A dynamic programming approach for the alignment of signal peaks in multiple gas chromatography-mass spectrometry experiments

BMC Bioinformatics

Volumn 8, Issue , 2007, Pages

  Robinson, Mark D ^a,b   De Souza, David P ^c   Keen, Woon Wai ^c   Saunders, Eleanor C ^c   McConville, Malcolm J ^c   Speed, Terence P ^a,d   Likić, Vladimir A ^c  

^a WALTER AND ELIZA HALL INSTITUTE OF MEDICAL RESEARCH   (Australia)

^b UNIVERSITY OF MELBOURNE   (Australia)

^c UNIVERSITY OF MELBOURNE   (Australia)

^d UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BIOLOGICAL SAMPLES; CHROMATOGRAPHIC PROFILES; GAS CHROMATOGRAPHY-MASS SPECTROMETRIES (GC-MS); GAS CHROMATOGRAPHY-MASS SPECTROMETRY; METABOLIC PROFILING; METABOLOMICS DATA; OPTIMAL ALIGNMENTS; SIMILARITY FUNCTIONS;

CHROMATOGRAPHIC ANALYSIS; DYNAMIC PROGRAMMING; EXPERIMENTS; FORESTRY; GAS CHROMATOGRAPHY; MASS SPECTROMETERS; MASS SPECTROMETRY;

ALIGNMENT;

ARTICLE; DATA ANALYSIS; DIAGNOSTIC ACCURACY; DNA FINGERPRINTING; GAS CHROMATOGRAPHY; GENE REPLICATION; INTERMETHOD COMPARISON; LEISHMANIA MEXICANA; MASS SPECTROMETRY; METABOLOMICS; MICROBIAL METABOLISM; NONHUMAN; SEQUENCE ALIGNMENT; SEQUENTIAL ANALYSIS; SIGNAL DETECTION; SIGNAL PROCESSING; STATISTICAL ANALYSIS; ALGORITHM; ARTIFICIAL INTELLIGENCE; AUTOMATED PATTERN RECOGNITION; GENE EXPRESSION PROFILING; MASS FRAGMENTOGRAPHY; METHODOLOGY; PEPTIDE MAPPING;

LEISHMANIA MEXICANA;

ALGORITHMS; ARTIFICIAL INTELLIGENCE; GAS CHROMATOGRAPHY-MASS SPECTROMETRY; GENE EXPRESSION PROFILING; PATTERN RECOGNITION, AUTOMATED; PEPTIDE MAPPING;

EID: 38049148514     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-8-419     Document Type: Article

References (39)

