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

Herzog R, Schwudke D, Schuhmann K, Sampaio JL, Bornstein SR, Schroeder M, Shevchenko A - Genome Biol. (2011)

Bottom Line: Shotgun lipidome profiling relies on direct mass spectrometric analysis of total lipid extracts from cells, tissues or organisms and is a powerful tool to elucidate the molecular composition of lipidomes.We present a novel informatics concept of the molecular fragmentation query language implemented within the LipidXplorer open source software kit that supports accurate quantification of individual species of any ionizable lipid class in shotgun spectra acquired on any mass spectrometry platform.

View Article: PubMed Central - HTML - PubMed

Affiliation: Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108, 01307 Dresden, Germany.

ABSTRACT
Shotgun lipidome profiling relies on direct mass spectrometric analysis of total lipid extracts from cells, tissues or organisms and is a powerful tool to elucidate the molecular composition of lipidomes. We present a novel informatics concept of the molecular fragmentation query language implemented within the LipidXplorer open source software kit that supports accurate quantification of individual species of any ionizable lipid class in shotgun spectra acquired on any mass spectrometry platform.

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Related in: MedlinePlus

Making a shotgun lipidomics dataset. Experiments are repeated in several independent biological replicates for each studied phenotype. Each biological replicate is split into several samples from which lipids are extracted and extracts are independently analyzed by MS. Spectra acquired from the total lipid extract survey molecular ions of lipid precursors, which are subsequently fragmented in MS/MS experiments, yielding MS/MS spectra. Each spectrum is acquired in several scans that are subsequently averaged. A set of MS and MS/MS spectra is termed as an 'acquisition' and several acquisitions are performed continuously making a 'technical replicate'.
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Figure 1: Making a shotgun lipidomics dataset. Experiments are repeated in several independent biological replicates for each studied phenotype. Each biological replicate is split into several samples from which lipids are extracted and extracts are independently analyzed by MS. Spectra acquired from the total lipid extract survey molecular ions of lipid precursors, which are subsequently fragmented in MS/MS experiments, yielding MS/MS spectra. Each spectrum is acquired in several scans that are subsequently averaged. A set of MS and MS/MS spectra is termed as an 'acquisition' and several acquisitions are performed continuously making a 'technical replicate'.

Mentions: Each biological experiment is performed in parallel in several independent replicates. To determine the lipidome in each of these experiments, each biological replicate is split into several samples that are processed and analyzed independently. Total lipid extracts obtained from each sample are infused into a tandem mass spectrometer a few times and several technical replicates are acquired, each providing a full set of MS and MS/MS spectra further termed as an acquisition. Therefore, a typical shotgun experiment yields several hundreds of MS and MS/MS spectra (Figure 1), although many spectra might be redundant because they are acquired in replicated analyses.


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

Herzog R, Schwudke D, Schuhmann K, Sampaio JL, Bornstein SR, Schroeder M, Shevchenko A - Genome Biol. (2011)

Making a shotgun lipidomics dataset. Experiments are repeated in several independent biological replicates for each studied phenotype. Each biological replicate is split into several samples from which lipids are extracted and extracts are independently analyzed by MS. Spectra acquired from the total lipid extract survey molecular ions of lipid precursors, which are subsequently fragmented in MS/MS experiments, yielding MS/MS spectra. Each spectrum is acquired in several scans that are subsequently averaged. A set of MS and MS/MS spectra is termed as an 'acquisition' and several acquisitions are performed continuously making a 'technical replicate'.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3091306&req=5

Figure 1: Making a shotgun lipidomics dataset. Experiments are repeated in several independent biological replicates for each studied phenotype. Each biological replicate is split into several samples from which lipids are extracted and extracts are independently analyzed by MS. Spectra acquired from the total lipid extract survey molecular ions of lipid precursors, which are subsequently fragmented in MS/MS experiments, yielding MS/MS spectra. Each spectrum is acquired in several scans that are subsequently averaged. A set of MS and MS/MS spectra is termed as an 'acquisition' and several acquisitions are performed continuously making a 'technical replicate'.
Mentions: Each biological experiment is performed in parallel in several independent replicates. To determine the lipidome in each of these experiments, each biological replicate is split into several samples that are processed and analyzed independently. Total lipid extracts obtained from each sample are infused into a tandem mass spectrometer a few times and several technical replicates are acquired, each providing a full set of MS and MS/MS spectra further termed as an acquisition. Therefore, a typical shotgun experiment yields several hundreds of MS and MS/MS spectra (Figure 1), although many spectra might be redundant because they are acquired in replicated analyses.

Bottom Line: Shotgun lipidome profiling relies on direct mass spectrometric analysis of total lipid extracts from cells, tissues or organisms and is a powerful tool to elucidate the molecular composition of lipidomes.We present a novel informatics concept of the molecular fragmentation query language implemented within the LipidXplorer open source software kit that supports accurate quantification of individual species of any ionizable lipid class in shotgun spectra acquired on any mass spectrometry platform.

View Article: PubMed Central - HTML - PubMed

Affiliation: Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108, 01307 Dresden, Germany.

ABSTRACT
Shotgun lipidome profiling relies on direct mass spectrometric analysis of total lipid extracts from cells, tissues or organisms and is a powerful tool to elucidate the molecular composition of lipidomes. We present a novel informatics concept of the molecular fragmentation query language implemented within the LipidXplorer open source software kit that supports accurate quantification of individual species of any ionizable lipid class in shotgun spectra acquired on any mass spectrometry platform.

Show MeSH
Related in: MedlinePlus