LIFS Training Workshops @ Lipidomics Forum 2019

Before this year's Lipidomics Forum 2019 in Borstel, Germany kicks off on the evening of Sunday, November 10th, 2019, LIFS will host two lipidomics tool and workflow workshops. Based on the participant surveys of previous trainings, we will offer two separate courses this year to allow for more hands-on time with the tools and data.

Please go to the Lipidomics Forum registration to sign up for one of the courses (they will be taught in parallel).

Workshop 1 - Lipidomics MS Data processing, identification & quantification

"What is it and how much?"

10:00 - 10:45 Common Introduction
10:45 - 12:30 LipidXplorer Shotgun Lipidomics
12:30 - 13:30 Lunch break
13:30 - 16:30 LipidCreator & Skyline Targeted LC-MS lipidomics

Educators:
Jacobo Miranda Ackermann, Nils Hoffmann (BioInfra.Prot / LIFS)

Date:
November 10th, 2019

Location:
Forschungszentrum Borstel, Borstel, Germany (as part of Lipidomics Forum 2019)

Contents:
In this course, we will work through a typical use-case for bioinformatics processing lipidomics data following MS acquisition. The first part of the course will start with PeakStrainer and LipidXplorer for filtering, identification and quantification of lipid signals from shotgun lipidomics. The second part of the course will work through an example for targeted LC-MS lipidomics with LipidCreator and Skyline. The course will consist of a short theory and background overview of the employed programs complemented by the application of the tools to a provided data set.
 
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. Participants are required to bring their own laptop in order to work on the hands-on exercises.

Keywords:
Lipidomics, Shotgun, Targeted, LC-MS

Tools:
PeakStrainer and LipidXplorer, LipidCreator and Skyline.


Workshop 2 - Statistical analysis & qualitative and quantitative comparison of lipidomics data

"How do I compare? Fancy graphics & convincing plots"

10:00 - 10:45 Common Introduction
10:45 - 12:30 R Scripting for LipidXplorer data quantification
          Quantitative lipidome comparison wiht ClovR
12:30 - 13:30 Lunch break
13:30 - 16:30 Qualitative lipidome with LUX Score
          Machine learning, clustering and classification for lipidomics data

Educators:
Fadi al Machot, Nils Hoffmann (BioInfra.Prot / LIFS)

Date:
November 10th, 2019

Location:
Forschungszentrum Borstel, Borstel, Germany (as part of Lipidomics Forum 2019)

Contents:
In this course, we will work through a typical use-case of downstream data processing of shotgun lipidomics data following MS acquisition with LipidXplorer. We will  absolute quantification against internal class-specific standards comparison of the lipidomes using the LUX Score lipidome homology, before finally comparing and visualizing our quantitative lipidome results with ClovR. 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.
 
Learning goals:
Participants will be able to understand and explain the shotgun lipidomics data analysis workflow. 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 applications. Basic knowledge of R and RStudio is a plus to understand the quantitation workflow. Participants are required to bring their own laptop in order to work on the hands-on exercises.

Keywords:
Lipidomics, Statistical Analysis, Visualization

Tools:
R and RStudio, LUX Score, ClovR.


Contact

If you have any questions about the training workshops, please use our Service & Support form.

 

Acknowlegements

We thank de.NBI - the German Network for Bioinformatics Infrastructure and Elixir for their support.

 

 

Release Note: SpeCS Database Update- Lipid Mediators

A new version of a spectral library for the Thermo Fisher Scientific Q Exactive mass spectrometer with new lipid mediators is now available for SpeCS. You can download the database here:

QExactive Mediator Library 

 

The spectral comparison score (SCS) algorithm provides a well-defined quality control approach for PRM based quantitation of lipid mediators. The score is based on the correlation between structural similarity and MS/MS fragmentation profile. All fragment ions above a user defined threshold are considered to calculate a score based on matching m/z and Spearman’s rank correlation between fragment intensities. SpeCSwas developed to

1) process raw peak lists,

2) generate customized spectral libraries,

3) perform SCS calculations, and

4) help to identify quantifier ions.

A set of filters can be employed to delete background signals and/or select only fragments that fit the user-defined compositional constraints.

Read more about SpeCS 

Release 1.0.2 of the jmzTab-m library was published to Maven Central

Please find the full release notes at https://github.com/lifs-tools/jmzTab-m/releases/tag/release-1.0.2 and in the next paragraphs:

It implements the draft of mzTab-m 2.0 at https://github.com/HUPO-PSI/mzTab.

