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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:
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:
Prof. Corinne Spickett, Aston University
Coordination:
Dr Alan Goddard
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]
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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:
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.
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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:
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:
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.
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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, Dominik Schwudke, Fadi Al Machot, |
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) |
| 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) |
| 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) |
| 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) |
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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: 25, January, 2019
