Bits & Bites: Short Course Series 2023 (Online)

 

When: January -December 2023
Where: online
Registration: here
Payment: here  
email: Jeannette Martins This email address is being protected from spambots. You need JavaScript enabled to view it.
phone: +1-530-754-5357

 

 
 
Bites & Bites 2023
 
UC Davis offers 1-week and 2-week intensive courses in Metabolomics, but many researchers cannot contribute so much time! Coming back now in its 3rd year, we are offering some of the most popular Bites in our short course series 'Bits & Bites' plus newly added short courses.

This 9-part short course series will feature in-depth topics in untargeted metabolomics such as a deeper look into MS-DIAL, mass spectrometry for metabolomics, lipidomics, GNPS, MetaboAnalyst, and so many others. 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 a highly interactive manner, with the use of freely available software and databases. The tuition is $175 per Bite, except for #5. The tuition for #5 is $350 as it will take approx. 8 hours

Bits & Bites # 01: Fundamentals of Lipidomics
Date: January 26, 2023
Instructor: Dr. Tong Shen, UC Davis
Required software: None
Participant prerequisites: None
Short description of the course: In this short course, we will cover topics related to lipids and systems-level scale analysis of lipids (lipidomics):

  • Introduction to lipids, classification, and functions
  • Mass spectrometry-based lipidomics, separation techniques, and perspectives on other novel technologies Case studies of lipidomics applications
  • Entire experimental pipeline—study design, sample extraction, analysis, data processing, identification, statistical methods, and visualization/interpretation resources
  • Quality control and standardization

Participants will gain a high-level overview of lipidomics in order to determine suitable strategies for their own research.

Bits & Bites # 02: Introduction to the GNPS Ecosystem - Tools, Visualizations, and Data
Date: February 9, 2023
Instructor: Dr. Mingxun Wang, UC Riverside
Required software: None
Participant prerequisites: GNPS Account, no programming experience necessary.
Short description of the course: Back by popular demand, in this short course we want to familiarize the entire community with how to look at their data using classical molecular networking on GNPS by reanalyzing public MassIVE data with classical molecular networking, visualizing raw mass spec data with GNPS Dashboard, and searching/contextualizing MS/MS data with MASST. The goals of the short course are to:

  • Select spectrum files and metadata from MassIVE public dataset
  • Run classical molecular network workflow
  • Qualitatively comparison of cohorts with molecular networks
  • Visualize LC/MS Data Interactively - GNPS Dashboard
  • Search Public Data with MASSTIdentify putative compounds
  • Visualize your molecular families

Bits & Bites # 03: Mass Spectrometry Imaging 101: Sample Preparation *New course*
Date: April 27, 2023
Instructor: Dr. Elizabeth Neumann, UC Davis
Required software: None
Participant prerequisites: None
Short description of the course: Have you ever looked at some mass spectrometry images and thought: "That is so cool! Can I do that?" Yes. Yes, you can! In this short course, we will cover the basics of sample preparation for mass spectrometry imaging analysis. We will start from the tissue and move all the way through the start of the data acquisition. This short course will include a mixture of video, PowerPoint content, and group discussion. By the end of the course, every researcher will have enough knowledge to start their own mass spectrometry imaging journey.

Bits & Bites # 04: Using MS-DIAL to generate accurate comprehensive LC-MS/MS metabolomics datasets
Date: May 25, 2023
Instructor: Dr. Jacob Folz, ETH Zurich
Required software: MS-DIAL for Windows. Versions of the tool to be used will be announced closer to the course date.
Participant prerequisites: Basic understanding of LC-MS and understanding of how MS/MS spectra are used in metabolite identification.
Short description of the course: Back by popular demand, this short course will focus on how to perform fine-tuned curation of processed LC-MS/MS data generated through MS-DIAL including compound identification, data quality analysis, and unknown feature reduction. Data from rat blood plasma analyzed using LC-MS/MS with MS/MS data collected in a data-dependent manner will be used to generate an example dataset, but the methods and techniques are applicable to many different sample types.

Bits & Bites # 05: Identification of unknown compounds in untargeted metabolomics using freely available software
Date: September 7, 2023 * 8-hrs
Instructor: Dr. Arpana Vaniya, UC Davis
Required software: Versions of tools to be used will be announced closer to the course date.

