CMFI Mass Spec Seminar #7 - MZmine3 Hands-On Feature Finding

Hands-On Tutorial for Feature Finding with MZmine3, with Robin Schmid (UC San Diego)

Slides: https://docs.google.com/presentation/...

Download the latest stable MZmine 3 release from the MZmine GitHub page:
https://github.com/mzmine/mzmine3/rel...

Installers and portable versions are available for all major operating systems. macOS users currently have to manually trust the MZmine software, as we are still in the process of signing MZmine with Apple. More information here:
https://github.com/mzmine/mzmine3#run...

Download data files from google drive (6 mzML files): https://drive.google.com/drive/folder...
The data is also shared on MassIVE under the following ID: MSV000084628

Batch file:
https://drive.google.com/file/d/1ViKv...

Output files (for GNPS and SIRIUS):
https://drive.google.com/drive/folder...

Download any spectral library for compound annotation in MZmine:
https://mona.fiehnlab.ucdavis.edu/dow...
Fhttps://gnps-external.ucsd.edu/gnpsli...


Seminar Description:
This bi-weekly seminar series is targeted to give a general introduction to contemporary mass spectrometry, and in particular how to analyze biomolecules. We will cover fundamental hardware principles on how a mass spectrometer works and application focused data analysis approaches. The seminar is meant to be very interactive and will have a large hands-on component for the data analysis tools.
The goal is to start from zero and bring everybody to a level of executing independently different mass spec data analysis tasks within a few sessions.
As the seminar will be very user focused, the content will only be set for the first lectures and will then evolve based on the participants interest. The idea is hereby that we will have guest lectures from experts in the field (e.g. mass spec software developers) as well as participants of the seminar who want to highlight their own data acquisition and data analysis approaches. That said, the seminar shall serve as a dynamic platform to teach and exchange ideas and concepts in mass spectrometry.
The focus will be at the beginning on non-targeted LC-MS/MS and data analysis with GNPS (gnps.ucsd.edu) and MZmine (mzmine.github.io) environment but might then shift to other metabolomics approaches (e.g. targeted metabolomics and other non-targeted approaches such as flow-injection analysis) as well as proteomics methods (e.g. shot-gun and top-down proteomics).

More Infos: https://www.functional-metabolomics.c...