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Release 1.0.5 of the jmzTab-m library was published to Maven Central
This is release 1.0.5 of the jmztab-m libraries that was published to Maven Central.
Please find the full release notes at https://github.com/lifs-tools/jmzTab-m/releases/tag/release-1.0.5.
jmzTab-M is the Java reference implementation to read, write and validate the mzTab-m 2.0 specification for metabolomics.
This release comes with an updated Maven site and JavaDoc and fixes issue #26.
Release 1.0.5 should be backwards compatible to 1.0.4, 1.0.3 and 1.0.2.
However, due to a stricter validation of the ms scan id referencing, files that have validated before may now fail to validate. Please contact us if you need help fixing your files.
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 and have increased the unit test coverage.
This release is also available from Bioconda and the CLI is available as a Docker container.
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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.
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!
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Early bird registration will close on September 8th 2019. Abstract submission will close on September 15th 2019. Applications for student travel grants will still be possible after the deadline.
We are very happy to announce the 5th International Lipidomics Forum in Borstel (FZ-Borstel) between 10th and 12th of November 2019. This symposium is the 5th 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)
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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.
