A peaklet-based generic strategy for the untargeted analysis of comprehensive two-dimensional gas chromatography mass spectrometry data sets

Journal of Chromatography A

Volumn 1405, Issue , 2015, Pages 168-177

  Egert, Björn ^a   Weinert, Christoph H ^a   Kulling, Sabine E ^a  

^a FEDERAL RESEARCH INSTITUTE OF NUTRITION AND FOOD   (Germany)

Author keywords

Comprehensive two dimensional gas chromatography mass spectrometry (GC GC MS); Data alignment algorithm; Peak modulation; Untargeted metabolomics

Indexed keywords

ALIGNMENT; MASS SPECTROMETRY; MODULATION; QUALITY CONTROL; SMOKE DETECTORS;

AUTOMATED PROCESSING; COMPREHENSIVE TWO-DIMENSIONAL GAS CHROMATOGRAPHY; DATA ALIGNMENTS; DENSITY-BASED CLUSTERING; GENERIC STRATEGIES; METABOLOMICS; SIMILARITY MATRIX; TRANSPARENT WORKFLOW;

GAS CHROMATOGRAPHY;

ALGORITHM; ARTICLE; AUTOMATION; CONTROLLED STUDY; DATA ANALYSIS; DATA PROCESSING; MASS FRAGMENTOGRAPHY; METABOLOMICS; PHYSICAL PARAMETERS; PRIORITY JOURNAL; QUALITY CONTROL; RELIABILITY; RETENTION TIME; TWO DIMENSIONAL GAS CHROMATOGRAPHY MASS SPECTROMETRY; URINALYSIS; CLUSTER ANALYSIS; HUMAN; METABOLOME; PROCEDURES;

ALGORITHMS; CLUSTER ANALYSIS; GAS CHROMATOGRAPHY-MASS SPECTROMETRY; HUMANS; METABOLOME; METABOLOMICS; URINALYSIS;

EID: 84937513495     PISSN: 00219673     EISSN: 18733778     Source Type: Journal    
DOI: 10.1016/j.chroma.2015.05.056     Document Type: Article

References (44)

