Short Courses | IBERO2022

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Short Courses Description (pre-conference)

Fundamentals of Mass Spectrometry (Copacabana Room)

SHORT-COURSE OUTLINE & TOPICS

Target Audience: It will it be mainly for beginners but also useful to consolidate concepts for advanced students.

Description

A one-day course on fundamentals of mass spectrometry aimed to give principles and applications of MS of organic and bioorganic molecules.

The course starts with an overview of modern mass spectrometry and a description of the main ionization techniques, for volatile and polar molecules, and ambient MS techniques, followed by an overview on in-space and in- time analyzers.

The course develops presenting isotopic patterns, ion formation and ion internal energy, together with some criteria for interpretation of mass spectra both for EI-MS and ESI-MS.

High-resolution MS and accurate mass measurements for molecular formula determination and different techniques of tandem mass spectrometry complete the 1st part of the course.

For the 2nd part, the most innovative and relevant applications of MS in science today will be discussed, their fundaments, and current examples from most recent literature will be highlighted, including ion imaging, ion spectroscopy, MS proteomic, metabolomic and petroleomics, ion mobility and forensic science.

For each topic, exercises involving active participation by students and applications in different fields will be presented.

Summary

Part 1

Mass spectrometry: history and overview
Ionization techniques: volatile molecules: EI
Ionization techniques: polar molecules : ESI, APCI, APPI and MALDI
Ambient MS
Analyzers: BE, Q, Tof, Ion trap, Orbitrap, FTICR & hibrids
High resolution mass spectrometry and accurate mass measurements
Molecular formula determination
Tandem mass spectrometry
Principles of interpretation of MS and MS/MS spectra for both EI-MS and ESI-MS

Part 2

Most innovative and relevant applications of MS in science today with fundaments and current examples from most recent literature including ion imaging, ion spectroscopy, MS proteomic, metabolomic and petroleomics, ion mobility and forensic science.

Methodology

Lectures

Language

English

Course Coordinators

Dr. Marcos Nogueira Eberlin

Professor, researcher and coordinator of the Center for Research in Science, Faith and Society - Discovery-Mackenzie - of Universidade Presbiteriana Mackenzie and of MackMass - Mackenzie Laboratory of Mass Spectrometry. Since 2002 he has been a member of the Brazilian Academy of Science and in 2005 he was appointed Commander of the National Order of Scientific Merit. In 2002 he received the Zeferino Vaz Academic Award (2002), in 2008 the Scopus-Capes Award for excellence in publications, and in 2016 the Thomson Medal (2016) from the International Society of Mass Spectrometry (IMSF), the highest honor given to spectrometrists. of pasta. In 2020 he was included in the "Power List - Around the World in 60 scientists" by the journal "The Analytical Scientist" and among the 50 most influential Brazilian Scientists by Stanford University. He was deputy director of the Institute of Chemistry at UNICAMP (1998-2002) and president for two terms (2009-2014) of the International Society for Mass Spectrometry (IMSF). He is currently director-president of the Brazilian Society of Mass Spectrometry (BrMASS) and of the Brazilian Society of Intelligent Design (TDI BRASIL). He is also editor of the Journal of Mass Spectrometry (JMS-Willey). He has supervised about 200 masters, doctoral students and post-docs, today spread across Brazil and around the world as researchers and professionals. It has already published about 1100 scientific articles that received about 30 thousand citations in several scientific areas, such as Chemistry, Physics, Biochemistry, Biology, Forensic Sciences, Pharmaceuticals, Food, Veterinary, Medical and Materials.

MSc. Alex Aparecido Rosini Silva

Pharmacist and Master graduated from the University of São Francisco - Campus Bragança Paulista. He is currently a PhD student at the Postgraduate Program in Health Sciences - Stricto Sensu at the São Francisco University - USF (Bragança Paulista Campus) as a CAPES Scholarship, under the guidance of Prof. Dr. Andréia de Melo Porcari, with experience in analytical chemistry, and metabolomic studies with an emphasis on various pathologies, such as: COVID-19, breast cancer and ovarian cancer.