Participant prerequisites: Basic knowledge of computer skills. No coding experience is 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 of the current status of compound ID in metabolomics, participants will learn how to use freely available in silico fragmentation tools MS-FINDER and SIRIUS+CSI: FingerID, web-based tools such as MetFrag and CFM-ID and learn how to use MassBank of North America in NIST MS Search. Participants will get a chance to apply those skills to unknown challenges.

Bits & Bites # 06: Mass Spectrometry for Metabolomics
Date: October 5, 2023
Instructor: Dr. Uri Keshet, UC Davis
Required software: None
Participant prerequisites: None
Short description of the course: Mass spectrometry (MS) is an important analytical technique in many metabolomics labs. With GC-MS, LC-MS, EI, ESI, TOF, QQQ, Orbitrap, and many other different MS systems in the market, it can be challenging to make the right choice of instrument for your specific needs and constraints. In this short course, we will cover the fundamental principles of MS, including the different sample introduction types, ionization techniques, and mass analyzer varieties, and how they are used in metabolomics. Whether it is for targeted or untargeted applications, we will cover the basics of reading and understanding MS output data (i.e., EI-MS, ESI-MS, or ESI-MS/MS spectra). We will also cover tips & tricks for developing high-throughput MS methods (i.e., short 5-min method) that can be used in metabolomics. By the end of the course you will have a solid understanding of the available MS systems in the market, the pitfalls in using such systems, the basics of designing a study using the different MS approaches, and the tools for reading and processing MS data files.

Bits & Bites # 07: Introduction to Metaboanalyst
Date: November 2, 2023
Instructor:  Dr. Jeff Xia, McGill University
Required software: None
Participant prerequisites:  Basic knowledge of computer skills. No coding experience is needed.
Short description of the course:  In this short course, we will cover how to use MetaboAnalyst 5.0, a comprehensive platform dedicated to metabolomics data analysis. There will be a brief overview of data input, processing, and general workflow to perform PCA/PLS-DA/OPLS-DA analysis in MetaboAnalyst. More importantly, this course will cover how to use different functional analysis methods such as Enrichment Analysis, Pathway Analysis, Joint Pathway Analysis, and Network Analysis. Lastly, participants will also learn how to perform biomarker analysis and statistical analysis with complex metadata.

Bits & Bites # 08: Tips & Tricks of GC-MS in Metabolomics
Date: November 16, 2023
Instructor:  Dr. Oliver Fiehn, UC Davis
Required software: MS-DIAL for Windows. Versions of the tool to be used will be announced closer to the course date.
Participant prerequisites: Basic knowledge of computer skills. No coding experience is needed.
Short description of the course: While LC-MS is all the hype in today's portfolio of metabolomics assays, ranges of small molecules are difficult to impossible to screen in this manner. Volatile compounds in breath, urine, or plant analyses can best be analyzed by GC-MS. Additionally, swaths of primary metabolic intermediates ranging from glycolysis and pentose phosphates to TCA compounds, sugars, and small microbial metabolites are readily and cost-efficiently analyzed by GC-MS. In this short course, we discuss the fundamentals of GC-MS, tips for best practices, and aspects of instrumentation, and demonstrate data processing and use of databases. Participants will also learn the current challenges, trends, and developments of GC-MS-based metabolomics.

Bits & Bites #09: Metabolomics for Epidemiologists *New course*
Date: December 7, 2023
Instructor: Dr. Oliver Fiehn, UC Davis
Required software: None
Participant prerequisites: None
Short description of the course: Epidemiologists increasingly use metabolomic data in large human cohort studies that focus on public health problems and risk factor analyses. Classically, only a few variables were used in epidemiological analyses which were then stratified by multiple adjustments to find robust associations with phenotypes. Now, GWAS analyses have led the way for metabolite-wide association studies. How robust are metabolite data? What are the best normalization strategies? How should we deal with missing data, QC pools, and blanks? How can different studies be combined to increase power? Which identifiers could be used, and what is good coverage for metabolomic studies? These questions will be discussed in this short course to provide an overview of metabolomics including realistic goals and considerations for study designs, and metabolite coverage from commercial providers versus core facilities.