LIFS Course - ILS 2021 & LipidomicsForum 2021
5 October 2021
Regensburg, GermanyLIFS Course - ILS 2021 & LipidomicsForum 2021 https://www.denbi.de/training/1151-lifs-course-ils-2021-lipidomicsforum-2021 https://tess.elixir-europe.org/events/lifs-course-ils-2021-lipidomicsforum-2021 Educators: Jacobo Miranda Ackerman, Daniel Krause, Nils Hoffmann (de.NBI, BioInfra.Prot / LIFS) Date: October 5th, 2021, 9:00 – 12:00 (CEST) & 13:00 – 17:00 (CEST) Deadline for Workshop Registration: Until capacity is reached. Location: On-Site, Regensburg (if local COVID-19 rules allow, on-line otherwise) Contents: In the first part of the course, we will work through an example for targeted LC-MS lipidomics with LipidCreator and Skyline. In the second part of the course, we will apply PeakStrainer and LipidXplorer for filtering, identification and quantification of lipid signals from shotgun lipidomics. The course will consist of a short theory and background overview of the employed programs complemented by the application of the tools to provided data sets. The third part of this course will work through a typical use-case of downstream data processing of shotgun lipidomics data following MS acquisition with LipidXplorer. We will inspect, check and normalize the data as well as calculate absolute quantities using internal class-specific standards with lxPostman. In part four, we will then perform a qualitative comparison of the lipidomes using the LUX Score lipidome homology. Morning 09:00 – 09:45 Welcome and Introduction 10:00 – 10:30 Targeted Lipidomics with LipidCreator and Skyline 10:30 – 12:00 LipidCreator and Skyline Exercises Afternoon 13:00 – 14:30 Shotgun Lipidomics with LipidXplorer 14:30 – 15:30 Quantification of Shotgun Lipidomics data with lxPostman 15:30 – 17:00 Lipidome comparison with LUX Score Learning goals: Participants will be able to understand and explain the shotgun MS and targeted LC-MS workflows for lipidomics. They will learn the fundamentals of the software tools used and how to choose parameters for them. They will learn to understand and interpret the results of each step of the pipeline. Prerequisites: Basic knowledge of lipidomics, analytical workflows in lipidomics and basic familiarity with web-based and desktop applications. Please note that you may need to install software on your computer to fully participate in all exercises which may require the proper rights. The workshop will be a mix of small lecture segments and hands-on exercises. The trainers will be available for questions and assistance during the workshop. Keywords: Lipidomics, Shotgun, Targeted, LC-MS Tools: PeakStrainer and LipidXplorer, LipidCreator, Skyline, lxPostman, LUX Score Registration: Please select the “LIFS Training session I & II” in the Workshops section of the conference registration. Capacity is limited to 30 participants. 2G (vaccinated or fully recovered) - with either certificate of full vaccination or certificate of recovery / positive PCR test not older than six months. Nose+mouth protection - FFP2 mask or medical mouth nose protection have to be worn inside of buildings. 2021-10-05 09:00:00 UTC 2021-10-05 17:00:00 UTC de.NBI Regensburg, Regensburg, Germany Regensburg Regensburg Oberpfalz Germany      
3rd de.NBI/ELIXIR-DE metaRbolomics Hackathon
22 - 24 November 2021
Lutherstadt Wittenberg, Germany3rd de.NBI/ELIXIR-DE metaRbolomics Hackathon https://www.denbi.de/training/1177-3rd-de-nbi-elixir-de-metarbolomics-hackathon https://tess.elixir-europe.org/events/3rd-de-nbi-elixir-de-metarbolomics-hackathon de.NBI Organisers: Marr / Schmidt / Meier / Neumann Date: 22.11. - 24.11.2021 Location: Leucorea, Lutherstadt Wittenberg Information on travel and accommodation: https://docs.google.com/document/d/1tM9mzGmTNT11p3cYRdHjm-CT3gb-yEDbZ-xoAUKixGs Workshop goals: Aim of the workshop is to improve the interoperability of packages (e.g. using common data structures and interfaces), combine efforts (use single implementation of common functions), create and demonstrate complex workflows by integrating existing tools, identify gaps in the metaRbolomics ecosystem that need to be covered. We will also have enough discussion time to ponder challenges of the future, taking metaRbolomics into the next decade. Prerequisites: Laptop, understanding in Metabolomics, R language skills Keywords: Metabolomics, mass spectrometry, R, Bioconductor, data processing, metabolite annotation, metabolite identification 2021-11-22 09:00:00 UTC 2021-11-24 17:00:00 UTC de.NBI Lutherstadt Wittenberg, Lutherstadt Wittenberg, Germany Lutherstadt Wittenberg Lutherstadt Wittenberg Germany    workshops_and_courses  