Note: The mini-course will happen only upon the minimal amount of 10 registrations/mini-course. In case of cancelation, the attendee should choose other mini-course (the registration fee will not be reimbursed).

Hands on Metabolomics (GNPS - Ipanema Room)

SHORT-COURSE OUTLINE & TOPICS

Target Audience: It will it be mainly for beginners and also for advanced students.

Description

In this hands-on course, we want to familiarize the participants on how to analyze mass
spectrometry-based metabolomics data using the Global Natural Products Social Molecular Networking (GNPS) analysis infrastructure (https://gnps.ucsd.edu) by reanalyzing public data and contextualizing MS/MS data with reference data.

Summary

 Basics of MS-based untargeted metabolomics.
 Global Natural Products Social Molecular Networking (GNPS) analysis infrastructure: an
overview.
 Hands on GNPS analysis of untargeted metabolomics using classical molecular
networking with provided public data. Here, the participant will learn how to use and
import publicly available data.
 Learn how to use reference data to readout information on diet, microbes, exposomics
(etc) from any sample, including clinical samples.
 Analyze data and learn how molecular networking and other recently developed specific
tools can be used to understand metabolism or role/relationship of microbes with its
microbiome.

Language

English

Course Coordinator

Anelize Bauermeister - University of São Paulo (USP)

She obtained her PhD in Sciences by University of São Paulo (USP) under supervision of Prof. Luiz Alberto Beraldo de Moraes. Her postdoctoral researches were developed at USP under supervision of Prof. Leticia V. Costa-Lotufo and at UCSD, USA under supervision of Prof. Pieter Dorrestein. Her research focus is mass spectrometry and MS-based metabolomics data analysis applied to investigations of microbial metabolites in association with host organisms. One of her career goals is to share metabolomics knowledge in Brazil towards open-science through free workshops and promoting collaborations, which led to the creation of the group "Rede Metabolomica" with more than 550 members from all over Brazil and other countries.

Tiago Leão - University of São Paulo (USP)

Dr. Tiago Leao, postdoc at University of São Paulo, Center for Nuclear Energy in Agriculture (CENA, Brazil).

He did his Ph.D. in Marine Biology at University of California, San Diego, working on marine cyanobacteria and developing BioCompass. His first postdoc was at the same university but at the Pharmacy and Pharmaceutical Sciences department, developing NPOmix. His current postdoc is at the University of São Paulo, CENA, developing AlphaOmix and BioGeneClassifier.

His research is focused on developing new tools (usually via machine learning) for genome mining, attempting to better understanding the DNA information and use it to find novel bioactive metabolite/natural products. For example, gene similarity can be used for identifying the least common BGC is a repository, prioritizing the most promising targets (like in the genus Moorena when analyzed with BioCompass). However, this information needs to relate to the metabolites so it can be useful for isolation of novel natural products, therefore, NPOmix links metabolites to BGCs. One last focus is to predict bioactivity of new analogs (BioGeneClassifier performs a database search) or entirely novel metabolites with predicted structures (we are creating AlphaOmix structure predictor and combining it with docking to protein targets).

Top Down Proteomics (Leblom Room)

SHORT-COURSE OUTLINE & TOPICS

Target Audience: Beginners on high resolution mass spectrometry

Description:

One-day course with the fundamentals, principles, and applications of Top-Down Proteomics. The course will start with an overview of proteomics techniques and a description of proteforms and their biological importance. Further, it will explore the state-of-art of protein fractionation, mass spectrometry, and data analysis techniques/methodologies used on Top-down Proteomics. Finally, some of the most important applications of Top-down Proteomics will be in depth presented in a friendly and openly environment.

