Release Note: LipidXplorer 1.2.8

DOI

Release Note: LipidXplorer 1.2.8, October 14th, 2019

Improved Import Performance and Implementation of Frequency Filtering

Fadi Al Machot, Nils Hoffmann, Jacobo Miranda Ackerman and Dominik Schwudke

Aim:

This release is focused on improving the import module and implementing the recently introduced filtering approach based on counting reoccurrences of peaks in MS-scans and MS/MS-scans conceptually following Schuhmann et al. [1]. All other general functionalities of the former releases should not be affected [2-5]. Further changes were made for better documentation and simpler user guidance. Some experimental and/or unused options were deactivated (grouping samples, heuristic hierarchical alignment, dta/csv import). Details are listed below.

Usage:

The frequency based filtering is active for the *.mzXML and *.mzML import module. For this release we have tested both *.mzXML and *.mzML files after conversion with msConvert of *.raw files of a Q Exactive instrument (Thermo Fisher Scientific, Bremen, Germany)[6]. The LipidXplorer (LX) software and also this improved import module were developed for shotgun lipidomics experiments.

Please see the full release notes document for further details on the evaluation.

Download:

LipidXplorer for Windows  LipidXplorer for Linux  LipidXplorer benchmark data

Installation instructions and Tutorials for LipidXplorer are available here.

Detailed Changelog

New Functionality

  • Added frequency MS-Filter and MS/MS-FilterThe MS-Filter and MS/MS-Filter each take a value between 0 and 1. It represents the fraction of scans in which a certain peak has to be present.

The filter is applied for both MS and MS/MS according to the given import setting for each scan type.

For each precursor ion, all associated MS/MS scans are collected according to the selection window. Counting of MS/MS scans and association of precursor is done automatically.

Accordingly, the number of MS/MS scan can vary for each precursor ion in the shotgun acquisition, as might occur when using a DDA strategy.

  • Improved mzML file loading speed from O(n^2) to O(n).This improves loading speed of mzML files significantly and brings them on par with mzXML files considering import of data.
  • Added application and taskbar icons.(Developers) Anaconda package management.LX now comes with a dependency definition for an Anaconda environment for development under Windows. Please check the GitLab README.md file for further information.
  • LX executable distributions (convenience binaries).here.

Bug Fixes

- Updated Wiki locations to https://lifs.isas.de/wiki

- Fixed MFQL editor dialog closing error on Windows 10 and Python 2.7.

- Fixed application not exiting properly due to non-terminated threads.

- Improved file handle closing by switching to auto closing behaviour with 'with'.

- Fixed output file creation for user accounts with '.' characters in path.

- Fixed UI label truncations and spacing issues on Windows 10.

- Updated wxPython dependency from 3.0 to 4.0.4.

Removed Functionality

- Removed sample grouping

- Removed DTA/CSV + PIS support for input spectra (If you rely on this functionality, please contact us at Service & Support)

Deprecated Functionality

- We plan to remove the mzXML format in one of the next LipidXplorer releases. mzXML is not supported anymore by the mass spectrometry community and deprecated. If you need this feature, please contact us for help with migration.

Acknowledgements:

The current maintainers, developers and contributors for LX would like to thank Ronny Herzog – initial author of the software for his continued support.

References:

1.            Schuhmann, K., et al., Intensity-Independent Noise Filtering in FT MS and FT MS/MS Spectra for Shotgun Lipidomics. Anal Chem, 2017. 89(13): p. 7046-7052.

2.            Eggers, L.F. and D. Schwudke, Shotgun Lipidomics Approach for Clinical Samples. Methods Mol Biol, 2018. 1730: p. 163-174.

3.            Herzog, R., et al., LipidXplorer: a software for consensual cross-platform lipidomics. PLoS One, 2012. 7(1): p. e29851.

4.            Herzog, R., et al., A novel informatics concept for high-throughput shotgun lipidomics based on the molecular fragmentation query language. Genome Biol, 2011. 12(1): p. R8.

5.            Herzog, R., D. Schwudke, and A. Shevchenko, LipidXplorer: Software for Quantitative Shotgun Lipidomics Compatible with Multiple Mass Spectrometry Platforms. Curr Protoc Bioinformatics, 2013. 43: p. 14 12 1-30.

6.            Chambers, M.C., et al., A cross-platform toolkit for mass spectrometry and proteomics. Nat Biotechnol, 2012. 30(10): p. 918-20.

 

 

LipidomicsForum Banner 2018 regOpen

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)

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]

 

 

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