Workshops

Novice Track Workshops

New in 2018! Introducing the Novice Track, a group of workshops aimed at students and other researchers who are new to or less experienced in the field of metabolomics. These 5 workshops walk through the major steps in a typical metabolomics analysis from Experimental Design, Mass Spec Analysis, Statistical Analysis, Pathway Analysis, followed by a Career Workshop. Novice Track workshops are open to everyone.

Hands-On Workshops

Some sessions listed below have a “Hands-On Session” indicator. These sessions will require you to bring your own laptop to the workshop. Hands On Workshops are open to everyone.

 

Sunday 12:00pm - 2:00pm

QA and QC in Untargeted Metabolomics
Organizers: Dan Bearden, Bianca Bethan (Metanomics Health), Clary Clish (Broad Institute), Annie Evans (Metabolon Inc.), Rick Higashi (University of Kentucky), Ping-Ching Hsu (University of Arkansas for Medical Sciences), Christina Jones (National Institute of Standards and Technology), Jonathan Mosley (Environmental Protection Agency), Claire O’Donovan (European Bioinformatics Institute), Susan Sumner (University of North Carolina), Krista Zanetti (National Cancer Institute)

A recent National Cancer Institute-sponsored Think Tank highlighted the need for a community-wide consensus on systematizing quality assurance (QA) and quality control (QC) practices for untargeted metabolomics. This workshop is intended to inform attendees about the Think Tank and discuss QA and QC principles. For the purposes of the workshop, QA will be defined as the set of LC-MS-based procedures that are performed in advance of sample analysis used to improve data quality (e.g., education, method development, and documentation); and QC will be defined as the set of activities that a laboratory conducts during and after LC-MS analysis to demonstrate the quality of project data (e.g., utilization of data quality metrics). The overall goal of the workshop is to provide a forum at which experienced investigators performing untargeted metabolomics studies will share real-life examples of ‘good’ and ‘bad’ QA and QC practices to highlight the current state of the field. By the end of the workshop, attendees will have an improved knowledge of this topic and learn about opportunities to participate in ongoing activities that have emerged from the Think Tank.

EMN - Experimental Design in Metabolomics: Choosing Suitable Strategies (Novice Track)
Organizers: Tim Causon, University of Natural Resources and Life Sciences, Vienna, Austria; Julia Kuligowski, Health Research Institute La Fe, Valencia, Spain; Candice Z. Ulmer, Centers for Disease Control and Prevention, Atlanta, GA, USA

Over the last 15 years, the application of metabolomics has become an important part of biological hypothesis generation and testing. With a wide range of research questions now requiring metabolome-level information, metabolomics entails the use of multidisciplinary skillsets to combine biological, analytical, statistical, and computational elements. Hence, the experimental design of a successful metabolomics study must be well-planned to ensure robust datasets are produced for meaningful statistical analysis and biological interpretation. The experimental design includes sampling considerations, choice of appropriate analytical strategies (platforms and methods), and quality control assessment. This workshop will showcase experts introducing and discussing the principles of experimental design in metabolomics. Possible solutions for commonly encountered challenges in both planning metabolomics studies and selection of suitable analytical strategies including quantification and data quality considerations will also be addressed.

Metabolomics Data Analysis with XCMS and Galaxy (Hands-On Session)
Organizers: Michael Witting, Helmholtz Zentrum München; Jan Stanstrup, University of Copenhagen; Jules Griffin, University of Cambridge

*HANDS-ON SESSION – you will need to bring your laptop to the Workshop*
Processing large amounts of untargeted metabolomics data can be a daunting task. The software rarely comes with a full and easy to understand walk-through; thus understanding the different steps, optimizing settings, and assessing final processing quality is challenging. This workshop will discuss two processing platforms (XCMS and Galaxy) that provide options for advanced processing. XCMS3 (available from github) offers several new features and implementations that improve the usability. XCMS3 global workflows, targeted workflows, interactive visualization, and working with DDA and DIA MS2 data will be discussed. Second, we will present Galaxy, which has transformed genomics research by massively increasing the accessibility to powerful data analysis tools, and allowing non-programmers to create workflows from an expanding suite of tools (https://galaxyproject.org/) in different languages and on the cloud for easy execution. An overview of Galaxy, along with several metabolomics workflows that have recently been reported (W4M, PhenoMeNal and MetaboFlow will be provided. We will focus on practical skills and pitfalls so that the participants have an understanding of how to approach different problems after the workshops.