Summary:

Course Coordinator: Dr. Rafael D. Melani (NU - USA)

Dr. Rafael Melani is a Senior Research Associate in the Kelleher Research Group at Northwestern University (Evanston, IL - USA) since 2017. He earned his BS degree in Biology (2010) and a master degree in Animal Biology (2012) from the University of Brasilia (Brasilia, DF - Brazil), and a PhD degree in Biochemistry (2016) from the Federal University of Rio de Janeiro (Rio de Janeiro, Rj – Brazil). During his PhD he spent 18 months at the Kelleher Research Group as a visiting scholar learning Top-down proteomics and expanding his expertise in mass spectrometry under the mentoring of Dr. Neil Kelleher. His thesis was awarded with the CAPES Thesis Award as one of the three best Biochemistry theses from Brazil in 2016. Rafael's postdoctoral research (2016-2017) was performed in the Proteomics Unit at Federal University of Rio de Janeiro (Rio de Janeiro, Rj – Brazil) under supervision of Dr. Gilberto Domont. Dr. Melani has large experience and extensive training on proteomics (especially Top-down proteomics), venomics, protein fractionation, mass spectrometry, and native mass spectrometry. Through direct work and fruitful collaborations, Rafael was privileged to have published over 15 peer-reviewed research papers and book chapters in topics related to proteomics, venomics, native mass spectrometry, charge detection mass spectrometry, and mass spectrometry.

Data Science & Artificial Intelligence Application In Health Science (Leme Room)

SHORT-COURSE OUTLINE & TOPICS

Target Audience: Beginners on high resolution mass spectrometry

Course Coordinators:

Dr. Patrick Mathias: School of Medicine – UW, USA

Dr. Aline M A Martins: The Scripps Research Institute - CA, USA

Getting the Basics of Reproducible Data Analysis: developing skills on R Programming and application of Machine Learning and Artificial Intelligence in Health Science

Course date: 10-11th December

Course Information:

Do you have little to no experience in programming but a desire to learn this valuable skill? Or do you rely on scripts in R or another programming language for your data analysis needs but feel you don’t have the basics down? In this course, we will focus on foundational workflows for completing data analyses in R, an open source statistical programming language. By walking through the core steps of an analysis with representative data sets, this highly interactive course will take learners from data import through transformation, summarization, and visualization. Coding and workflow exercises will be frequent to reinforce concepts shortly after discussion. Best practices for completing data analyses reproducibly will be built into the content, exposing learners to concepts such as literate programming (using R Markdown), optimal project organization, and version control. By the last part of the course, you will be introduce to successful examples on how you can use Machine Learning and Artificial Intelligence to integrate data in Health Science. These skills are increasingly important for fully utilizing and extracting value from the data we collect every day so this course will emphasize tips and practices to make your work efficient and reproducible.

Topics:

- Introduction to RStudio

- Reproducibility through R Markdown

- Importing data from files

- Transforming and summarizing data using Tidyverse tools

- Visualizing data with ggplot

- Joining multiple data sets

- Structuring projects to optimize your efficiency

- Version control using Git

- Modeling data

- Application of successful examples of Machine Learning and Artificial Intelligence in Health Science

Participant Requirements:

Course attendees must have a laptop to complete exercises. Course material will be available in RStudio Cloud, which requires access to the Internet. Alternately learners can download RStudio and required packages to their computer prior to the course.

Proteomic Data Analysis with PatternLab (Urca Room)

SHORT-COURSE OUTLINE & TOPICS

Target Audience: For beginners and also for advanced students.

Description:

This course shows how to analyze shotgun proteomic data using PatternLab for proteomics. We will review peptide spectrum matching concepts and concepts converging into reliable results. We will use modules for the application of differential proteomics for label-free and chemically labeled data. The course will be taught by the authors of the computational tool.

