Journal of Pharmaceutical and Biomedical Sciences

Identification of Metabolites through GC/LC–MS Processed Data using Different Reference Libraries and Their Comparison

Sarika Srivastava, Priya Ranjan Kumar, Santosh Kumar Mishra

Abstract


Much significant advancement has been reported in the last few years in the field of metabolomics studies. The high-end computer applications are already contributing to the research and analysis in the field of life sciences. There are many hardware and softwares available, which can be used with various biomolecular separation and analysis instruments like chromatography, mass spectroscopy (MS), NMR, etc. The metabolite identification is the crucial part of the metabolomics study. The biosample collected from any resource need to be analysed from GC/LC–MS or NMR-type instrumentation to precisely identify the compounds present in the sample qualitatively and quantitatively. There are many tools and databases already available which can be used for the pre-processing, processing and analysis of raw data generated from these instruments. Various reference libraries are also available, which can be used for the identification of metabolites present in the sample after the processing of raw data. In this study, we have reviewed and compared different libraries and tools available for the metabolite identification from GC/ LC–MS data.

Keywords


metabolomics, reference libraries, GC–MS, LC–MS, metabolite profiling

Full Text:

References


Brown M, Wedge DC, Goodacre R, Kell DB, Baker PN, Kenny LC, et al. Automated workflows for accurate mass-based putative metabolite identification in LC/MS-derived metabolomic datasets. Bioinformatics. 2011;27:1108–1112.

Aggio RB, Mayor A, Reade S, Probert CS, Ruggiero K. Identifying and quantifying metabolites by scoring peaks of GC–MS data. BMC Bioinformatics. 2014;15:374.

Smith CA, Want EJ, O’Maille G, Abagyan R, Siuzdak G. XCMS: processing mass spectrometry data for metabolite profiling using nonlinear peak alignment, matching, and identification. Anal Chem. 2006;78:779–787.

Stein SE. An integrated method for spectrum extraction and compound identification from gas chromatography/mass spectrometry data. J Am Soc Mass Spectrom. 1999;10:770–781.

Qualitative methods of GC/MS analysis: library search. Retrieved from: http://www.shimadzu.com/an/gcms/support/fundamentals/library.html

Kopka J, Schauer N, Krueger S, Birkemeyer C, Usadel B, Bergmüller E, et al. GMD@CSB.DB: the Golm metabolome database. Bioinformatics. 2005;21:1635–1638.

Kind T, Wohlgemuth G, Lee DY, Lu Y, Palazoglu M, Shahbaz S, et al. FiehnLib: mass spectral and retention index libraries for metabolomics based on quadrupole and time-of-flight gas chromatography/mass spectrometry. Anal Chem. 2009;81:10038–10048.

Wishart DS, Knox C, Guo AC, Eisner R, Young N, Gautam B, et al. HMDB: a knowledgebase for the human metabolome. Nucleic Acids Res. 2009;37:603–610.

Warwick B, Dunn WB, Erban A, Weber RJM, Creek DJ, Brown M, et al. Mass appeal: metabolite identification in mass spectrometry- focused untargeted metabolomics. Metabolomics. 2013;9:44–66.

Tiller PR, Yu S, Castro-Perez J, Fillgrove KL, Baillie TA. Highthroughput, accurate mass liquid chromatography/tandem mass spectrometry on a quadrupole time?of?flight system as a ‘first?line’ approach for metabolite identification studies. Rapid Commun Mass Spectrom. 2008;22:1053–1061.

Schauer N, Steinhauser D, Strelkov S, Schomburg D, Allison G, Moritz T, et al. GC–MS libraries for the rapid identification of metabolites in complex biological samples. FEBS Lett. 2005;579:1332–1337.

Zhu ZJ, Schultz AW, Wang J, Johnson CH, Yannone SM, Patti GJ, et al. Liquid chromatography quadrupole time-of-flight characterization of metabolites guided by the METLIN database. Nat Protoc. 2013;8:451–460.

