Dorrestein Lab
Dorrestein Lab
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Reverse metabolomics - CMMC workshop
Reverse metabolomics workshop provided as part of the Collaborative Microbial Metabolite Center (CMMC) on December 10th, 2024.
USIs used:
Phe-CA: mzspec:gnps:GNPS-LIBRARY:accession:CCMSLIB00006582001
Phe-C4: mzspec:GNPS:GNPS-LIBRARY:accession:CCMSLIB00010010601
His-C4: mzspec:GNPS:GNPS-LIBRARY:accession:CCMSLIB00011434738
Important links:
GNPS libraries: library.gnps2.org/
Reverse metabolomics tutorial Github repository: github.com/VCLamoureux/reverse-metabolomics
Fast search: fasst.gnps2.org/fastsearch/
Metabolomics Spectrum Resolver: metabolomics-usi.gnps2.org
microbeMASST: masst.gnps2.org/microbemasst/
Office Hours planned on reverse metabolomics:
December 12 - 9am PST
December 17- 9am PST
January 7- 9am PST
Join Zoom Meeting: ucsd.zoom.us/j/92750601296
Meeting ID: 927 5060 1296
มุมมอง: 419

วีดีโอ

QC-MXP Demo
มุมมอง 2427 หลายเดือนก่อน
In this video, Prof. David Broadhurst (Edith Cowan University) kindly provided a demo of his recently developed app QC:MXP (broadhurstdavid.github.io/QC-MXP/) based on his 2018 paper (link.springer.com/article/10.1007/s11306-018-1367-3). Watch the recorded session and discussion with him.
Library generation tutorial - MZmine3
มุมมอง 5147 หลายเดือนก่อน
Hands-on workshop on library generation with MZmine (version 3.9.0). April 19th, 2024.
Network Enrichment analysis and Deposition workflow - CMMC workshop
มุมมอง 695ปีที่แล้ว
Network enrichment and deposition workflow workshop provided as part of the Collaborative Microbial Metabolite Center (CMMC) on October 31st, 2023.
microbeMASST - CMMC Workshop
มุมมอง 873ปีที่แล้ว
microbeMASST workshop provided as part of the Collaborative Microbial Metabolite Center (CMMC) on July 5th, 2023.
Classical Molecular Networking - CMMC Workshop
มุมมอง 559ปีที่แล้ว
Classical Molecular Networking workshop provided as part of the Collaborative Microbial Metabolite Center (CMMC) on May 30th, 2023.
GNPS Molecular Networking with GCMS data in Portuguese - Part 1
มุมมอง 1.7K2 ปีที่แล้ว
Learn how to create a molecular networking with your GCMS data. Aprenda a gerar uma rede molecular com seus dados de CGMS.
GNPS Molecular Networking with GCMS data in Portuguese - Part 2
มุมมอง 1.2K2 ปีที่แล้ว
Learn how to create a molecular networking with your GCMS data. Aprenda a gerar uma rede molecular com seus dados de CGMS.
GNPS MANA 2021 Workshop
มุมมอง 1.3K3 ปีที่แล้ว
We want to familiarize the entire community on how to look at their data using classical molecular networking on GNPS by reanalyzing public MassIVE data with classical molecular networking, visualize raw mass spec data with GNPS Dashboard, and search/contextualize MS/MS data with MASST. Goals Select spectrum files and metadata from MassIVE public dataset Run classical molecular network workflow...
GNPS Dashboard - Use Case - Monika Thukral - MultiInstrument Analysis
มุมมอง 4153 ปีที่แล้ว
GNPS Dashboard - Use Case - Monika Thukral - MultiInstrument Analysis
GNPS Dashboard - GC/MS - Gregor
มุมมอง 2853 ปีที่แล้ว
GNPS Dashboard - GC/MS - Gregor
GNPS Dashboard - Metabolomics Workbench Integration
มุมมอง 3393 ปีที่แล้ว
GNPS Dashboard - Metabolomics Workbench Integration
GNPS Dashboard - Use Case GOB Tiny Earth course
มุมมอง 1853 ปีที่แล้ว
GNPS Dashboard - Use Case GOB Tiny Earth course
GNPS Dashboard - Puri Cummings - Quick data analysis of MS1 single quad data
มุมมอง 2333 ปีที่แล้ว
GNPS Dashboard - Puri Cummings - Quick data analysis of MS1 single quad data
GNPS Dashboard - Daniel Petras - Use Case 1
มุมมอง 3553 ปีที่แล้ว
GNPS Dashboard - Daniel Petras - Use Case 1
GNPS Dashboard - Tutorial Analysis
มุมมอง 6693 ปีที่แล้ว
GNPS Dashboard - Tutorial Analysis
GNPS Dashboard - Use Case 9 - Vanessa Phelan
มุมมอง 913 ปีที่แล้ว
GNPS Dashboard - Use Case 9 - Vanessa Phelan
GNPS Dashboard - Garg/Deutsch
มุมมอง 1313 ปีที่แล้ว
GNPS Dashboard - Garg/Deutsch
GNPS Dashboard - Use Case 18 - Navarro/Vasquez-Castro - Full Collaborative Exploration
มุมมอง 1833 ปีที่แล้ว
GNPS Dashboard - Use Case 18 - Navarro/Vasquez-Castro - Full Collaborative Exploration
GNPS Dashboard - Tutorial - Data Selection/Upload
มุมมอง 9213 ปีที่แล้ว
GNPS Dashboard - Tutorial - Data Selection/Upload
GNPS Dashboard- Tutorial 1
มุมมอง 2K3 ปีที่แล้ว
GNPS Dashboard- Tutorial 1
GNPS Dashboard - Tutorial - Synchronization/Collaboration
มุมมอง 3023 ปีที่แล้ว
Learn how to synchronize and collaboratively look at data with collaborators or in the classroom.
GNPS Dashboard Simon - Use Case 15
มุมมอง 963 ปีที่แล้ว
GNPS Dashboard Simon - Use Case 15
GNPS Dashboard - Use Case - Tiny Earth Classroom Exploration
มุมมอง 1613 ปีที่แล้ว
Join Allegra Aron to learn how Tiny Earth is using the GNPS Dashboard in the undergraduate classroom.
GNPS Dashboard - Scott Jarmusch - Targeted dereplication and evaluation of culture conditions
มุมมอง 4803 ปีที่แล้ว
GNPS Dashboard - Scott Jarmusch - Targeted dereplication and evaluation of culture conditions
Spatial distribution of molecules detected by LC-MS/MS from Atta texana fungus garden
มุมมอง 2103 ปีที่แล้ว
Spatial distribution of molecules detected by LC-MS/MS from Atta texana fungus garden
GNPS Dashboard Workshop
มุมมอง 1.4K3 ปีที่แล้ว
GNPS Dashboard Workshop
GNPS for GC-MS in petroleomics: using molecular networks to find incorrect annotations
มุมมอง 2283 ปีที่แล้ว
GNPS for GC-MS in petroleomics: using molecular networks to find incorrect annotations
GNPS for GC-MS in microbiology: using networks to explore chemistry of cheese
มุมมอง 3833 ปีที่แล้ว
GNPS for GC-MS in microbiology: using networks to explore chemistry of cheese
GNPS for GC-MS in biology: using molecular networks for compound discovery in dart frogs
มุมมอง 7013 ปีที่แล้ว
GNPS for GC-MS in biology: using molecular networks for compound discovery in dart frogs