This release also includes any amendments that were made as a result of the publication reviewers' feedback and the feedback from the PSI document review process. We have substantially updated the API documentation and have added examples from the specification document.

Release 1.0.2 should be backwards compatible to 1.0.1. However, due to fixes in the handling of optional columns using CV parameters, files written with the old version may need to be updated to follow the optional column specification for CV parameters, namely only the value for the affected row MUST be reported in the table. The column header name must follow the opt_global_cv_MS_MS:12189_parameter_name pattern or the opt_assay[1]_cv_MS_MS:12189_parameter_name pattern (please change the values accordingly).

Also, the MZTabFileParser class has been renamed to MzTabFileParser and was moved from the uk.ac.ebi.pride.jmztab2.utils package to the de.isas.mztab2.io package.

The mapping file has been updated to use the https://www.ebi.ac.uk/ols/ontologies/msio[Metabolomics Standards Society MSIO ontology] for sample processing related terms and the https://www.ebi.ac.uk/ols/ontologies/chebi[CHEBI ontology] for derivatization groups to replace the SEP and XLMOD ontologies. Semantic validation should in this case report a warning to alert you to these changes. Please update your files and implementations accordingly.

To access the release artefacts, please go to Maven Central:

https://search.maven.org/#search%7Cga%7C1%7Cde.isas.mztab

For everyone who is working off any generated code, please update to the latest version:

R: https://search.maven.org/remotecontent?filepath=de/isas/mztab/jmztabm-api/1.0.2/jmztabm-api-1.0.2-r.zip,

Python: https://search.maven.org/remotecontent?filepath=de/isas/mztab/jmztabm-api/1.0.2/jmztabm-api-1.0.2-python.zip

Please note that these packages do not include parser or writer code yet. However, the JSON created can be converted to proper mzTab using the Java CLI.

The CLI package bundles parser and semantic validator and contains sample files and the latest mapping file:

https://search.maven.org/remotecontent?filepath=de/isas/mztab/jmztabm-cli/1.0.2/jmztabm-cli-1.0.2-bin.zip

Running

java -jar jmztabm-cli-1.0.2.jar

on your command line will show you the possible arguments (staying close to the old jmztab).

Run a basic parse and validation on Error level:

java -jar jmztabm-cli-1.0.2.jar -check inFile=examples/MTBLS263.mztab

Run a basic parse and validation followed by applying a provided mapping file on Error level:

java -jar jmztabm-cli-1.0.2.jar -check inFile=examples/MTBLS263.mztab -checkSemantic mappingFile=cv-mapping/mzTab-M-mapping.xml

Running the same on Info level yields additional messages (for optional parameters):

java -jar jmztabm-cli-1.0.2.jar -check inFile=examples/MTBLS263.mztab -checkSemantic mappingFile=cv-mapping/mzTab-M-mapping.xml -level Info

To use the IO libraries (reading, writing and structural and logical validation) in your own Maven projects, use the following dependency:

<dependency>
    <groupId>de.isas.mztab</groupId>
    <artifactId>jmztabm-io</artifactId>
    <version>1.0.2</version>
</dependency>

To use the semantic validation with the mapping file in your own Maven project, use the following dependency:

<dependency>
    <groupId>de.isas.mztab</groupId>
    <artifactId>jmztabm-validation</artifactId>
    <version>1.0.2</version>
</dependency>

The semantic validation requires access to EBI's Ontology Lookup Service to resolve child terms in the mzTab file against their potential parents in the mapping file.

The validator web-application has been updated to release 1.0.14, which includes jmzTab-m 1.0.2 as well.

The 52nd annual conference of the DGMS will take place from the 10th to the 13th of March, 2019, in Rostock, Germany.

Members of LIFS will be present at the event, presenting software tools and applications for lipidomics.

The following table gives an overview of the timetable of LIFS-related events at the venue.

Day Time Session What Who Affiliation
March 10th 14:00 - 17:00 I. Workshops

Targeted lipidomics-beyond the spreadsheet, new ways for assay development and data evaluation.

The workshop will offer a presentation of current tools developed in the LIFS consortium (de.NBI). The user will be guided how to develop a targeted assay for lipidomics. Therefore, different strategies for MS workflows such as SRM or PRM will be presented. The attendee will also get a brief overview about the dos and don’ts using these strategies. We are looking forward to your attendance!

Please note that the last hour of the workshop time will be dedicated to the inaugural meeting of the Lipid Analysis and Lipidomics Integerest Group within DGMS, led by Dr. Dominik Schwudke and Dr. Robert Ahrends.