Smith CA, O’Maille G, Want EJ, Qin C, Trauger SA, Brandon TR, et al. METLIN: a metabolite mass spectral database. Ther Drug Monit. 2005;27:747–751.

Tautenhahn R, Cho K, Uritboonthai W, Zhu Z, Patti GJ, Siuzdak G. An accelerated workflow for untargeted metabolomics using the METLIN database. Nat Biotechnol. 2012;30:826–828.

Giarrocco V, Quimby B, Klee M. Retention time locking: concepts and applications. Little falls: Agilent Technologies Publication. 1997.

Agilent G1676AA Fiehn GC/MS metabolomics RTL library, user guide. Retrieved from: http://www.agilent.com/cs/library/usermanuals/ Public/G1676-90001_Fiehn.pdf.

NIST 14 mass spectral & search software. Retrieved from: http:// www.sisweb.com/software/ms/nist.htm.

NIST/EPA/NIH mass spectral library (NIST 14) and NIST mass spectral search program (Version 2.2), user guide. Retrieved from: http://www.nist.gov/srd/upload/NIST1aVer22Man.pdf.

Automated mass spectrometry deconvolution and identification system (AMDIS), user guide. Retrieved from: http://chemdata.nist.gov/mass-spc/amdis/docs/amdis.pdf.

Tautenhahn R, Patti GJ, Rinehart D, Siuzdak G. XCMS online: a web-based platform to process untargeted metabolomic data. Anal Chem. 2012;84:5035–5039.

Horai H, Arita M, Kanaya S, Nihei Y, Ikeda T, Suwa K, et al. MassBank: a public repository for sharing mass spectral data for life sciences. J Mass Spectrom. 2010;45:703–714.

Madison-Qingdao Metabolomics Consortium Database. Retrieved from: http://mmcd.nmrfam.wisc.ed /main.html.

Cui Q, Lewis IA, Hegeman AD, Anderson ME, Schulte JLCF, Westler WM, et al. Metabolite identification via the Madison Metabolomics Consortium Database. Nat Biotechnol. 2008;26:162–164.

Creek DJ, Jankevics A, Burgess KE, Breitling R, Barrett MP. IDEOM: an excel interface for analysis of LC–MS-based metabolomics data. Bioinformatics. 2012;28:1048–1049.

Wang J, Peake DA, Mistrik R, Huang Y. A platform to identify endogenous metabolites using a novel high performance Orbitrap MS and the mzCloud Library. Blood. 2013;4:2–8.

Sheldon MT, Mistrik R, Croley TR. Determination of ion structures in structurally related compounds using precursor ion fingerprinting. J Am Soc Mass Spectrom. 2009;20:370–376.

Kanehisa M, Goto S. KEGG: kyoto encyclopedia of genes and genomes. Nucleic Acids Res. 2000;28:27–30.

Brown M, Dunn WB, Dobson P, Patel Y, Winder CL, Francis-McIntyre S, et al. Mass spectrometry tools and metabolite-specific databases for molecular identification in metabolomics. Analyst. 2009;134:1322–1332.

Brown M, Wedge DC, Goodacre R, Kell DB, Baker PN, Kenny LC, et al. Automated workflows for accurate mass-based putative metabolite identification in LC/MS-derived metabolomic datasets. Bioinformatics. 2011;27:1108–1112.

Kuhl C, Tautenhahn R, Böttcher C, Larson TR, Neumann S. CAMERA: an integrated strategy for compound spectra extraction and annotation of liquid chromatography/mass spectrometry data sets. Anal Chem. 2011;84:283–289.

Kessler N, Walter F, Persicke M, Albaum SP, Kalinowski J, Goesmann A, 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:e113909.


Refbacks

  • There are currently no refbacks.


Copyright (c) 2016 Journal of Pharmaceutical and Biomedical Sciences

Creative Commons License
This work is licensed under a Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License.