Combining peak- and chromatogram-based retention time alignment algorithms for multiple chromatography-mass spectrometry datasets
Hoffmann N, Keck M, Neuweger H, Wilhelm M, Högy P, Niehaus K, Stoye J (2012)
BMC Bioinformatics 13(1): 21.
Zeitschriftenaufsatz
| Veröffentlicht | Englisch
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Autor*in
Einrichtung
Centrum für Biotechnologie > Institut für Genomforschung und Systembiologie
Centrum für Biotechnologie > Institut für Bioinformatik
Centrum für Biotechnologie > Arbeitsgruppe J. Stoye
Fakultät für Biologie > Proteom- und Metabolomforschung
Technische Fakultät > AG Genominformatik
Centrum für Biotechnologie > Arbeitsgruppe K. Niehaus
Centrum für Biotechnologie > Institut für Bioinformatik
Centrum für Biotechnologie > Arbeitsgruppe J. Stoye
Fakultät für Biologie > Proteom- und Metabolomforschung
Technische Fakultät > AG Genominformatik
Centrum für Biotechnologie > Arbeitsgruppe K. Niehaus
Abstract / Bemerkung
Background
Modern analytical methods in biology and chemistry use separation techniques coupled to sensitive detectors, such as gas chromatography-mass spectrometry (GC-MS) and liquid chromatography-mass spectrometry (LC-MS). These hyphenated methods provide high-dimensional data. Comparing such data manually to find corresponding signals is a laborious task, as each experiment usually consists of thousands of individual scans, each containing hundreds or even thousands of distinct signals. In order to allow for successful identification of metabolites or proteins within such data, especially in the context of metabolomics and proteomics, an accurate alignment and matching of corresponding features between two or more experiments is required. Such a matching algorithm should capture fluctuations in the chromatographic system which lead to non-linear distortions on the time axis, as well as systematic changes in recorded intensities. Many different algorithms for the retention time alignment of GC-MS and LC-MS data have been proposed and published, but all of them focus either on aligning previously extracted peak features or on aligning and comparing the complete raw data containing all available features.
Results
In this paper we introduce two algorithms for retention time alignment of multiple GC-MS datasets: multiple alignment by bidirectional best hits peak assignment and cluster extension (BIPACE) and center-star multiple alignment by pairwise partitioned dynamic time warping (CEMAPP-DTW). We show how the similarity-based peak group matching method BIPACE may be used for multiple alignment calculation individually and how it can be used as a preprocessing step for the pairwise alignments performed by CEMAPP-DTW. We evaluate the algorithms individually and in combination on a previously published small GC-MS dataset studying the Leishmania parasite and on a larger GC-MS dataset studying grains of wheat (Triticum aestivum).
Conclusions
We have shown that BIPACE achieves very high precision and recall and a very low number of false positive peak assignments on both evaluation datasets. CEMAPP-DTW finds a high number of true positives when executed on its own, but achieves even better results when BIPACE is used to constrain its search space. The source code of both algorithms is included in the OpenSource software framework Maltcms, which is available from http://maltcms.sf.net webcite. The evaluation scripts of the present study are available from the same source.
Erscheinungsjahr
2012
Zeitschriftentitel
BMC Bioinformatics
Band
13
Ausgabe
1
Art.-Nr.
21
ISSN
1471-2105
Finanzierungs-Informationen
Open-Access-Publikationskosten wurden durch die Deutsche Forschungsgemeinschaft und die Universität Bielefeld gefördert.
Page URI
https://pub.uni-bielefeld.de/record/2517239
Zitieren
Hoffmann N, Keck M, Neuweger H, et al. Combining peak- and chromatogram-based retention time alignment algorithms for multiple chromatography-mass spectrometry datasets. BMC Bioinformatics. 2012;13(1): 21.
Hoffmann, N., Keck, M., Neuweger, H., Wilhelm, M., Högy, P., Niehaus, K., & Stoye, J. (2012). Combining peak- and chromatogram-based retention time alignment algorithms for multiple chromatography-mass spectrometry datasets. BMC Bioinformatics, 13(1), 21. doi:10.1186/1471-2105-13-21
Hoffmann, Nils, Keck, Matthias, Neuweger, Heiko, Wilhelm, Mathias, Högy, Petra, Niehaus, Karsten, and Stoye, Jens. 2012. “Combining peak- and chromatogram-based retention time alignment algorithms for multiple chromatography-mass spectrometry datasets”. BMC Bioinformatics 13 (1): 21.