 

Sunday 2:15pm - 4:15pm

Targeted MS and Skyline
Organizers: Haiwei Gu and Brian Pratt

This workshop is focused on targeted mass spectrometry (MS) and its applications in metabolomics. We will introduce traditional targeted MS assays. In addition, we will introduce a recently-developed approach, globally optimized targeted (GOT)-MS, which has many advantages of traditional targeted detection and global profiling, including the capability to detect unknowns, broad metabolite coverage, and excellent sensitivity. Furthermore, selected examples of targeted metabolomics studies will be highlighted, including the development of a targeted assay with Skyline. Skyline is a freely-available and open source Windows client application for building quantitative methods for Selected Reaction Monitoring (SRM), Parallel Reaction Monitoring (PRM), Data Independent Acquisition (DIA/SWATH) and MS1 filtering, and analyzing the resulting mass spectrometry data.

The workshop participants can interact with experts in targeted mass spectrometry for metabolomics, and to talk with the Skyline development team about what's possible, what's new, and what's coming in targeted metabolomics analysis. We hope participants will share their experiences and communicate their needs in metabolomics.

EMN - Introduction to Mass Spectrometry-based Metabolomics (Novice Track)
Organizers: Umaporn Uawisetwathana (BIOTEC, NSTDA, Thailand), Ricardo Heredia (University College London, UK), Charmion Cruickshank-Quinn (University of Colorado, Denver, CO, USA)

In a general metabolomics workflow, a major challenge in untargeted metabolomics is the detection of a large range and number of small molecules, while targeted metabolomics aims to detect very low levels of small molecules. Since there is no perfect analytical tool to detect all these small molecules at a time, knowledge on the principle of each analytical instrument will be useful to relevant scientists to enable them to select the suitable tools for their research. In this workshop, participants will learn the advantages and limitations of each analytical instrument and the methods to get them started on instruments. Participants will also get insights into tips and tricks of how to troubleshoot the instruments and the essential issues to their maintenance. This workshop primarily targets beginners to the field of metabolomics and instrument analysis. However, intermediates and experts in the metabolomics field can also benefit, including postgraduate students and early-career researchers who are working with or are about to work with mass spectrometry-based metabolomics and lipidomics in their own studies.

Advanced Multivariate Statistics (Hands-On Session)
Organizers: Min Zhang (Purdue University) and Dabao Zhang (Purdue University)

*HANDS-ON SESSION – you will need to bring your laptop to the Workshop*
Despite the successful application of multivariate statistical methods to identify biomarkers and probe systems biology, it remains challenging to handle large numbers of variables when the sample size is small or to select significant biomarkers in the presence of strong confounding factors.

This workshop will first provide an overview of some popular multivariate methods used in metabolomics, including PLS-DA, O-PLS, random forests, logistic regression, and then focus on the utility of two new methods, seemingly unrelated regression (SUR) and penalized orthogonal components regression (POCRE), which have been developed and applied to metabolomic data. The workshop will feature hands-on exercises, developed by an NIH-funded project “New Statistical Methods to Model Metabolite Profiles for Disease Detection”. The workshop will introduce data pre-processing procedures, guide the participants to run through several hands-on exercises including NMR and targeted LC-MS/MS data, visualize the results, interpret the outputs, and discuss follow-up analysis. To assist participants in analyzing metabolomic data using advanced multivariate statistical methods, this workshop is designed for metabolomics researchers with relatively limited statistical background and computational skills.

 

Sunday 4:30pm - 6:30pm

Stable Isotope Approaches in Metabolomics
Organizers: Fred Stevens and Charmion Cruickshank Quinn

This workshop will focus on the integration of stable-isotope tracer approaches in metabolomics. Topics: 1) Carbon-13 and Nitrogen-15 labeled substrates for measurement of metabolic flux; 2) Metabolic labeling using 2H- and O-18 labeled water; 3) Pathway modeling using mass isotopomer distribution data; 4) Approaches for detection of labeled metabolites using untargeted and targeted mass spectrometry techniques.