Robert Ahrends, Nils Hoffmann,
Leibniz Institute for Analytical Sciences – ISAS, Dortmund, Germany

Dominik Schwudke, Fadi Al Machot,
Research Center Borstel - Leibniz-Lung-Center, Borstel, Germany

Lipidomics Informatics for Life Sciences

 

The following table gives an overview of the timetable of LIFS related posters at the venue.

Day Time Session No. What Who
March 11th 17:15 - 19:00 N.A. 162 A Web-Tool to Compute Lipidomes Homologies based on Template SMILES

Al Machot, Fadi (1); Hoffmann, Nils (2); Krause, Daniel (1); Schwudke, Dominik (1)
Organization(s): 1: Research Center Borstel - Leibniz Lung Center; 2: Leibniz Institute for Analytical Sciences

March 11th 17:15 - 19:00 N.A. 206 LipidCompass

Hoffmann, Nils (1); Al Machot, Fadi (2); Schwudke, Dominik (2); Haug, Kenneth (3); O'Donovan, Claire (3); Ahrends, Robert (1)
Organization(s): 1: Leibniz-Institut für Analytische Wissenschaften – ISAS – e.V., Otto-Hahn-Straße 6b, 44227 Dortmund, Germany; 2: Bioanalytical Chemistry, Research Center Borstel – Leibniz Lung Center, Parkallee 1-40, 23845 Borstel; 3: EMBL-EBI Hinxton, Metabolomics, Wellcome Genome Campus, CB10 1SD, United Kingdom

March 11th 17:15 - 19:00 N.A.     210 LipidCreator: A workbench to probe the lipidomic landscape

Peng, Bing (1); Kopczynski, Dominik (1); Pratt, Brian S (2); Ejsing, Christer S (3,4); Hermansson, Martin (3); Schwudke, Dominik (5); Meckelmann, Sven (6); Schmitz, Oliver J (6); MacLean, Brendan (2); Borst, Oliver (7); Hoffmann, Nils (1); Ahrends, Robert (1)
Organization(s): 1: Leibniz-Institut für Analytische Wissenschaften – ISAS – e.V., Germany; 2: University of Washington, Department of Genome Sciences, Seattle, USA; 3: Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark; 4: Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany; 5: Research Center Borstel, Leibniz Lung Center, Borstel, Germany; 6: Institute of Applied Analytical Chemistry, University of Duisburg-Essen, Essen, Germany; 7: Department of Cardiology and Cardiovascular Medicine, University of Tübingen, Tübingen, Germany

March 11th 17:15 - 19:00 N.A. 218 SIMPLEX: A multi-omics approach for screening of modified hippocampal lipid signaling pathways triggered by lifestyle condition

Schött, Hans-Frieder (1); Westhoff, Philipp (1); Coman, Cristina (1); Li, Tingting (1); Borgmeyer, Maximillian (2); Borutzki, Corinna (3); Confettura, Alessandro-Dario (3); Has, Canan (1); Kreutz, Michael R (2,3); Ahrends, Robert (1)
Organization(s): 1: Leibniz-Institut für Analytische Wissenschaften-ISAS e .V, Otto-Hahn-Str. 6b, 44227 Dortmund, Germany; 2: Leibniz Group 'Dendritic Organelles and Synaptic Function', Center for Molecular Neurobiology (ZMNH), University Medical Center Hamburg-Eppendorf Hamburg, Germany.; 3: RG Neuroplasticity, Leibniz Institute for Neurobiology Magdeburg, Germany.

LIFS is co-organizing the Summer school on Integration of Large Scale Lipidomics Data in Systems Medicine Research (LipoSysMed) in Leipzig will introduce young researchers into the field of lipidomics data acquisition and analysis strategies with the focus of Omics data integration into the systems medicine research.

LipoSysMed is planned as an educational and training event based on the interdisciplinary exchange between biochemists, clinicians, analytical chemists, and computer scientists to provide the participants with the full overview of the current status of lipidome analysis strategies and data integration solutions.

The main aims of the summer school are to introduce early stage researches into the field of lipidomics with the focus on understanding the nature of clinical data and associated mass spectrometry derived datasets as well as bioinformatics solutions for lipidomics data analysis and further integration into multi-dimensional datasets.

The goal of LipoSysMed is to provide to all participants the training necessary to work with raw lipidomics datasets aiming its integration in systems medicine workflows via intensive interdisciplinary knowledge exchange and networking between young scientists, advanced PhD students, postdoctoral trainers and a panel of outstanding international experts.

Application deadline has been extended till: 25January, 2019

>>> Apply here ! <<<