Hoffmann, N., Keck, M., Neuweger, H., Wilhelm, M., Högy, P., Niehaus, K., and Stoye, J. (2012). Combining peak- and chromatogram-based retention time alignment algorithms for multiple chromatography-mass spectrometry datasets. BMC Bioinformatics 13:21.
Hoffmann, N., et al., 2012. Combining peak- and chromatogram-based retention time alignment algorithms for multiple chromatography-mass spectrometry datasets. BMC Bioinformatics, 13(1): 21.
N. Hoffmann, et al., “Combining peak- and chromatogram-based retention time alignment algorithms for multiple chromatography-mass spectrometry datasets”, BMC Bioinformatics, vol. 13, 2012, : 21.
Hoffmann, N., Keck, M., Neuweger, H., Wilhelm, M., Högy, P., Niehaus, K., Stoye, J.: Combining peak- and chromatogram-based retention time alignment algorithms for multiple chromatography-mass spectrometry datasets. BMC Bioinformatics. 13, : 21 (2012).
Hoffmann, Nils, Keck, Matthias, Neuweger, Heiko, Wilhelm, Mathias, Högy, Petra, Niehaus, Karsten, and Stoye, Jens. “Combining peak- and chromatogram-based retention time alignment algorithms for multiple chromatography-mass spectrometry datasets”. BMC Bioinformatics 13.1 (2012): 21.
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2019-09-06T09:18:04Z
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11 Zitationen in Europe PMC
Daten bereitgestellt von Europe PubMed Central.
Elucidation of chromatographic peak shifts in complex samples using a chemometrical approach.
Sousa PFM, de Waard A, Åberg KM., Anal Bioanal Chem 410(21), 2018
PMID: 29947907
Sousa PFM, de Waard A, Åberg KM., Anal Bioanal Chem 410(21), 2018
PMID: 29947907
Supporting metabolomics with adaptable software: design architectures for the end-user.
Sarpe V, Schriemer DC., Curr Opin Biotechnol 43(), 2017
PMID: 27870998
Sarpe V, Schriemer DC., Curr Opin Biotechnol 43(), 2017
PMID: 27870998
Joint Bounding of Peaks Across Samples Improves Differential Analysis in Mass Spectrometry-Based Metabolomics.
Myint L, Kleensang A, Zhao L, Hartung T, Hansen KD., Anal Chem 89(6), 2017
PMID: 28221771
Myint L, Kleensang A, Zhao L, Hartung T, Hansen KD., Anal Chem 89(6), 2017
PMID: 28221771
Further development of biomarkers in amyotrophic lateral sclerosis.
Blasco H, Vourc'h P, Pradat PF, Gordon PH, Andres CR, Corcia P., Expert Rev Mol Diagn 16(8), 2016
PMID: 27275785
Blasco H, Vourc'h P, Pradat PF, Gordon PH, Andres CR, Corcia P., Expert Rev Mol Diagn 16(8), 2016
PMID: 27275785
A hybrid retention time alignment algorithm for SWATH-MS data.
Wu L, Amon S, Lam H., Proteomics 16(15-16), 2016
PMID: 27302277
Wu L, Amon S, Lam H., Proteomics 16(15-16), 2016
PMID: 27302277
Comparative analysis of targeted metabolomics: dominance-based rough set approach versus orthogonal partial least square-discriminant analysis.
Blasco H, Błaszczyński J, Billaut JC, Nadal-Desbarats L, Pradat PF, Devos D, Moreau C, Andres CR, Emond P, Corcia P, Słowiński R., J Biomed Inform 53(), 2015
PMID: 25499899
Blasco H, Błaszczyński J, Billaut JC, Nadal-Desbarats L, Pradat PF, Devos D, Moreau C, Andres CR, Emond P, Corcia P, Słowiński R., J Biomed Inform 53(), 2015
PMID: 25499899
Incorporating peak grouping information for alignment of multiple liquid chromatography-mass spectrometry datasets.
Wandy J, Daly R, Breitling R, Rogers S., Bioinformatics 31(12), 2015
PMID: 25649621
Wandy J, Daly R, Breitling R, Rogers S., Bioinformatics 31(12), 2015
PMID: 25649621
Metabolomics and systems pharmacology: why and how to model the human metabolic network for drug discovery.