EMN - Principles of Multivariate Data Analysis for Metabolomics (Novice Track)
Organizers: Ricardo Suarez-Heredia (University College London, UK), Dara Daygon (University of Queensland, St. Lucia, Australia) and Charmion Cruickshank-Quinn (University of Colorado, Denver, CO, USA)

This workshop is designed to provide the principles, challenges and usual processing techniques in Multivariate Data Analysis for metabolomics data analysis and interpretation. This workshop is divided into four parts and primarily targets beginners in multivariate data analysis, including early-career researchers and experienced researchers in metabolomics. It is designed to provide powerful statistical tools for data analysis and interpretation. Section one will discuss univariate and multivariate analysis, provide an overview and applications of multivariate analysis, and basic theory. Section two will discuss principal component analysis (PCA) and PCA models including parameters and diagnostics. Section three will give an overview of projection to latent structure (PLS), its principles, features, mechanisms, and conclude with parameters and diagnostics. The workshop will conclude with an overview of software for multivariate data analysis with focus on JMP. This session will provide an introduction to strategies for data pre-processing and provide case studies for metabolomics datasets.

Mining the Metabolome - Annotation Strategies & Visualization (Hands-On Session)
Organizers: Justin van der Hooft

*HANDS-ON SESSION – you will need to bring your laptop to the Workshop*
The cost of mass spectrometry ($/data volume) has decreased by two orders of magnitude in the past decade. It is now fairly straightforward to obtain large volumes of untargeted mass spectrometry data, which analysis is the focus of the workshop, from large cohorts of samples resulting in millions of MS/MS spectra. Because it is becoming so cost effective, using and interpreting the large volume of data now becomes one of the key challenges to optimally profit from these data. To start from scratch with emerging technologies can be daunting and this workshop will ease the introduction by providing practical sessions so participants get a head-start in implementing metabolomics analysis tools. This workshop offers a hands-on introduction in emerging data annotation and visualization tools, covering the infrastructure of GNPS, the motivation and fundamentals behind metabolome mining tools Molecular Networking and MS2LDA and the ‘ili’ visualisation tool. We will explain how to submit jobs, which important analysis parameters to consider, and how to browse the results at the GNPS (https://gnps.ucsd.edu) and MS2LDA (www.ms2lda.org) and ‘ili’ web interfaces.

 

Monday 8:30am - 10:15am

Improving Metabolite ID Approaches – Confidence and CASMI
Organizers: Coral Barbas, Steffen Neumann, Lloyd Sumner

Despite huge advances in analytical instrumentation and software developments, metabolite identification is still far from trivial. We will give an overview of metabolite identification approaches and spectral libraries from both the technical and software perspective. We will also present the updated identification confidence levels, which have been under discussion recently.

The Critical Assessment of Small Molecule Identification contest: (CASMI) is an open contest on the identification of small molecules from mass spectrometry data. The challenge spectra, solutions and participant submissions are available www.casmi-contest.org. Several teams have participated with manual, semi-automated and fully automatic metabolite annotation methods and pipelines. The workshop will give an overview of past and current efforts in the CASMI contest, which was organized for the fifth time in 2017.

Special attention will be paid to lipid annotation process using CEU Mass Mediator platform (CMM) http://ceumass.eps.uspceu.es/mediator/. CMM is a knowledge-based metabolite annotation tool, also designed for the annotation of oxidized phosphatidylcholines and quality assessment of MSMS spectra prior to the interpretation process.

Systems Biology Workflows for Data Analysis and Integration
Organizers: Douglas McCloskey

Medical clinics, industrial biotechnology, and research labs are increasingly facing more and more complex and challenging biological questions that cannot be addressed using traditional approaches. Systems biology offers a unique tool set of modern analytical tools that integrates multiple –omics data sources (i.e., metabolomics, fluxomics, phenomics, transcriptomics, and genomics) to better address these ever increasing challenges. This workshop will cover current state-of-the art systems biology workflows starting from experimental design to data acquisition to integrated data analysis that can be applied to derive meaningful conclusions about complex biological questions. In particular, this workshop will focus heavily on the integration of metabolomics and fluxomics data with biochemical modeling (e.g., Metabolic flux analysis (MFA), thermodynamics analysis, and kinetic modeling). In addition, techniques for integrating metabolomics and fluxomics data with other –omics data types will be detailed. Examples from recent research involving clinical applications and industrial biotechnology applications will be provided.

