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 ! <<<

The 7th European Lipidomics Meeting will take place from 26-29 September 2018 in Leipzig, Germany.

Members of LIFS and the lipidomics standards initiative will be present at the event, giving various keynote presentations and presenting software tools and standardization guidelines for lipidomics.

The following table gives an overview of the timetable of LIFS and LSI related talks and workshop at the venue.

DayTimeSessionWhatWhoAffiliation
September 26th 16:15 - 18:00 Satellite workshop Satellite workshop organized by Lipidomics Standards
Initiative
Kim Ekroos, Lipidomics Consulting Ltd, Finland
Gerhard Liebisch, University of Regensburg, Regensburg, Germany
Lipidomics Standards Initiative (LSI)
September 27th 9:10 - 9:40 Session 1: Analytical Methods Development for Lipidomics Ultra-high-resolution mass spectrometry  and what it brings  to shotgun lipidomics Andrej Shevchenko, MPI-CBG Dresden, Dresden, Germany Lipidomics Informatics for Life Sciences
September 28th 13:30 – 14:30 Lipidomics Software Demo PeakStrainer and LipidXplorer Eduardo Jacobo Miranda Ackerman, MPI-CBG Dresden, Dresden, Germany Lipidomics Informatics for Life Sciences
September 28th 8:30 - 9:00 Session 3:
Bioinformatics solutions for Lipidomics
LIFS: Lipidomics informatics for life-science Robert Ahrends,
Leibniz Institute for Analytical Sciences – ISAS, Dortmund, Germany
Lipidomics Informatics for Life Sciences
September 28th 15:10 - 15:40 Session 5: Clinical Lipidomics Tissue lipidomics: about the challenge to correlate clinical data and
histological phenotypes with lipid metabolic snapshots
Dominik Schwudke,
Research Center Borstel, Borstel, Germany
Lipidomics Informatics for Life Sciences
September 29th 11:50 - 12:10 Session 6: Integration of Lipidomics into Systems
Medicine Research
Guidelines for lipidomics analysis and reporting – the Lipidomics Standards Initiative (LSI) Gerhard Liebisch, University of Regensburg, Regensburg, Germany Lipidomics Standards Initiative (LSI)

 

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

DayTimeSessionWhatWhoAbstract
September 27th 17:40 - 19:00 Poster Session (odd numbers) P3.3: Peakstrainer and LipidXplorerWeb for Online Shotgun Lipidomics Processing Pipeline Jacobo Miranda Ackermann, MPI CBG, Dresden, Germany LipidXplorerWeb is an enhanced online version of the free and open-source software kit LipidXplorer. It supports the identification and quantification of molecular species of any lipid class detected by shotgun experiments performed on any mass spectrometry platform. In contrast to the local installation, the internet version provides continuous enhancements and corrections to simplify the lipid identification routines based on users experience and requirement. For example users can select predefined collections of MFQL files (molecular fragmentation query language), or create their own and share them with other. Automated configuration generation, as well as warning for unexpected setting, make it easier for the user to implement the workflow. The major drawback of online processing is the large file sizes that need to be transferred, to mitigate this issue PeakStrainer can be run on a local installation and generate files where noise peaks are filtered out (without loosing low intensity signals) and the data is efficiently packed to minimize upload time, this allows batch processing of multiple shotgun acquisitions by high-resolution mass mapping, precursor and neutral-loss scanning, and data-dependent MS/MS. While the internet version is suitable for a variety of lipidomics applications in cell biology and molecular medicine, the flexible nature of MFQL and potential for collaboration and interaction lends itself to diverse applications of small molecule identification in experiments where molecules are consistently processed on a mass spectrometry platform.

LipidomicsForum Banner 2018

Early bird registration and abstract submission have been extended until September 15th 2018. Applications for student travel grants will still be possible after the deadline.

We are very happy to announce the 4th International Lipidomics Forum in Dortmund (ISAS) between 11th and 13th of November 2018 (lipidomics-forum.isas.de/ lipidomics-forum.fz-borstel.de). This symposium is the 4th meeting of an annual series of conferences on lipid biology and lipidomics. The forum provides a platform for interaction of international acknowledged scientists, students and young researchers. Specifically, we encourage young researchers to participate by poster presentations and short talks allowing them to receive advice from experts in the field. This symposium series will not only cover research highlights but also will offer tutorials on selected medical and methodical topics, which are in the focus of the Special Interest Group Lipid Analytics and Lipidomics of the DGMS. Students will be financially supported by travel grants of the DGMS. We are very excited to present this meeting and looking forward to lively discussions and many interactions.

The registration is open; we warmly welcome you to the ISAS Dortmund and looking forward to your visit and contribution.

The Organizers

Robert Ahrends (ISAS), Nils Hoffmann (ISAS), Dominik Kopczynski (ISAS), Nicolas Gisch (RCB) and Dominik Schwudke (RCB)