Kell DB, Goodacre R., Drug Discov Today 19(2), 2014
PMID: 23892182
Kell DB, Goodacre R., Drug Discov Today 19(2), 2014
PMID: 23892182
BiPACE 2D--graph-based multiple alignment for comprehensive 2D gas chromatography-mass spectrometry.
Hoffmann N, Wilhelm M, Doebbe A, Niehaus K, Stoye J., Bioinformatics 30(7), 2014
PMID: 24363380
Hoffmann N, Wilhelm M, Doebbe A, Niehaus K, Stoye J., Bioinformatics 30(7), 2014
PMID: 24363380
Maui-VIA: A User-Friendly Software for Visual Identification, Alignment, Correction, and Quantification of Gas Chromatography-Mass Spectrometry Data.
Kuich PH, Hoffmann N, Kempa S., Front Bioeng Biotechnol 2(), 2014
PMID: 25654076
Kuich PH, Hoffmann N, Kempa S., Front Bioeng Biotechnol 2(), 2014
PMID: 25654076
Nonlinear alignment of chromatograms by means of moving window fast Fourier transfrom cross-correlation.
Li Z, Wang JJ, Huang J, Zhang ZM, Lu HM, Zheng YB, Zhan DJ, Liang YZ., J Sep Sci 36(9-10), 2013
PMID: 23436496
Li Z, Wang JJ, Huang J, Zhang ZM, Lu HM, Zheng YB, Zhan DJ, Liang YZ., J Sep Sci 36(9-10), 2013
PMID: 23436496
35 References
Daten bereitgestellt von Europe PubMed Central.
Retention time alignment algorithms for LC/MS data must consider non-linear shifts.
Podwojski K, Fritsch A, Chamrad DC, Paul W, Sitek B, Stuhler K, Mutzel P, Stephan C, Meyer HE, Urfer W, Ickstadt K, Rahnenfuhrer J., Bioinformatics 25(6), 2009
PMID: 19176558
Podwojski K, Fritsch A, Chamrad DC, Paul W, Sitek B, Stuhler K, Mutzel P, Stephan C, Meyer HE, Urfer W, Ickstadt K, Rahnenfuhrer J., Bioinformatics 25(6), 2009
PMID: 19176558
Retention index thresholds for compound matching in GC-MS metabolite profiling.
Strehmel N, Hummel J, Erban A, Strassburg K, Kopka J., J. Chromatogr. B Analyt. Technol. Biomed. Life Sci. 871(2), 2008
PMID: 18501684
Strehmel N, Hummel J, Erban A, Strassburg K, Kopka J., J. Chromatogr. B Analyt. Technol. Biomed. Life Sci. 871(2), 2008
PMID: 18501684
An iterative block-shifting approach to retention time alignment that preserves the shape and area of gas chromatography-mass spectrometry peaks.
Chae M, Shmookler Reis RJ, Thaden JJ., BMC Bioinformatics 9 Suppl 9(), 2008
PMID: 18793460
Chae M, Shmookler Reis RJ, Thaden JJ., BMC Bioinformatics 9 Suppl 9(), 2008
PMID: 18793460
Systematic identification of conserved metabolites in GC/MS data for metabolomics and biomarker discovery.
Styczynski MP, Moxley JF, Tong LV, Walther JL, Jensen KL, Stephanopoulos GN., Anal. Chem. 79(3), 2007
PMID: 17263323
Styczynski MP, Moxley JF, Tong LV, Walther JL, Jensen KL, Stephanopoulos GN., Anal. Chem. 79(3), 2007
PMID: 17263323
A geometric approach for the alignment of liquid chromatography-mass spectrometry data.
Lange E, Gropl C, Schulz-Trieglaff O, Leinenbach A, Huber C, Reinert K., Bioinformatics 23(13), 2007
PMID: 17646306
Lange E, Gropl C, Schulz-Trieglaff O, Leinenbach A, Huber C, Reinert K., Bioinformatics 23(13), 2007
PMID: 17646306
Alignment of gas chromatography-mass spectrometry data by landmark selection from complex chemical mixtures
AUTHOR UNKNOWN, 2006
AUTHOR UNKNOWN, 2006
XCMS: processing mass spectrometry data for metabolite profiling using nonlinear peak alignment, matching, and identification.