Introduction to Data Workflows – Metaboanalyst 4.0 (Hands-On Session) (Novice Track)
Organizers: Jeff Xia

*HANDS-ON SESSION – you will need to bring your laptop to the Workshop*
The workshop aims to introduce participants to the key features of the most recent release of MetaboAnalyst (version 4.0), including a companion R package (MetaboAnalystR) for more transparent and flexible analysis, an expanded knowledge base of metabolite sets and metabolic pathways for functional analysis, a new module for pathway activity prediction from MS peak lists (mummichog), a new module for biomarker meta-analysis, and a new module for network-based integrative analysis with other omics data. During the workshop participants will be given a brief overview of these new modules in MetaboAnalyst and most of its main functionalities. Then selected example data sets will be processed by the instructors using different MetaboAnalyst features as part of a live demonstration. After this 45-minute introduction, workshop participants will continue with a 90 minute “hands-on” lab where they will be encouraged to use their own data and to process it with MetaboAnalyst 4.0. Alternately, participants may work with “canned” data sets and an accompanying written tutorial to explore MetaboAnalyst 4.0 on their own. The instructors (plus TAs) will assist participants in completing these tasks.

 

Monday 10:30am - 12:15pm

Visualizing Metabolic Data: Introduction to Visual Analytics
Organizers: Caroline (Lindy) Rae (University of New South Wales), Thomas Bednarz (University of New South Wales)

Visual analytics (VA) is an important tool to gain insights from complex data. The more complex and large data are, VA have even stronger value. Today’s challenges are about visualising unstructured data, real-time analytics, adoption of advanced visualisation techniques and human supported predictive analytics. Using VA tools, we enable people to see patterns and relationships in data, especially those they would never see or would take them a very long time to measure.

This workshop will introduce attendees to the basic principles of visual analytics and the reasons why adopting these principles is useful. It will showcase the current state of data visualisation in metabolomics including visualisation for data interaction, for drawing conclusions from data, for exploring data and for presenting and communicating data. We will explore ways in which these approaches can be improved and the methods that can be used. On top of it, we will also cover modern techniques, such as immersive visualisation, collaborative visualisation, and mixed reality systems, and how they can be used in the context of metabolomics.

Metabolomics and Precision Medicine
Organizers: Dr. Kaddurah-Daouk, Nichole Reisdorph and Dr. Ulmer

Our metabolomics community believes that inclusion of metabolomics data in Precision Medicine Initiatives is timely and will provide an extremely valuable layer of data that compliments and informs other data obtained by these important large initiatives. Our Metabolomics Society, through its “Pharmacometabolomics and Precision Medicine Task Group”, with input from our metabolomics community, has developed a White Paper where we discuss the value and approaches for including metabolomics data in large precision medicine initiatives. This White Paper offers recommendations for the selection of state of-the-art metabolomics platforms and approaches that offer the widest biochemical coverage, considers critical sample collection and preservation, and standardization of measurements, among other important topics. In this session we will tackle bottlenecks and issues we as a metabolomics community need to address to enable our community to have representation in precision medicine large initiatives. Topics we need to debate include sample acquisition/preservation, selection of optimal ‘omics technologies and key issues regarding data collection, interpretation and dissemination.

EMN - Professional Career Development: The Survival Kit (Novice Track)
Organizers: Ricardo Suarez-Heredia (University College London, UK), Dara Daygon (University of Queensland, St. Lucia, Australia) and Charmion Cruickshank-Quinn (University of Colorado, Denver, CO, USA)

The “Professional Career Development: The Survival Kit” workshop primarily targets Early Career Researchers (Undergraduate, Graduate, Postdoctoral Associates) to create awareness on career development and planning. It meant to get participants thinking about their career path, where they would like to be, and how to get there. This workshop will briefly discuss building up your career development strategy, establishing your professional brand, communicating effectively with focus on public speaking and pitching skills, and the essentials of networking and how to assess, map and create your network establish collaborations. If time permits, the session will conclude with speakers from a variety of sectors such as academia, consulting, entrepreneurship and new ventures, and industry. They will discuss professional career pathways and how to get there. Participants will leave this workshop with a better understanding of the tools that are available to them and how they can use the resources around them to propel their career transition.