News - LIFS Tools web portal

Details: Category: News; Published: 18 November 2019

This year's Lipidomics Forum in Borstel hosted the founding event of the International Lipidomics Society, on November 12th.

What are the aims of the society?
Quoting from the ILS Home Page - About:

The International Lipidomics Society (ILS) is a scientific non-profit organization representing and promoting lipidomics through worldwide cooperation and collaborations by fostering the development of new technologies, techniques, resources, skills and training.

The point of contact for lipidomics research, development and commercialization activities worldwide

Foster global collaboration and transparent communication in lipidomics projects by gathering leading international laboratories from a wide range of disciplines

Organize annual international meetings, workshops and training courses

Foster the translation of lipidomics data to biological meaning in all aspects of research to human health

Support large-scale inter-lab lipidomics projects

Foster and coordinate communication among funding agencies and industry partners with the lipidomics community and coordinate the

Activities of groups and organizations interested in ILS’s scientific initiatives and Interest Groups

If you are interested in contributing to or joining the ILS and any of its interest groups, please visit the ILS homepage and get in contact!

Details: Category: News; Published: 22 August 2019

Early bird registration will close on September 8^th 2019. Abstract submission will close on September 15^th 2019. Applications for student travel grants will still be possible after the deadline.

We are very happy to announce the 5^th International Lipidomics Forum in Borstel (FZ-Borstel) between 10^th and 12^th of November 2019. This symposium is the 5^th 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.

Workshops

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).

More information on the course may be found [here].

Foundation of the International Lipidomics Society (ILS):

Dear Lipidomics Forum attendee, it is with great pleasure that we announce to host the foundation of the International Lipidomics Society (ILS) during our conference. The main aim of the society is to bring together the worldwide lipid community, and represent and promote lipidomics through worldwide cooperation and collaborations. ILS will foster the development of new technologies, resources and skills needed for tackling important research questions in lipid research. If you are interested please join us for the inaugural ceremony.

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

The Organizers

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

Details: Category: News; Published: 22 August 2019

The Department of Biosciences at Aston University has recently been awarded the EU Marie Skłodowska-Curie funded COFUND Doctoral Programme entitled MemTrain (Cell Membranes in Industrial Processes Training). The Programme is coordinated by Dr Alan Goddard who is a member of the Aston Membrane Protein and Lipid Research Group (AMPL). More information about AMPL can be found at:

https://www2.aston.ac.uk/lhs/research/centres-facilities/molecular-biomedical-research/ampl/Aston%20Membrane%20Proteins%20and%20Lipids%20(AMPL)

Over five years, MemTrain will train 12 Early Stage Researchers (ESRs; within 4 years of Masters qualification) undertaking a PhD in an area of research within the remit of AMPL, each of which is expected to have an intersectoral focus. Possible projects involve determining the roles of biological membranes in biotechnology or medicines discovery and the application of novel methodologies to investigate these membranes. Our 11 industrial partners will contribute to training of the researchers to generate a unique, integrated, learning environment in which graduate students benefit from industrial links, employability and entrepreneurial skills, and will leave as researchers who are highly competitive for jobs within academia and industry, as well as public policy, intellectual property law or as entrepreneurs. We are now recruiting for the following project.

Analysis of membrane lipids and their interaction with proteins by mass spectrometry (Waters Ltd).

Cell membrane lipid composition is critical for membrane functionality. The activity of membrane proteins is dependent on their interaction with surrounding membrane lipids, and membrane lipids also act as signals to other cells through recognition by receptors and antibodies. Membrane lipids can also be modified in stress conditions, for example by oxidation. In order to understand membrane properties, detailed analysis of local lipid environment is
needed, using sophisticated analytical methods such as mass spectrometry. The project will focus on 2 related biological areas: i) Analysis of antibody recognition of glycolipids relevant to the development of autoimmune diseases of the nervous system, and ii) Analysis of membrane lipids associated with membrane transporters and their functional effects. The project will be a collaboration with Waters Ltd, and will utilize their new generation cyclic ion mobility mass spectrometry (cIM-MS) instrument for enhanced ability to separate and identify membrane lipids and oxidised lipids, and determine their interactions with membrane proteins. The project will run with support and collaboration from scientists at Waters.

Project contacts

Scientific:
Prof Andy Pitt, Aston University: This email address is being protected from spambots. You need JavaScript enabled to view it. or
Prof. Corinne Spickett, Aston University This email address is being protected from spambots. You need JavaScript enabled to view it.

Coordination:
Dr Alan Goddard This email address is being protected from spambots. You need JavaScript enabled to view it.

Further Information

Please visit the website https://jobs.aston.ac.uk/Vacancy.aspx?ref=R190342 for further information and to apply online.

Download Full Job Advertisement [PDF]

Details: Category: News; Published: 30 April 2019

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

Details: Category: News; Published: 20 February 2019

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.