1. Mondello L., Tranchida P.Q., Dugo P., Dugo G. Comprehensive two-dimensional gas chromatography-mass spectrometry: a review. Mass Spectrom. Rev. 2008, 27:101-124.
2. Purcaro G., Quinto Tranchida P., Conte L., Obiedzinska A., Dugo P., Dugo G., Mondello L. Performance evaluation of a rapid-scanning quadrupole mass spectrometer in the comprehensive two-dimensional gas chromatography analysis of pesticides in water. J. Sep. Sci. 2011, 34:2411-2417.
3. Purcaro G., Tranchida P.Q., Ragonese C., Conte L., Dugo P., Dugo G., Mondello L. Evaluation of a rapid-scanning quadrupole mass spectrometer in an apolar×ionic-liquid comprehensive two-dimensional gas chromatography system. Anal. Chem. 2010, 82:8583-8590.
4. Silva B.J., Tranchida P.Q., Purcaro G., Queiroz M.E., Mondello L., Lancas F.M. Evaluation of comprehensive two-dimensional gas chromatography coupled to rapid scanning quadrupole mass spectrometry for quantitative analysis. J. Chromatogr. A 2012, 1255:177-183.
5. Wojciechowska E., Weinert C., Egert B., Trierweiler B., Schmidt-Heydt M., Horneburg B., Graeff-Hönninger S., Kulling S., Geisen R. Chlorogenic acid, a metabolite identified by untargeted metabolome analysis in resistant tomatoes, inhibits the colonization by Alternaria alternata by inhibiting alternariol biosynthesis. Eur. J. Plant Pathol. 2014, 139:735-747.
6. Oh C., Huang X., Regnier F.E., Buck C., Zhang X. Comprehensive two-dimensional gas chromatography/time-of-flight mass spectrometry peak sorting algorithm. J. Chromatogr. A 2008, 1179:205-215.
7. Wang B., Fang A., Heim J., Bogdanov B., Pugh S., Libardoni M., Zhang X. DISCO: Distance and spectrum correlation optimization alignment for two-dimensional gas chromatography time-of-flight mass spectrometry-based metabolomics. Anal. Chem. 2010, 82:5069-5081.
8. Wang B. A two-stage peak alignment algorithm for two-dimensional gas chromatography time-of-flight mass spectrometry-based metabolomics. Comput. Struct. Biotechnol. J. 2013, 7:e201304002.
9. Wang B., Fang A., Shi X., Kim S., Zhang X. Bio-inspired Computing and Applications 2012, 486-491. Springer, Berlin Heidelberg. D.-S. Huang, Y. Gan, P. Premaratne, K. Han (Eds.).
10. Almstetter M.F., Appel I.J., Dettmer K., Gruber M.A., Oefner P.J. Comparison of two algorithmic data processing strategies for metabolic fingerprinting by comprehensive two-dimensional gas chromatography-time-of-flight mass spectrometry. J. Chromatogr. A 2011, 1218:7031-7038.
11. Almstetter M.F., Appel I.J., Gruber M.A., Lottaz C., Timischl B., Spang R., Dettmer K., Oefner P.J. Integrative normalization and comparative analysis for metabolic fingerprinting by comprehensive two-dimensional gas chromatography-time-of-flight mass spectrometry. Anal. Chem. 2009, 81:5731-5739.
12. Castillo S., Mattila I., Miettinen J., Oresic M., Hyotylainen T. Data analysis tool for comprehensive two-dimensional gas chromatography/time-of-flight mass spectrometry. Anal. Chem. 2011, 83:3058-3067.
13. Wei X., Shi X., Koo I., Kim S., Schmidt R.H., Arteel G.E., Watson W.H., McClain C., Zhang X. MetPP: a computational platform for comprehensive two-dimensional gas chromatography time-of-flight mass spectrometry-based metabolomics. Bioinformatics 2013, 29:1786-1792.
14. Hoffmann N., Wilhelm M., Doebbe A., Niehaus K., Stoye J. BiPACE 2D - Graph-based multiple alignment for comprehensive 2D gas chromatography-mass spectrometry. Bioinformatics 2014, 30:988-995.
15. Kim S., Fang A.Q., Wang B., Jeong J., Zhang X. An optimal peak alignment for comprehensive two-dimensional gas chromatography mass spectrometry using mixture similarity measure. Bioinformatics 2011, 27:1660-1666.
16. Kim S., Koo I., Fang A., Zhang X. Smith-Waterman peak alignment for comprehensive two-dimensional gas chromatography-mass spectrometry. BMC Bioinform. 2011, 12:235.
17. Stein S.E., Scott D.R. Optimization and testing of mass-spectral library search algorithms for compound identification. J. Am. Soc. Mass Spectrom. 1994, 5:859-866.
18. Robinson M.D., De Souza D.P., Keen W.W., Saunders E.C., McConville M.J., Speed T.P., Likic V.A. A dynamic programming approach for the alignment of signal peaks in multiple gas chromatography-mass spectrometry experiments. BMC Bioinform. 2007, 8:419.
19. Weusten J.J., Derks E.P., Mommers J.H., van der Wal S. Alignment and clustering strategies for GCxGC-MS features using a cylindrical mapping. Anal. Chim. Acta 2012, 726:9-21.
20. Reichenbach S.E., Tian X., Tao Q., Ledford E.B., Wu Z., Fiehn O. Informatics for cross-sample analysis with comprehensive two-dimensional gas chromatography and high-resolution mass spectrometry (GCxGC-HRMS). Talanta 2011, 83:1279-1288.
