Limits...
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.

Show MeSH

Related in: MedlinePlus

Pearson correlation factors of peak abundances in the MasterScan and individual spectra. In total, the dataset consisted of 128 high resolution MS spectra of total lipid extracts in which 219 peaks of individual lipid species were recognized. The exact number of peaks assigned to lipid species is provided for each PCF bin. The average PCF calculated for the entire dataset had a value of 0.94
© Copyright Policy - open-access
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC3091306&req=5

Figure 8: Pearson correlation factors of peak abundances in the MasterScan and individual spectra. In total, the dataset consisted of 128 high resolution MS spectra of total lipid extracts in which 219 peaks of individual lipid species were recognized. The exact number of peaks assigned to lipid species is provided for each PCF bin. The average PCF calculated for the entire dataset had a value of 0.94

Mentions: Using 128 MS spectra of total lipid extracts of different human blood plasma samples [25], we compiled a MasterScan file in which individual spectra were mass-aligned as described above. In parallel, each of these 128 spectra was submitted to LipidXplorer, lipid species were identified under the same settings, and then the spectra were aligned by identified species (not by peak masses, as in the MasterScan). We note that, in both tests, the intensities of peaks in individual spectra were preserved. We then computed Pearson correlation factors (PCFs) between the intensities of peaks of the same lipid species in the same acquisition, either determined in the raw 'as submitted' spectrum (lipids were identified in individual spectra), or aligned within the MasterScan file (lipids were identified by probing the MasterScan). We anticipated that accurate alignment of multiple spectra would increase the mass accuracy of each individual peak and improve peak identifications. A total of 218 lipid species was recognized by both methods. Of these, three and six species were not identified in the MasterScan and in individually processed spectra, respectively. We compared the intensities of lipid peaks identified by both methods by calculating the PCFs of their intensity vectors (Figure 8) and found that the PCFs of 15 lipid species out of the total of 218 fell below 0.8. Case-by-case inspection of these showed that isotopic clusters of three species in individual spectra were altered by background or spray instability. The remaining 12 lipid species were very low abundance and their peak intensities were below 0.1% of the intensities of base peaks in corresponding spectra. We therefore concluded that, while building a MasterScan, mass-alignment of peaks was, in general, correct. The full test dataset is available in Additional file 10.


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)

Pearson correlation factors of peak abundances in the MasterScan and individual spectra. In total, the dataset consisted of 128 high resolution MS spectra of total lipid extracts in which 219 peaks of individual lipid species were recognized. The exact number of peaks assigned to lipid species is provided for each PCF bin. The average PCF calculated for the entire dataset had a value of 0.94
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 8: Pearson correlation factors of peak abundances in the MasterScan and individual spectra. In total, the dataset consisted of 128 high resolution MS spectra of total lipid extracts in which 219 peaks of individual lipid species were recognized. The exact number of peaks assigned to lipid species is provided for each PCF bin. The average PCF calculated for the entire dataset had a value of 0.94
Mentions: Using 128 MS spectra of total lipid extracts of different human blood plasma samples [25], we compiled a MasterScan file in which individual spectra were mass-aligned as described above. In parallel, each of these 128 spectra was submitted to LipidXplorer, lipid species were identified under the same settings, and then the spectra were aligned by identified species (not by peak masses, as in the MasterScan). We note that, in both tests, the intensities of peaks in individual spectra were preserved. We then computed Pearson correlation factors (PCFs) between the intensities of peaks of the same lipid species in the same acquisition, either determined in the raw 'as submitted' spectrum (lipids were identified in individual spectra), or aligned within the MasterScan file (lipids were identified by probing the MasterScan). We anticipated that accurate alignment of multiple spectra would increase the mass accuracy of each individual peak and improve peak identifications. A total of 218 lipid species was recognized by both methods. Of these, three and six species were not identified in the MasterScan and in individually processed spectra, respectively. We compared the intensities of lipid peaks identified by both methods by calculating the PCFs of their intensity vectors (Figure 8) and found that the PCFs of 15 lipid species out of the total of 218 fell below 0.8. Case-by-case inspection of these showed that isotopic clusters of three species in individual spectra were altered by background or spray instability. The remaining 12 lipid species were very low abundance and their peak intensities were below 0.1% of the intensities of base peaks in corresponding spectra. We therefore concluded that, while building a MasterScan, mass-alignment of peaks was, in general, correct. The full test dataset is available in Additional file 10.

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