Applied Metaproteomics Workshop Magdeburg 2021
22 - 26 November 2021
Magdeburg, GermanyApplied Metaproteomics Workshop Magdeburg 2021 https://www.denbi.de/training/979-applied-metaproteomics-workshop-magdeburg-2021 https://tess.elixir-europe.org/events/applied-metaproteomics-workshop-magdeburg-2021 Educators: Dirk Benndorf, Stephan Fuchs, Robert Heyer, Kay Schallert (BiGi/MetaProtServ) Date: 22.11.2021 – 26.11.2021 Location: Magdeburg, Germany (Universitätsplatz 2, Building 28.205) Contents: Microbiome research is rapidly increasing. Meta-Omics data provide insights into microbial community influencing human health and biochemical cycle. Metaproteomics focusses on proteins representing the expressed genes and functions. In contrast to metagenomics or metatranscriptomics, the extraction and the analysis of proteins from human or environmental samples is challenging. The de.NBI course on Applied Metaproteomics trains the participants to apply a complete workflow starting from design of experiments via sample preparation to measurement and bioinformatics analysis of high-resolution MS data. Maximum 10 participants are strongly encouraged to analyze their own samples to start their own metaproteomics project. The workshop takes place at chair of bioprocess engineering at Otto-von-Guericke University Magdeburg. The team of microbial communities head by Dr. Dirk Benndorf is well experienced in metaproteomics. The samples will be measured on newly purchased timsTOF Pro MS. His group devellopes the MetaProteomAnalyzer service facilitating the analysis of of metaproteomic data. The provision of service is supported by the German Network for Bioinformatics Infrastructure - de.NBI. Monday 09:00-10:00 Arrival 10:00-11:00 Introduction to metaproteomics (lecture: Dirk Benndorf) 11:00-12:00 Design of experiments and sample preparation (lecture: Robert Heyer) 12:00-13:00 Lunch 13:00-18:00 Sample preparation I (protein extraction, protein quantification: Robert Heyer) during the afternoon short presentations of participant´s about their samples (each participant max. 10 min) Tuesday 08:00-11:00 Sample preparation II (FASP digest, SDS-PAGE: Robert Heyer) 11:00-13:00 Introduction to high resolution mass spectrometry (lecture: Dirk Benndorf) 13:00-14:00 Lunch 13:00-14:00 Sample preparation II (peptide extraction: Robert Heyer) 14:00-16:00 Introduction to the MPA 2.0 (lecture: Kay Schallert) non-stop: measurement of participant’s samples I Wednesday non-stop: measurement of participant’s samples I: Dirk Benndorf, Patrick Hellwig 09:00-11:00 MPA 2.0 exercise I (working with a small reference dataset, db searching, metaprotein concept: Kay Schallert, Robert Heyer) 11:00-13:00 MPA 2.0 exercise II (loading user db, BLAST search of unknown hits, quantitative comparison of datasets, visualization and data export: Kay Schallert, Robert Heyer) 13:00-14:00 Lunch 14:00-17:00 Prophane workflow (lecture and training: Stefan Fuchs, external speaker) Thursday 09:00-13:00 MPA 2.0 exercise III (analyzing own data: Kay Schallert, Robert Heyer) 13:00-14:00 Lunch 14:00-17:00 Training at MS (calibration, setup of LC-MS methods, solvent exchange, trouble shooting, Patrick Hellwig) Friday 08:00-10:00 MPA 2.0 exercise IV (visualization of data: Robert Heyer) 10:00-12:00 Individual discussion of results and preparation of presentations (Dirk Benndorf, Robert Heyer, Kay Schallert) 12:00-13:00 Short presentations of participant‘s results and conclusion 13:00 Lunch and departure Learning goals: To apply a complete workflow starting from design of experiments via sample preparation to measurement and bioinformatics analysis of high-resolution MS data. Prerequisites: Fee: 70 € -> The so-called “3G rule” (the course is only open to those that are vaccinated, recovered, or tested - geimpft, genesen, getestet) will be applied! Keywords: Microbiome, MPA, Metaproteomics, MetaProteomeAnalyzer, Tools: MetaproteomeAnalyzer 2021-11-22 09:00:00 UTC 2021-11-26 17:00:00 UTC de.NBI Magdeburg, Magdeburg, Germany Magdeburg Magdeburg Sachsen-Anhalt Germany    workshops_and_courses  
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