Course date: December 10th, 9:00 am - 5:00pm

Course Coordinators:

Researchers Paulo Carvalho, Marlon Santos, Milan Clasen and Louise Kurt

Paulo Costa Carvalho

Paulo obtained his undergraduate degree in Engineering by PUC-Rio; Master degree in Cellular and Molecular Biology (2006) by Instituto Oswaldo Cruz (CAPES 7), Fiocruz; PhD by the Program of Computer Systems Engineering (2010) COPPE/UFRJ (CAPES 7) with a period of sandwich fellowship at the Scripps Research Institute, California, under the supervision of Dr. John R Yates, III (index H: 168). Paulo is a level two CNPq productivity researcher (Computer Science Committee), member of the permanent board of graduate professors in Biosciences and Biotecnology at ICC-Fiocruz, permanent professor of the graduate program in Biochemostry at the Institute of Chemistry- UFRJ. He is an adviser by the Program of Computer Systems Engineering (2010) COPPE/UFRJ. Paulo has two patent files, more than 100 published articles, highlighting: first and last authorship in Nature Methods, Nature Protocols, and Bioinformatics. His awards deserving attention: Google Award for Academic Excellence, honorable mention in CAPES PhD thesis award, another honorable mention in CAPES PhD thesis (2016) jointly with his student Diogo Borges Lima, Innovation by Fleury Laboratory and recently he has been granted with the Talent Award of the Institute Pasteur network. He was a member of the features panel of the journal Analytical Chemistry and is the executive editor of the Journal of Proteomics – Elsevier. Paulo coordinates events and courses at international level, delivers lectures in international meetings, and is part of a lot of committees. From August 2018, Paulo created and started to lead the Structural and Computational Proteomics Laboratory at Fiocruz Paraná.

Marlon Dias Mariano dos Santos

He obtained his undergraduate degree in Engineering of Bioprocesses and Biotechnology by Universidade Positivo (2017) and Master degree in Biosciences and Biotechnology by Instituto Carlos Chagas, Fiocruz (2019). He is currently a PhD fellow at the Structural and Computational Proteomics Laboratory at Instituto Carlos Chagas, Fiocruz, Paraná. He works in the field of development of experimental and computational methods applied to mass spectrometry and proteomic data analysis.

Milan Avila Clasen

PhD fellow in Biosciences and Biotechnology at the Structural and Computational Proteomics Laboratory of Instituto Carlos Chagas - Fiocruz. He has experience in the development of tools and methodologies for mass spectrometry data analysis.

Louise Kurt

PhD fellow in Biosciences and Biotechnology at the Structural and Computational Proteomics Laboratory of Instituto Carlos Chagas - Fiocruz. She has experience in the development of tools and methodologies for mass spectrometry data analysis.

The Metabolomics Workflow (Vidgal Room)

SHORT-COURSE OUTLINE & TOPICS

Course Coordinator:

Dr. Marina Tavares

Co-Coordinator:

Daniel Rossado Oliveira

Duration: 4h teoretical class and 4h (Hands-on/Laptop required)

Objective:

To introduce fundamental and practical aspects of metabolomics, in both targeted and untargeted formats, describing in detail the metabolomics workflow, from the design of experiments to the biological interpretation of the problem under examination, with emphasis on modern analytical techniques commonly used for data acquisition, the statistical concepts involved in the processing of omics data, as well as on a general revision of human metabolism and major metabolic routes.

Justification:

Among the omics sciences and in the context of systems biology, metabolomics has occupied an important niche, because it offers the revolutionary possibility of characterizing the phenotype of an individual to the molecular level, so necessary to aid the understanding of cellular biology towards personalized medicine. Interests in metabolomics have grown considerably in many areas, not only the discovery of biomarkers for early diagnosis of diseases, but include applications in biotechnology and agriculture, development of new pharmaceuticals, nutrition, food quality and safety, environmental chemistry, toxicology, among others.

Syllabus:

This course intends to review the terminology and to discuss the denominations in use in the field of metabolomics, as well to describe systematically its workflow for both untargeted and targeted metabolomics, from the metabolite selection (targeted metabolomics), biological sample collection and preparation, introducing general principles of multiplatform instrumental analysis in current use for data acquisition, the statistical concepts involved in data processing (using R platform), and finally, to provide an overview of human metabolism and principal biological routes to support biological interpretation of results. Among the analytical instrumentation, GC-MS, LC-MS in both reversed-phase and hydrophilic interaction modes, and CE-MS will be reviewed. The processing of omics data, the methods used for group discrimination, discriminant metabolite selection and structural identification of putative metabolites by assessing metabolomics databases (FiehnLib, KEGG, Metlin, HMDB, MassBank, etc.) as well as MS/MS fragmentation strategies will all be addressed by theoretical and practical lectures using the institution multimedia facility, where the students will have access to real metabolomics datasets and pertinent softwares (XCMS and SIMCA-P). Finally, examples of representative applications of metabolomics will be presented in supervised group discussions.

