Identification of unknown compounds in untargeted metabolomics using freely available software for compound ID with Dr. Arpana Vaniya, UC Davis
Date: August 05, 2021
Instructor: Dr. Arpana Vaniya, UC Davis
Required software: MS-FINDER (http://prime.psc.riken.jp/compms/msfinder/main.html) & SIRIUS+CSI:FingerID (https://bio.informatik.uni-jena.de/software/sirius/). CFM-ID will be as the web-based tool. Versions of tools to be used will be announced closer to the course date.
Participant prerequisites: Basic knowledge of computer skills. No coding experience needed.
Short description of the course: Compound identification is known as the bottleneck in metabolomics. However, there are many approaches one may consider while tackling this challenge (i.e. mass spectral library search, in silico fragmentation tools, or database searching). This short course will provide an overview on the current status of compound ID in metabolomics, participants will learn how to use some current tools for compound ID (i.e. CFM-ID, MS-FINDER, and SIRIUS+CSI:FingerID), and apply those skills to some unknown challenges.
More information: UC Davis offers 1-week and 2-week intensive courses in Metabolomics, but many researchers cannot contribute so much time! We therefore offer 'Bits and Bites' of some of our most popular parts of our intensive courses, see below. We hope to see you there!
This 6-part short course series will feature in-depth topics in untargeted metabolomics such as pathway-based interpretation, Bayesian statistics, and a deeper look into MS-DIAL version 4.0. Each short course can be taken individually or you can select multiple Bites. Participants will gain a deeper insight into current software, methods, and pitfalls. Each session starts promptly at 9 a.m. (Pacific Time) and will take approx. 4 hours. The courses will be conducted in highly interactive manner, with use of freely available software and databases. The tuition is $150 per Bite. We do offer a discounted price when you take 5 Bites for $700 or 6 Bites for $800.