ความคิดเห็น

  • @thiagobrito9979
    @thiagobrito9979 27 วันที่ผ่านมา

    I don't know where to find this option called "gnps Export" in the new versions of the MS Dial software. Can someone help me?

  • @flyinginmssim-solo4668
    @flyinginmssim-solo4668 หลายเดือนก่อน

    I was the final test engineer in the development of this MALDI benchtop. I tested every part of this mass spec during development, all the special memories just rushed back into my head, I spent a lot of hours testing almost every single part of the machine. You guys did a fabulous deep cleaning. Well done and thank you for the video.

  • @ZhiyuWan-y1o
    @ZhiyuWan-y1o 2 หลายเดือนก่อน

    Regarding [8:01](th-cam.com/video/KIOim2h8i64/w-d-xo.html), is it no longer supported to use custom MGF libraries? I found that if the SPECTRUMID item is missing (e.g., missing "SPECTRUMID=CCMSLIB00003134487") or this item is empty (e.g., "SPECTRUMID=") in the mgf library uploaded by oneself, it is impossible to perform library search and view the deconvolution results. Is this a bug?

  • @elisaguerra5239
    @elisaguerra5239 2 หลายเดือนก่อน

    Sensacional! Obrigada 👏🏼

  • @SamanehChaharmiri
    @SamanehChaharmiri 4 หลายเดือนก่อน

    your lab is incredible

  • @surendersehrawat3753
    @surendersehrawat3753 4 หลายเดือนก่อน

    is there any publication related to this

  • @lunadiao8876
    @lunadiao8876 5 หลายเดือนก่อน

    Is that the MS file format must to be MzXML? I didn't see this in the ReDU guide tutorial..., the data has been converted into MZML in MASSIVE, whats the relevance with this google document?