Bibliography:

G.A.B. Canuto, J.L. da Costa, P.L.R. da Cruz, A.R.L. de Souza, A.T. Faccio, A. Klassen, K.T. Rodrigues, M.F.M. Tavares, Metabolômica: definições, estado-da-arte e aplicações representativas, Quimica Nova 2018, http://dx.doi.org/10.21577/0100-4042.20170134.
A. Klassen, A.T. Faccio, G.A.B. Canuto, P.L.R. da Cruz, H.C. Ribeiro, M.F.M. Tavares, A. Sussulini, Metabolomics: definitions and significance in systems biology, In Metabolomics: from fundamentals to clinical applications, (Ed. A. Sussulini), Series "Proteomics, Metabolomics, Interactomics and Systems Biology" (Ed. Daniel Martins-de-Souza), Springer, 2017, p3-17.
J.M. Berg, J.L. Tymoczko, G.J. Gatoo Jr, L. Stryer, Biochemistry, W.H. Freeman, 2015, 8th edition.
L. Eriksson, T. Byrne, E. Johansson, J. Trygg and C. Vikström, Multi- and Megavariate Data Analysis - Basic Principles and Applications, Umetrics Academy, 2013, 3rd edition.
https://masspec.scripps.edu/landing_page.php?pgcontent=whatIsMassSpec

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Conference Courses Description

Introduction of High Resolution Mass Spectrometry for Qualitative and Quantitative Analysis (Free of charge - Ipanema room)

Target audience: For beginners and also for advanced MS students

Description: This course is intended to give an overview on high resolution MS systems and how to identify the best analyzer for your application, the advantages, limitations and the workflow from sample preparation to data processing for analyses using high resolution mass spectrometry. The fundamental concepts of high resolution and accurate mass measurement as well mass calibration will be discussed during the course. The history of the development of HRMS analyzers and instrument options including Time of flight (TOF) and Fourier transform mass spectrometry (FTMS) will be covered, including hybrid instrumentation. Ion mobility-mass spectrometry (IM-MS) is an innovative 2D detection technique that integrates ion mobility separation (IMS) and mass spectrometry (MS). Ion mobility principle, hardware innovations, and data acquisition methods will be discussed. Applications include small molecule, biologics (antibody drug conjugates, peptides, and proteins) and biomarkers using HRMS as part of this course covering the qualitative and quantitative applications.

Course coordinators: Michael Murgu and Viviane Nascimento

Michael Murgu, PhD
Mass Spectrometry Applications Specialist working for Waters since 2006 with customer support and training and MS method development.
Chemist, with Master and PhD degree in Organic Chemistry/Mass Spectrometry at the Universidade Federal de São Carlos. Has been working with Mass Spectrometry since 1996, with experience in different applications, including Natural Products, Metabolomics, Proteomics, Pharmaceutical analysis on biological samples and medicines, Residual and contaminants analysis on Food and Environmental samples, Toxicology, Forensic and Clinical applications.

Viviane Nascimento
Viviane Nascimento is a MS Specialist at Waters Corporation. Viviane has worked as Mass Spec Specialist for more than 10 years with applications and support in the areas of Food and Environment, Clinical Research and Toxicology, Pharmaceuticals and Academic Research. Following a career in Field MS Application, Viviane joined Waters in 2019. She has a bachelor's degree in Chemistry from UFSCar and a master's degree in Analytical Chemistry from USP, where he developed research on electrophoretic and spectrometric characterization of plant extracts.

Duration: Monday 01:00 p.m. - 03:00 p.m.

Tuesday 01:00 p.m. - 03:00 p.m.

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