Method
A novel informatics concept for high-throughput shotgun lipidomics based on the molecular fragmentation query language
- † Equal contributors
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
Genome Biology 2011, 12:R8 doi:10.1186/gb-2011-12-1-r8
Published: 19 January 2011Additional 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.
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Additional file 2:
Scan averaging algorithm. A detailed mathematical description of the algorithm.
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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.
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Additional file 4:
Spectra alignment algorithm. A detailed mathematical description of the algorithm.
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Additional file 5:
Common peak attributes considered by LipidXplorer.
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Additional file 6:
Backus-Naur-Form (BNF) of the molecular fragmentation query language (MFQL).
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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
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
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
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.
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Additional file 11:
MFQL scripts used for LipidXplorer benchmarking.
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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
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
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
Additional file 15:
MFQL scripts used for the lipid identification in a bovine heart total extract.
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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