  • @shahidnawaz126
    @shahidnawaz126 5 หลายเดือนก่อน

    every time I execute molecular networking option it comes up with error saying, ERROR: main_specnets.cpp : 244: Input spectra set is empty for file inputspectra/spec-00000.mzXML ERROR: main_specnets.cpp : 244: Input spectra set is empty for file inputspectra/spectwo-00000.mzXML ERROR: main_specnets.cpp : 244: Input spectra set is empty for file inputspectra/specthree-00000.mzXML ERROR: main_specnets.cpp : 244: Input spectra set is empty for file inputspectra/specfour-00000.mzXML ERROR: main_specnets.cpp : 244: Input spectra set is empty for file inputspectra/specfive-00000.mzXML ERROR: main_specnets.cpp : 262: Input spectra set is empty ERROR: main_specnets.cpp : 263: Please make sure input files are 32-bit uncompressed mzXML files that contain MS/MS spectra ERROR: main_specnets.cpp : 949: Failed loading initial data. Tool execution terminates abnormally with exit code [1], can somebody help with that? the data is of LRMS not from HRMS

  • @robsonalmeida2562
    @robsonalmeida2562 6 หลายเดือนก่อน

    Poderiam disponibilizar o material?

  • @shahidnawaz126
    @shahidnawaz126 8 หลายเดือนก่อน

    I have a question , When we grow a certain microorganism in a media we process its LC-MS data as a blank (control). Is there any quick way to substract the metabolites produced by the media itself from those that are produced by the organism of interest?

  • @afzaalashraf9218
    @afzaalashraf9218 10 หลายเดือนก่อน

    I am using MZmine 3. And i am using LC-MS ADAP Chromatogram builder. After mass detection of MS1 and MS2 (following this tutorial), when i tried ADAP chromatogram it says the due to MS1 and MS2 data the results might be wrong, after building, i compared it with above tutorial, it is wrong, what should i do?

  • @lisaarnquist2197
    @lisaarnquist2197 10 หลายเดือนก่อน

    List of cables to be disconnected? want to share 🙂

  • @captainwheelbarrow649
    @captainwheelbarrow649 11 หลายเดือนก่อน

    Cool idea and great tutorial! Just wish I got more matches. Having to manually check each spectral database match by googling is compound X known made by fungi is a big pain

  • @NohaElzeny-u5q
    @NohaElzeny-u5q 11 หลายเดือนก่อน

    Can i upload mzxml files ? i did that but it gave me "failed" status

  • @YasminMounir-x7i
    @YasminMounir-x7i 11 หลายเดือนก่อน

    How can I obtain CDF. file to be able to upload to MassIVE? and IS this process can be used in MS/MS?

  • @YasminMounir-x7i
    @YasminMounir-x7i 11 หลายเดือนก่อน

    Firstly, I want to thank you for this workshop and all questions, you covered all points I need. Secondly, I want to ask "Can I use GNPS for only one sample or not? and if available which tools should i use?"

  • @silviahandayani5816
    @silviahandayani5816 ปีที่แล้ว

    Sir, In my cytoscape software is not CF_superclass menu in column style. Could you explain for me, Why is that?

  • @rafaelfeitosa6923
    @rafaelfeitosa6923 ปีที่แล้ว

    Excelente! Ajudou bastante!

  • @nikoandriansyah211
    @nikoandriansyah211 ปีที่แล้ว

    Filezilla not working in my pc, they said “server it does not support FTP over TLS

  • @christalho9386
    @christalho9386 ปีที่แล้ว

    nice job

  • @Nooruddinsadiq
    @Nooruddinsadiq ปีที่แล้ว

    can you please explain one thing that is this data set contain biological replicates or not and how those biological replicates will be represented in networking files

  • @quimi921
    @quimi921 ปีที่แล้ว

    Molnet enhancer for GC-MS?

  • @midiarodriguesdeoliveira4980
    @midiarodriguesdeoliveira4980 ปีที่แล้ว

    seria bom se disponibilizassem, na descrição do vídeo, o link para a documentação, pois o chat não aparece mais. Obrigada!

  • @renataporto3998
    @renataporto3998 2 ปีที่แล้ว

    I would like to thank you for this video. I unlock a new problem with WinSPC and thanks to this I learned Firezilla exists. !

