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Open Access Method

A novel informatics concept for high-throughput shotgun lipidomics based on the molecular fragmentation query language

Ronny Herzog12, Dominik Schwudke13, Kai Schuhmann12, Julio L Sampaio1, Stefan R Bornstein2, Michael Schroeder4 and Andrej Shevchenko1*

Author Affiliations

1 Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108, 01307 Dresden, Germany

2 Department of Internal Medicine III, Carl Gustav Carus Clinics of Dresden University of Technology, Fetscherstrasse 74, 01307 Dresden, Germany

3 National Centre for Biological Sciences, Tata Institute of Fundamental Research, GKVK, Bellary Road, Bangalore 560065, India

4 Biotechnology Centre, Dresden University of Technology, Tatzberg 47-51, 01307 Dresden, Germany

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Genome Biology 2011, 12:R8  doi:10.1186/gb-2011-12-1-r8

Published: 19 January 2011

Additional files

Additional file 1:

Screenshots of the graphical user interface (GUI) of LipidXplorer. Screenshots of four operational panels and explanations of their organization and available functionalities.

Format: PDF Size: 655KB Download file

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Open Data

Additional file 2:

Scan averaging algorithm. A detailed mathematical description of the algorithm.

Format: PDF Size: 127KB Download file

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Open Data

Additional file 3:

Binning of peaks during scan averaging. A figure showing a work scheme and explaining why the accuracy of average mass calculation improves with each binning cycle.

Format: PDF Size: 87KB Download file

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Open Data

Additional file 4:

Spectra alignment algorithm. A detailed mathematical description of the algorithm.

Format: PDF Size: 111KB Download file

This file can be viewed with: Adobe Acrobat Reader

Open Data

Additional file 5:

Common peak attributes considered by LipidXplorer.

Format: PDF Size: 65KB Download file

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Open Data

Additional file 6:

Backus-Naur-Form (BNF) of the molecular fragmentation query language (MFQL).

Format: PDF Size: 81KB Download file

This file can be viewed with: Adobe Acrobat Reader

Open Data

Additional file 7:

Comparison of 325 spectra independently averaged by Xcalibur and LipidXplorer. A spreadsheet providing alignment details for each pair of spectra at different intensity thresholds.

Format: XLSX Size: 100KB Download file

Open Data

Additional file 8:

Validation of the isotopic correction algorithm. A spreadsheet providing the abundances of peaks within partially overlapping isotopic clusters of PA lipids calculated with and without isotopic correction.

Format: XLSX Size: 26KB Download file

Open Data

Additional file 9:

Validation of the spectra alignment algorithm using a computationally generated spectra dataset. A spreadsheet providing details of alignments of spectra processed using different numbers of binning cycles.

Format: XLSX Size: 50KB Download file

Open Data

Additional file 10:

Validation of the spectra alignment algorithm using MS spectra acquired from 128 total lipid extracts. A spreadsheet providing a list of identified lipids and details of spectra alignment and correlation of peak intensities.

Format: XLSX Size: 1.1MB Download file

Open Data

Additional file 11:

MFQL scripts used for LipidXplorer benchmarking.

Format: PDF Size: 43KB Download file

This file can be viewed with: Adobe Acrobat Reader

Open Data

Additional file 12:

Benchmarking the LipidXplorer identification performance. A spreadsheet providing lists of lipid species identified in a total E. coli extract by different software and their alignment with species from the reference list.

Format: XLSX Size: 92KB Download file

Open Data

Additional file 13:

Lipid species identified by LipidXplorer in spectra acquired at different mass resolution from a total E. coli extract. A spreadsheet providing a list of species and intensities of their precursor and characteristic fragment ions in each individual spectrum.

Format: XLS Size: 168KB Download file

This file can be viewed with: Microsoft Excel Viewer

Open Data

Additional file 14:

Validation of LipidXplorer cross-platform lipid identification by correlating relative abundances of E. coli lipid species determined in independent MS and MS/MS experiments on QSTAR Pulsar i and LTQ Orbitrap Velos mass spectrometers. A spreadsheet providing LipidXplorer spectra processing settings, bar diagrams of relative abundances of individual species and statistical estimates of their correlation.

Format: XLSX Size: 113KB Download file

Open Data

Additional file 15:

MFQL scripts used for the lipid identification in a bovine heart total extract.

Format: PDF Size: 30KB Download file

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Open Data

Additional file 16:

Lipid species identified by LipidXplorer in a total extract of bovine heart. A spreadsheet providing a full list of lipid species and intensities of their precursor and characteristic fragment ions detected in independent MS and MS/MS experiments.

Format: XLSX Size: 55KB Download file

Open Data