Bileacids play a critical role in metabolism and immunity, but their structural diversity and isomeric complexity make them difficult to distinguish using conventional MS/MS spectral libraries. In the study of the #microbiome, bile acid characterization is of high importance, as multiple enzymes catalyze chemical modifications, including hydroxylation, dehydroxylation, dehydration, and oxidation, resulting in a large number of isomeric metabolites. Conventional spectral matching struggles with isomeric bile acids, due to their similar fragmentation patterns and limited spectral libraries restrict the identification of novel bile acids. This study from introduces a combination of utilizing #mzmine data processing with an open-source MassQL-Based Filtering Tree. Analysis of different data sets, including those analyzing the effects of diet on #Alzheimer’s disease, rheumatoid #arthritis and a #HIV neurobehavioral study, identified a common compound across studies. The workflow enabled the structural characterization of this compound, revealing it to be deoxycholyl-2-aminophenol, a novel bile acid linked to whole grain metabolism. This method can be applied retrospectively to public LC-MS/MS datasets, expanding unknown bile acid isomer annotation. Congratulations to the team for this impressive work! Ipsita Mohanty, Shipei Xing, Vanessa Castillo, Julius Agongo, Ph.D. Abubaker Patan, Ph.D., Yasin El Abiead, Helena Mannochio Russo,Simone Zuffa, Jasmine Zemlin, Alexandre Tronel, Audrey LE GOUELLEC, Thomas Soranzo, Jennifer Iudicello, Mohammadsobhan S. Andalibi, Ronald Ellis, David Moore, Donald Franklin Jr., Marta Sala Climent, PhD, Monica Guma, Robin Voigt, Rima Kaddaruh-Dauok, Dionicio Siegel , Mingxun Wang, Lee Hagey, Pieter Dorrestein Read more here: https://lnkd.in/gA9TGEHK

Happy Friday everyone! We are wrapping up a productive week with the release of a brand new update for mzmine 😎 Check out the latest feature-packed version at: https://lnkd.in/gySfsNgS #mzmine #Update #Productivity