  • @beatrizcostadesouza8133
    @beatrizcostadesouza8133 2 ปีที่แล้ว

    Acho que inverteram o "Part 2" com o "Part 1"

  • @aljuprannosh
    @aljuprannosh 2 ปีที่แล้ว

    how to take metadata from lcms/ms device for gnps?

  • @risanofiani2847
    @risanofiani2847 2 ปีที่แล้ว

    Is there a specific port I need to connect to ? My app is not connecting to the server.

    • @AliceMuller-mq9xz
      @AliceMuller-mq9xz ปีที่แล้ว

      Was this resolved? My filezilla is also not connecting to the massive server

  • @elianaalvarezvaldez3841
    @elianaalvarezvaldez3841 2 ปีที่แล้ว

    Hello, I would like to know if you have personalized courses for software management or do you know of any institute that does it and certifies the process?

  • @elianaalvarezvaldez3841
    @elianaalvarezvaldez3841 2 ปีที่แล้ว

    Hola, me gustaria saber si tienen cursos personalizados, para el manejo del software o conocen algun instituto que lo hagan y certifiquen el proceso? Hello, I would like to know if you have personalized courses for software management or do you know of any institute that does it and certifies the process?

  • @DrAkhtarAli08
    @DrAkhtarAli08 2 ปีที่แล้ว

    I learned data conversion; when I converted my data files, it was converted into a 3 GB file. I have been trying for the past 3 months, yet unable to upload the files.

  • @abdelhalimadel8425
    @abdelhalimadel8425 2 ปีที่แล้ว

    good

  • @abdelhalimadel8425
    @abdelhalimadel8425 2 ปีที่แล้ว

    Thanks alot

  • @wangjunhaowangjunhao8869
    @wangjunhaowangjunhao8869 2 ปีที่แล้ว

    can you share the file with email

  • @karolcarrillojaimes9025
    @karolcarrillojaimes9025 2 ปีที่แล้ว

    Quedó cortado :(

  • @DrAkhtarAli08
    @DrAkhtarAli08 2 ปีที่แล้ว

    I am trying to upload the file.

  • @rubiyeverino6415
    @rubiyeverino6415 2 ปีที่แล้ว

    Hi! How can i create this for my own samples? I don´t know what to upload on the iLi STL model box

  • @DrAkhtarAli08
    @DrAkhtarAli08 2 ปีที่แล้ว

    Appreciations, I want to learn molecular networking.

    • @2309649
      @2309649 ปีที่แล้ว

      me too

  • @handyhardyman
    @handyhardyman 3 ปีที่แล้ว

    Thank you so much for the good tutorial!

  • @tahirali4395
    @tahirali4395 3 ปีที่แล้ว

    Please share the link for the spreadsheet. Thanks. Warm regards to Prof. Dorresteine

  • @punamthapa1778
    @punamthapa1778 3 ปีที่แล้ว

    i have same hit at different retention time with same mass, how can i solve it?

  • @BioJAM156
    @BioJAM156 3 ปีที่แล้ว

    A very useful tutorial, indeed. Thank you so much.

  • @crystalconcepcion3887
    @crystalconcepcion3887 3 ปีที่แล้ว

    Beautiful presentation! Thank you!

  • @perriermentrude8466
    @perriermentrude8466 3 ปีที่แล้ว

    vzq4f vyn.fyi

  • @renataporto3998
    @renataporto3998 3 ปีที่แล้ว

    My Doubt is how to convert raw data to mzXML using a macbook, could you tell me? Thanks in advance

    • @dorresteinlab4428
      @dorresteinlab4428 3 ปีที่แล้ว

      you cant' do it on a Mac, you must use windows or you can use our GNPS quickstart convertor on the web

  • @tommasostefani3423
    @tommasostefani3423 3 ปีที่แล้ว

    Thanks a lot for the tutorial! Very useful!

  • @Abdullah_Al_Saud
    @Abdullah_Al_Saud 3 ปีที่แล้ว

    Panitchpakdi...why di except for the pronunciation?

  • @Michal-hardy
    @Michal-hardy 3 ปีที่แล้ว

    Thank you!

  • @omartovar7484
    @omartovar7484 3 ปีที่แล้ว

    Muchas gracias por esto!

  • @alokmishra8109
    @alokmishra8109 3 ปีที่แล้ว

    Thank you so much for uploading

  • @duaamagdy4740
    @duaamagdy4740 3 ปีที่แล้ว

    Keep the great work, Scott!!