ALLocator: An Interactive Web Platform for the Analysis of Metabolomic LC-ESI-MS Datasets, Enabling Semi-Automated, User-Revised Compound Annotation and Mass Isotopomer Ratio Analysis

Kessler N, Walter F, Persicke M, Albaum S, Kalinowski J, Goesmann A, Niehaus K, Nattkemper TW (2014)
PLoS ONE 9(11): e113909.

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Abstract
Adduct formation, fragmentation events and matrix effects impose special challenges to the identification and quantitation of metabolites in LC-ESI-MS datasets. An important step in compound identification is the deconvolution of mass signals. During this processing step, peaks representing adducts, fragments, and isotopologues of the same analyte are allocated to a distinct group, in order to separate peaks from coeluting compounds. From these peak groups, neutral masses and pseudo spectra are derived and used for metabolite identification via mass decomposition and database matching. Quantitation of metabolites is hampered by matrix effects and nonlinear responses in LC-ESI-MS measurements. A common approach to correct for these effects is the addition of a U-13C-labeled internal standard and the calculation of mass isotopomer ratios for each metabolite. Here we present a new web-platform for the analysis of LC-ESI-MS experiments. ALLocator covers the workflow from raw data processing to metabolite identification and mass isotopomer ratio analysis. The integrated processing pipeline for spectra deconvolution “ALLocatorSD” generates pseudo spectra and automatically identifies peaks emerging from the U-13C-labeled internal standard. Information from the latter improves mass decomposition and annotation of neutral losses. ALLocator provides an interactive and dynamic interface to explore and enhance the results in depth. Pseudo spectra of identified metabolites can be stored in user- and method-specific reference lists that can be applied on succeeding datasets. The potential of the software is exemplified in an experiment, in which abundance fold-changes of metabolites of the l-arginine biosynthesis in C. glutamicum type strain ATCC 13032 and l-arginine producing strain ATCC 21831 are compared. Furthermore, the capability for detection and annotation of uncommon large neutral losses is shown by the identification of (γ-)glutamyl dipeptides in the same strains. ALLocator is available online at: https://allocator.cebitec.uni-bielefeld.​de. A login is required, but freely available.
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Kessler N, Walter F, Persicke M, et al. ALLocator: An Interactive Web Platform for the Analysis of Metabolomic LC-ESI-MS Datasets, Enabling Semi-Automated, User-Revised Compound Annotation and Mass Isotopomer Ratio Analysis. PLoS ONE. 2014;9(11):e113909.
Kessler, N., Walter, F., Persicke, M., Albaum, S., Kalinowski, J., Goesmann, A., Niehaus, K., et al. (2014). ALLocator: An Interactive Web Platform for the Analysis of Metabolomic LC-ESI-MS Datasets, Enabling Semi-Automated, User-Revised Compound Annotation and Mass Isotopomer Ratio Analysis. PLoS ONE, 9(11), e113909. doi:10.1371/journal.pone.0113909
Kessler, N., Walter, F., Persicke, M., Albaum, S., Kalinowski, J., Goesmann, A., Niehaus, K., and Nattkemper, T. W. (2014). ALLocator: An Interactive Web Platform for the Analysis of Metabolomic LC-ESI-MS Datasets, Enabling Semi-Automated, User-Revised Compound Annotation and Mass Isotopomer Ratio Analysis. PLoS ONE 9, e113909.
Kessler, N., et al., 2014. ALLocator: An Interactive Web Platform for the Analysis of Metabolomic LC-ESI-MS Datasets, Enabling Semi-Automated, User-Revised Compound Annotation and Mass Isotopomer Ratio Analysis. PLoS ONE, 9(11), p e113909.
N. Kessler, et al., “ALLocator: An Interactive Web Platform for the Analysis of Metabolomic LC-ESI-MS Datasets, Enabling Semi-Automated, User-Revised Compound Annotation and Mass Isotopomer Ratio Analysis”, PLoS ONE, vol. 9, 2014, pp. e113909.
Kessler, N., Walter, F., Persicke, M., Albaum, S., Kalinowski, J., Goesmann, A., Niehaus, K., Nattkemper, T.W.: ALLocator: An Interactive Web Platform for the Analysis of Metabolomic LC-ESI-MS Datasets, Enabling Semi-Automated, User-Revised Compound Annotation and Mass Isotopomer Ratio Analysis. PLoS ONE. 9, e113909 (2014).
Kessler, Nikolas, Walter, Frederik, Persicke, Marcus, Albaum, Stefan, Kalinowski, Jörn, Goesmann, Alexander, Niehaus, Karsten, and Nattkemper, Tim Wilhelm. “ALLocator: An Interactive Web Platform for the Analysis of Metabolomic LC-ESI-MS Datasets, Enabling Semi-Automated, User-Revised Compound Annotation and Mass Isotopomer Ratio Analysis”. PLoS ONE 9.11 (2014): e113909.
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40 References

Data provided by Europe PubMed Central.

ChemSpider: an online chemical information resource. J Chem Educ
AUTHOR UNKNOWN, 2010
Seven Golden Rules for heuristic filtering of molecular formulas obtained by accurate mass spectrometry. BMC Bioinformatics
AUTHOR UNKNOWN, 2007

AUTHOR UNKNOWN, 0
A novel type of N-acetylglutamate synthase is involved in the first step of arginine biosynthesis in Corynebacterium glutamicum. BMC Genomics
AUTHOR UNKNOWN, 2013
The MetaboLights repository: curation challenges in metabolomics.
Salek RM, Haug K, Conesa P, Hastings J, Williams M, Mahendraker T, Maguire E, Gonzalez-Beltran AN, Rocca-Serra P, Sansone SA, Steinbeck C., Database (Oxford) 2013(), 2013
PMID: 23630246
The Isolation of y-L-Glutamyl Peptides from a Fermentation Broth. J Biol Chem
AUTHOR UNKNOWN, 1965
Gamma-Glutamylpeptide formative activity by Corynebacterium glutamicum by the reverse reaction of the gamma-glutamylpetide hydrolytic enzyme. Agric Biol Chem
AUTHOR UNKNOWN, 1978
Fragmentation reactions of protonated peptides containing glutamine or glutamic acid. J Mass Spectrom
AUTHOR UNKNOWN, 2003

AUTHOR UNKNOWN, 0
Balancing a heterologous mevalonate pathway for improved isoprenoid production in Escherichia coli. Metab Eng
AUTHOR UNKNOWN, 2007
Controlling the false discovery rate: a practical and powerful approach to multiple testing. J R Stat Soc Ser B
AUTHOR UNKNOWN, 1995
Metabolic engineering of Corynebacterium glutamicum for L-arginine production. Nat Commun
AUTHOR UNKNOWN, 2014
MeltDB 2.0-advances of the metabolomics software system. Bioinformatics
AUTHOR UNKNOWN, 2013
MetaboAnalyst: a web server for metabolomic data analysis and interpretation. Nucleic Acids Res
AUTHOR UNKNOWN, 2009
Isoleucine synthesis in Corynebacterium glutamicum: molecular analysis of the ilvB-ilvN-ilvC operon. J Bacteriol
AUTHOR UNKNOWN, 1993

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