Smith CA, Want EJ, O'Maille G, Abagyan R, Siuzdak G., Anal. Chem. 78(3), 2006
PMID: 16448051
Smith CA, Want EJ, O'Maille G, Abagyan R, Siuzdak G., Anal. Chem. 78(3), 2006
PMID: 16448051
Chromatographic alignment of ESI-LC-MS proteomics data sets by ordered bijective interpolated warping.
Prince JT, Marcotte EM., Anal. Chem. 78(17), 2006
PMID: 16944896
Prince JT, Marcotte EM., Anal. Chem. 78(17), 2006
PMID: 16944896
Signal maps for mass spectrometry-based comparative proteomics
AUTHOR UNKNOWN, 2006
AUTHOR UNKNOWN, 2006
A dynamic programming approach for the alignment of signal peaks in multiple gas chromatography-mass spectrometry experiments.
Robinson MD, De Souza DP, Keen WW, Saunders EC, McConville MJ, Speed TP, Likic VA., BMC Bioinformatics 8(), 2007
PMID: 17963529
Robinson MD, De Souza DP, Keen WW, Saunders EC, McConville MJ, Speed TP, Likic VA., BMC Bioinformatics 8(), 2007
PMID: 17963529
Critical assessment of alignment procedures for LC-MS proteomics and metabolomics measurements.
Lange E, Tautenhahn R, Neumann S, Gropl C., BMC Bioinformatics 9(), 2008
PMID: 18793413
Lange E, Tautenhahn R, Neumann S, Gropl C., BMC Bioinformatics 9(), 2008
PMID: 18793413
Robust algorithm for alignment of liquid chromatography-mass spectrometry analyses in an accurate mass and time tag data analysis pipeline.
Jaitly N, Monroe ME, Petyuk VA, Clauss TR, Adkins JN, Smith RD., Anal. Chem. 78(21), 2006
PMID: 17073405
Jaitly N, Monroe ME, Petyuk VA, Clauss TR, Adkins JN, Smith RD., Anal. Chem. 78(21), 2006
PMID: 17073405
The correspondence problem for metabonomics datasets.
Aberg KM, Alm E, Torgrip RJ., Anal Bioanal Chem 394(1), 2009
PMID: 19198812
Aberg KM, Alm E, Torgrip RJ., Anal Bioanal Chem 394(1), 2009
PMID: 19198812
Chromatographic alignment by warping and dynamic programming as a pre-processing tool for PARAFAC modelling of liquid chromatography-mass spectrometry data.
Bylund D, Danielsson R, Malmquist G, Markides KE., J Chromatogr A 961(2), 2002
PMID: 12184621
Bylund D, Danielsson R, Malmquist G, Markides KE., J Chromatogr A 961(2), 2002
PMID: 12184621
Time alignment algorithms based on selected mass traces for complex LC-MS data.
Christin C, Hoefsloot HC, Smilde AK, Suits F, Bischoff R, Horvatovich PL., J. Proteome Res. 9(3), 2010
PMID: 20070124
Christin C, Hoefsloot HC, Smilde AK, Suits F, Bischoff R, Horvatovich PL., J. Proteome Res. 9(3), 2010
PMID: 20070124
Dynamic time warping of spectroscopic BATCH data
AUTHOR UNKNOWN, 2003
AUTHOR UNKNOWN, 2003
Alignment using variable penalty dynamic time warping.
Clifford D, Stone G, Montoliu I, Rezzi S, Martin FP, Guy P, Bruce S, Kochhar S., Anal. Chem. 81(3), 2009
PMID: 19138127
Clifford D, Stone G, Montoliu I, Rezzi S, Martin FP, Guy P, Bruce S, Kochhar S., Anal. Chem. 81(3), 2009
PMID: 19138127
Unsupervised parameter optimization for automated retention time alignment of severely shifted gas chromatographic data using the piecewise alignment algorithm.
Pierce KM, Wright BW, Synovec RE., J Chromatogr A 1141(1), 2006
PMID: 17174960
Pierce KM, Wright BW, Synovec RE., J Chromatogr A 1141(1), 2006
PMID: 17174960
A genomic perspective on protein families.
Tatusov RL, Koonin EV, Lipman DJ., Science 278(5338), 1997
PMID: 9381173
Tatusov RL, Koonin EV, Lipman DJ., Science 278(5338), 1997
PMID: 9381173
The use of gene clusters to infer functional coupling.
