Mingxun Wang
@mingxunwang.bsky.social
Assistant Professor @ UCR Computational Mass Spectrometry, Bioinformatics. #massspec #molecularnetworking #GNPS #MassQL https://www.cs.ucr.edu/~mingxunw/
We are hiring for a metabolomics position here at UC Riverside! Come join the vibrant research and mass spectrometry community here! aprecruit.ucr.edu/JPF02151
Assistant Professor in Computational and/or Analytical Metabolomics
University of California, Riverside is hiring. Apply now!
aprecruit.ucr.edu
To help make more mass spec data accessible - we've just rolled out a change to enable universal spectrum identifier resolution and plotting directly from mzML files in Zenodo. We're growing support from more sources in GNPS2 for public data reanalysis! metabolomics-usi.gnps2.org/dashinterfac...
Interested in a co-authorship? We’re building a tool for repository-scale untargeted #metabolomics and #exposomics of #environmental data. To make it the best it can be, we’re looking for people willing to share high-resolution LC-MS/MS (DDA) data from #water, #soil, #sediment, and related samples.
GNPS2 and associated services will be down for power maintenance tonight and into tomorrow.
We just crossed the 800,000 files mark in Pan-ReDU. That's 800,000 public #metabolomics raw data files with harmonized metadata that can be re-analyzed to learn about new molecules and bio-distributions. 🎉 redu.gnps2.org
The Mass Spectrometry Query Language (MassQL) is an open-source language for instrument-independent searching across mass spectrometry data for complex patterns of interest via concise and expressive queries without the need for programming skills. www.nature.com/articles/s41...
Thanks @ucriverside.bsky.social for featuring our work! news.ucr.edu/articles/202...
New computer language helps spot hidden pollutants
Courtesy of UC Riverside, biologists and chemists have a new programming language to uncover previously unknown environmental pollutants and other information at breakneck speed – without requiring th...
news.ucr.edu
Mingxun Wang@mingxunwang.bsky.social · last yr.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.
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.
MS-RT: A Method for Evaluating MS/MS Clustering Performance for Metabolomics Data pubs.acs.org/doi/10.1021/...
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.
pubs.acs.org
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
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...
cell.com
#FeaturedProtocol this week is a #reversemetabolomics protocol, in which a tandem #massspec spectrum is used as a search term to probe public #metabolomic data, enabling discovery of new metabolic associations bit.ly/4hdyQQF
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...
bit.ly
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....
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.
doi.org
GNPS2 is planning on being down for server maintenance tomorrow at 12PM PST. We expect 5 hours of downtime to move servers, bring online new storage, and increase networking performance.
GNPS2 will be down for the next hour for a new release update!
🚨 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
EMN Metabolomics Society@emn-metsoc.bsky.social · 2y ago🎉 First webinar for 2025! On 22 January at 3pm UTC, we will host Dr Wout Bittremieux who will deliver a talk on an approach to untargeted metabolomics data annotation! ✒️ Register here for free: tinyurl.com/2v654vp9 We look forward to seeing you there 👋
It was a wonderful working with so many old friends again at #SIMB. Thank you to all the participants who were super engaged and asked amazing questions. This kind of feedback is what makes building tools so worthwhile for the community and improves future developments.
Pieter Dorrestein@pieterdorrestein.bsky.social · 2y agoSuch 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
GNPS2 will be in maintenance this morning with some electricity upgrades in our data center room. We anticipate GNPS2 will come back online in a few hours.
Remember to VOTE in the ASMS Board election. All current members started to receive online ballot via email on Dec 2. Polls close on December 19. Learn about the election & meet the candidates here: www.asms.org/about/board-...
Congrats Laura on passing your second year seminar! @ucsantacruz.bsky.social #MassSpectacular #FeMS
To register docs.google.com/forms/d/e/1F...
Sign up - CMMC Workshop - Introduction to Reverse Metabolomics- Dec. 10 9am PST
The CMMC invites PAR-21-253 Grantees, Collaborators, POs, and Lab Members to the beginner friendly, hands-on workshop to look for microbial metabolites in the public domain.
docs.google.com
Pieter Dorrestein@pieterdorrestein.bsky.social · 2y agoThe 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 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
Scripps Institution of Oceanography, UCSD is looking for an assistant prof in marine natural products / marine biotech apol-recruit.ucsd.edu/JPF04101 #naturalproducts
Marine Natural Products/Marine Biotechnology - Assistant Professor
University of California, San Diego is hiring. Apply now!
apol-recruit.ucsd.edu
Next Tuesday, Nov 19, 5 pm CET / 8 am PST we will have the next #VMOL seminar #mzmine series on multimodal data processing using mzwizard. And in case you wana watch the last mzmine seminar on non-targeted LC-MS/MS data processing, you can find the recording here: youtu.be/UnqVtZngzl0
Join us here at UC Riverside! I’ve been here a bit over two years and it’s been a wonderful environment with fantastic colleagues!
Joseph Genereux@josephgenereux.bsky.social · 2y agoCome to California! Still time left to apply for Assistant Professor positions in Analytical and Physical Chemistry at UC Riverside. It's a great place to live and to work. #chemjobs #chemsky chem.ucr.edu/careers/new-...
Side-directed open modification search for metabolites: If you wana boost your insights about putative analogs, you many wana give Modifinder a try. Big congrats to Reza and Ming @mingxunwang.bsky.social et al. and thanks a lot for letting us play around with it. www.biorxiv.org/content/10.1...