21. Groger T., Schaffer M., Putz M., Ahrens B., Drew K., Eschner M., Zimmermann R. Application of two-dimensional gas chromatography combined with pixel-based chemometric processing for the chemical profiling of illicit drug samples. J. Chromatogr. A 2008, 1200:8-16.
22. Schmarr H.G., Bernhardt J. Profiling analysis of volatile compounds from fruits using comprehensive two-dimensional gas chromatography and image processing techniques. J. Chromatogr. A 2010, 1217:565-574.
23. Skov T., Hoggard J.C., Bro R., Synovec R.E. Handling within run retention time shifts in two-dimensional chromatography data using shift correction and modeling. J. Chromatogr. A 2009, 1216:4020-4029.
24. Gros J., Nabi D., Dimitriou-Christidis P., Rutler R., Arey J.S. Robust algorithm for aligning two-dimensional chromatograms. Anal. Chem. 2012, 84:9033-9040.
25. Zhang D., Huang X., Regnier F.E., Zhang M. Two-dimensional correlation optimized warping algorithm for aligning GC x GC-MS data. Anal. Chem. 2008, 80:2664-2671.
26. Weinert C.H., Egert B., Kulling S.E. On the applicability of comprehensive two-dimensional gas chromatography combined with a fast-scanning quadrupole mass spectrometer for untargeted large-scale metabolomics. J. Chromatogr. A 2015, 1405:156-167.
27. Hummel J., Strehmel N., Selbig J., Walther D., Kopka J. Decision tree supported substructure prediction of metabolites from GC-MS profiles. Metabolomics 2010, 6:322-333.
28. C. Beleites, S. Valter, hyperSpec: a package to handle hyperspectral data sets in R. Package version 0.98-20140523. http://hyperspec.r-forge.r-project.org (2014).
29. Adahchour M., Beens J., Brinkman U.A.T. Recent developments in the application of comprehensive two-dimensional gas chromatography. J. Chromatogr. A 2008, 1186:67-108.
30. Demuth W., Karlovits M., Varmuza K. Spectral similarity versus structural similarity: mass spectrometry. Anal. Chim. Acta 2004, 516:75-85.
31. Kim S., Koo I., Jeong J., Wu S., Shi X., Zhang X. Compound identification using partial and semipartial correlations for gas chromatography-mass spectrometry data. Anal. Chem. 2012, 84:6477-6487.
32. Kim S., Zhang X. Comparative analysis of mass spectral similarity measures on peak alignment for comprehensive two-dimensional gas chromatography mass spectrometry. Comput. Math Methods Med. 2013, 2013:509761.
33. Koo I., Kim S., Zhang X. Comparative analysis of mass spectral matching-based compound identification in gas chromatography-mass spectrometry. J. Chromatogr. A 2013, 1298:132-138.
34. Liu J., Bell A., Bergeron J., Yanofsky C., Carrillo B., Beaudrie C., Kearney R. Methods for peptide identification by spectral comparison. Proteome Sci. 2007, 5:3.
35. Wan K.X., Vidavsky I., Gross M.L. Comparing similar spectra: from similarity index to spectral contrast angle. J. Am. Soc. Mass Spectrom. 2002, 13:85-88.
36. Ester M., Kriegel H., Sander J., Xu X. A Density-based Algorithm for Discovering Clusters in Large Spatial Databases with Noise 1996, 226-231. AAAI Press. E. Simoudis, J. Han, U. Fayyad (Eds.).
37. C. Hennig, fpc: Flexible procedures for clustering. R package version 2.1-7, 2010, http://CRAN.R-project.org/package=fpc.
38. Koek M.M., van der Kloet F.M., Kleemann R., Kooistra T., Verheij E.R., Hankemeier T. Semi-automated non-target processing in GC x GC-MS metabolomics analysis: applicability for biomedical studies. Metabolomics 2011, 7:1-14.
39. Wehrens R., Weingart G., Mattivi F. metaMS: an open-source pipeline for GC-MS-based untargeted metabolomics. J. Chromatogr. B Anal. Technol. Biomed. Life Sci. 2014.
40. Chan E.C.Y., Pasikanti K.K., Nicholson J.K. Global urinary metabolic profiling procedures using gas chromatography-mass spectrometry. Nat. Protocols 2011, 6:1483-1499.
41. Cuadros-Inostroza A., Caldana C., Redestig H., Kusano M., Lisec J., Pena-Cortes H., Willmitzer L., Hannah M. TargetSearch-a Bioconductor package for the efficient preprocessing of GC-MS metabolite profiling data. BMC Bioinform. 2009, 10:428.
42. Du X., Zeisel S.H. Spectral deconvolution for gas chromatography mass spectrometry-based metabolomics: current status and future perspectives. Comput. Struct. Biotechnol. J. 2013, 4:e201301013.
43. Lisec J., Schauer N., Kopka J., Willmitzer L., Fernie A.R. Gas chromatography mass spectrometry-based metabolite profiling in plants. Nat. Protocols 2006, 1:387-396.
44. Lu H., Liang Y., Dunn W.B., Shen H., Kell D.B. Comparative evaluation of software for deconvolution of metabolomics data based on GC-TOF-MS. TrAC Trends Anal. Chem. 2008, 27:215-227.