Overbeek R, Fonstein M, D'Souza M, Pusch GD, Maltsev N., Proc. Natl. Acad. Sci. U.S.A. 96(6), 1999
PMID: 10077608
Overbeek R, Fonstein M, D'Souza M, Pusch GD, Maltsev N., Proc. Natl. Acad. Sci. U.S.A. 96(6), 1999
PMID: 10077608
Minimum Prediction Residual Principle Applied to Speech Recognition
AUTHOR UNKNOWN, 1975
AUTHOR UNKNOWN, 1975
Dynamic Programming Algorithm Optimization for Spoken Word Recognition
AUTHOR UNKNOWN, 1978
AUTHOR UNKNOWN, 1978
The symmetric time-warping problem: from continuous to discrete
AUTHOR UNKNOWN, 1983
AUTHOR UNKNOWN, 1983
Characterization of normal human cells by pyrolysis gas chromatography mass spectrometry.
Reiner E, Abbey LE, Moran TF, Papamichalis P, Schafer RW., Biomed. Mass Spectrom. 6(11), 1979
PMID: 394768
Reiner E, Abbey LE, Moran TF, Papamichalis P, Schafer RW., Biomed. Mass Spectrom. 6(11), 1979
PMID: 394768
Multiple alignment of continuous time series
AUTHOR UNKNOWN, 2005
AUTHOR UNKNOWN, 2005
Time-series alignment by non-negative multiple generalized canonical correlation analysis.
Fischer B, Roth V, Buhmann JM., BMC Bioinformatics 8 Suppl 10(), 2007
PMID: 18269698
Fischer B, Roth V, Buhmann JM., BMC Bioinformatics 8 Suppl 10(), 2007
PMID: 18269698
ChromA: signal-based retention time alignment for chromatography-mass spectrometry data.
Hoffmann N, Stoye J., Bioinformatics 25(16), 2009
PMID: 19505941
Hoffmann N, Stoye J., Bioinformatics 25(16), 2009
PMID: 19505941
Reducibility Among Combinatorial Problems
AUTHOR UNKNOWN, 1972
AUTHOR UNKNOWN, 1972
Complexity Results on Graphs with Few Cliques
AUTHOR UNKNOWN, 2007
AUTHOR UNKNOWN, 2007
Optimized time alignment algorithm for LC-MS data: correlation optimized warping using component detection algorithm-selected mass chromatograms.
Christin C, Smilde AK, Hoefsloot HC, Suits F, Bischoff R, Horvatovich PL., Anal. Chem. 80(18), 2008
PMID: 18715018
Christin C, Smilde AK, Hoefsloot HC, Suits F, Bischoff R, Horvatovich PL., Anal. Chem. 80(18), 2008
PMID: 18715018
Symmetric time warping, Boltzmann pair probabilities and functional genomics.
Clote P, Straubhaar J., J Math Biol 53(1), 2006
PMID: 16791652
Clote P, Straubhaar J., J Math Biol 53(1), 2006
PMID: 16791652
Effects of atmospheric CO2 enrichment on biomass, yield and low molecular weight metabolites in wheat grain
Hogy P, Keck M, Niehaus K, Franzaring J, Fangmeier A., J. Cereal Sci. 52(2), 2010
PMID: IND44432855
Hogy P, Keck M, Niehaus K, Franzaring J, Fangmeier A., J. Cereal Sci. 52(2), 2010
PMID: IND44432855
Effects of elevated CO2 on grain yield and quality of wheat: results from a 3-year free-air CO2 enrichment experiment.
Hogy P, Wieser H, Kohler P, Schwadorf K, Breuer J, Franzaring J, Muntifering R, Fangmeier A., Plant Biol (Stuttg) 11 Suppl 1(), 2009
PMID: 19778369
Hogy P, Wieser H, Kohler P, Schwadorf K, Breuer J, Franzaring J, Muntifering R, Fangmeier A., Plant Biol (Stuttg) 11 Suppl 1(), 2009
PMID: 19778369
MeltDB: a software platform for the analysis and integration of metabolomics experiment data.
Neuweger H, Albaum SP, Dondrup M, Persicke M, Watt T, Niehaus K, Stoye J, Goesmann A., Bioinformatics 24(23), 2008
PMID: 18765459
Neuweger H, Albaum SP, Dondrup M, Persicke M, Watt T, Niehaus K, Stoye J, Goesmann A., Bioinformatics 24(23), 2008
PMID: 18765459
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