1. Fiehn O Kopka J Dormann P Altmann T Trethewey RN Willmitzer L Metabolite profiling for plant functional genomics Nat Biotechnol 2000, 18:1157-1161. 10.1038/81137 11062433
2. Allen J Davey HM Broadhurst D Heald JK Rowland JJ Oliver SG Kell DB High-throughput classification of yeast mutants for functional genomics using metabolic footprinting Nat Biotechnol 2003, 21:692-696. 10.1038/ nbt823 12740584
3. Sweetlove LJ Last RL Fernie AR Predictive Metabolic Engineering: A Goal for Systems Biology Plant Physiology 2003, 132:420-425. 1540321 12805573 10.1104/pp.103.022004
4. Fernie AR Trethewey RN Krotzky AJ Willmitzer L Metabolite profiling: from diagnostics to systems biology Nat Rev Mol Cell Biol 2004, 5:763-769. 10.1038/nrm1451 15340383
5. Koek MM Muilwijk B van der Werf MJ Hankemeier T Microbial metabolomics with gas chromatography/mass spectrometry Anal Chem 2006, 78:1272-1281. 10.1021/ac051683+ 16478122
6. Sabatine MS Liu E Morrow DA Heller E McCarroll R Wiegand R Berriz GF Roth FP Gerszten RE Metabolomic identification of novel biomarkers of myocardial ischemia Circulation 2005, 112:3868-3875. 10.1161/ CIRCULATIONAHA.105.569137 16344383
7. Robertson DG Metabonomics in toxicology: A review Toxicol Sci 2005, 85:809-822. 10.1093/toxsci/kfi102 15689416
8. Keun HC Metabonomic modeling of drug toxicity Pharmacol Ther 2006, 109:92-106. 10.1016/j.pharmthera.2005.06.008 16051371
9. Gibney MJ Walsh M Brennan L Roche HM German B van Ommen B Metabolomics in human nutrition: Opportunities and challenges Am J Clin Nutr 2005, 82:497-503. 16155259
10. German JB Watkins SM Fay LB Metabolomics in practice: Emerging knowledge to guide future dietetic advice toward individualized health J Am Diet Assoc 2005, 105:1425-1432. 10.1016/j.jada.2005.06.006 16129085
11. Nikiforova VJ Gakiere B Kempa S Adamik M Willmitzer L Hesse H Hoefgen R Towards dissecting nutrient metabolism in plants: A systems biology case study on sulphur metabolism J Exp Bot 2004, 55:1861-1870. 10.1093/jxb/ erh177 15208339
12. Roessner U Luedemann A Brust D Fiehn O Linke T Willmitzer L Fernie A Metabolic profiling allows comprehensive phenotyping of genetically or environmentally modified plant systems Plant Cell 2001, 13:11-29. 10.1105/tpc.13.1.11 11158526
13. Urbanczyk-Wochniak E Luedemann A Kopka J Selbig J Roessner-Tunali U Willmitzer L Fernie AR Parallel analysis of transcript and metabolic profiles: A new approach in systems biology EMBO Rep 2003, 4:989-993. 1326402 12973302 10.1038/sj.embor.embor944
14. Tolstikov VV Lommen A Nakanishi K Tanaka N Fiehn O Monolithic silica-based capillary reversed-phase liquid chromatography/electrospray mass spectrometry for plant metabolomics Anal Chem 2003, 75:6737-6740. 10.1021/ac034716z 14640754
15. Halket JM Waterman D Przyborowska AM Patel RK Fraser PD Bramley PM Chemical derivatization and mass spectral libraries in metabolic profiling by GC/MS and LC/MS/MS J Exp Bot 2005, 56:219-243. 10.1093/jxb/ eri069 15618298
16. 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. 10.1016/S1044-0305(99)00047-1
17. Malmquist G Danielsson R Alignment of chromatographic profiles for principal component analysis: A prerequisite for fingerprinting methods Journal of Chromatography A 1994, 687:71-88. 10.1016/0021-9673(94)00726-8
18. Johnson KJ Wright BW Jarman KH Synovec RE High-speed peak matching algorithm for retention time alignment of gas chromatographic data for chemometric analysis J Chromatogr A 2003, 996:141-155. 10.1016/ S0021-9673(03)00616-2 12830915
19. Duran AL Yang J Wang L Sumner LW Metabolomics spectral formatting, alignment and conversion tools (MSFACTs) Bioinformatics 2003, 19:2283-2293. 10.1093/bioinformatics/btg315 14630657
20. Katajamaa M Oresic M Processing methods for differential analysis of LC/ MS profile data BMC Bioinformatics 2005, 6:179. 1187873 16026613 10.1186/ 1471-2105-6-179
21. 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. 10.1021/ac051437y 16448051
22. De Souza DP Saunders EC McConville MJ Likic VA Progressive peak clustering in GC-MS Metabolomic experiments applied to Leishmania parasites Bioinformatics 2006, 22:1391-1396. 10.1093/bioinformatics/ btl085 16527833
23. Styczynski MP Moxley JF Tong LV Walther JL Jensen KL Stephanopoulos GN Systematic identification of conserved metabolites in GC/MS data for metabolomics and biomarker discovery Anal Chem 2007, 79:966-973. 10.1021/ ac0614846 17263323
24. Frenzel T Miller A Engel KH A methodology for automated comparative analysis of metabolite profiling data European Food Research and Technology 2004, 216:1438-2377.
25. Broeckling CD Reddy IR Duran AL Zhao X Sumner LW MET-IDEA: Data extraction tool for mass spectrometry-based metabolomics Anal Chem 2006, 78:4334-4341. 10.1021/ac0521596 16808440
26. Nielsen NPV Carstensen JM Smedsgaard J Aligning of single and multiple wavelength chromatographic profiles for chemometric data analysis using correlation optimised warping Journal of Chromatography A 1998, 805:17-35. 10.1016/S0021-9673(98)00021-1
27. Bylund D Danielsson R Malmquist G Markides KE Chromatographic alignment by warping and dynamic programming as a pre-processing tool for PARAFAC modelling of liquid chromatography-mass spectrometry data J Chromatogr A 2002, 961:237-244. 10.1016/S0021-9673(02)00588-5 12184621
28. Jonsson P Gullberg J Nordstrom A Kusano M Kowalczyk M Sjostrom M Moritz T A strategy for identifying differences in large series of metabolomic samples analyzed by GC/MS Anal Chem 2004, 76:1738-1745. 10.1021/ ac0352427 15018577
29. Eilers PH Parametric time warping Anal Chem 2004, 76:404-411. 10.1021/ ac034800e 14719890
30. Baran R Kochi H Saito N Suematsu M Soga T Nishioka T Robert M Tomita M MathDAMP: A package for differential analysis of metabolite profiles BMC Bioinformatics 2006, 7:530. 1764210 17166258 10.1186/1471-2105-7-530
31. Tikunov Y Lommen A de Vos CH Verhoeven HA Bino RJ Hall RD Bovy AG A novel approach for nontargeted data analysis for metabolomics. Large-scale profiling of tomato fruit volatiles Plant Physiol 2005, 139:1125-1137. 1283752 16286451 10.1104/pp.105.068130
32. Feng DF Doolittle RF Progressive sequence alignment as a prerequisite to correct phylogenetic trees J Mol Evol 1987, 25:351-360. 10.1007/ BF02603120 3118049
33. Thompson JD Higgins DG Gibson TJ CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice Nucleic Acids Res 1994, 22:4673-4680. 308517 7984417 10.1093/nar/22.22.4673
34. Needleman SB Wunsch CD A general method applicable to the search for similarities in the amino acid sequence of two proteins J Mol Biol 1970, 48:443-453. 10.1016/0022-2836(70)90057-4 5420325
35. Lipman DJ Altschul SF Kececioglu JD A tool for multiple sequence alignment Proc Natl Acad Sci U S A 1989, 86:4412-4415. 287279 2734293 10.1073/pnas.86.12.4412
36. Burchmore RJ Rodriguez-Contreras D McBride K Merkel P Barrett MP Modi G Sacks D Landfear SM Genetic characterization of glucose transporter function in Leishmania mexicana Proc Natl Acad Sci U S A 2003, 100:3901-3906. 153020 12651954 10.1073/pnas.0630165100
37. Prakash A Mallick P Whiteaker J Zhang H Paulovich A Flory M Lee H Aebersold R Schwikowski B Signal maps for mass spectrometry-based comparative proteomics Mol Cell Proteomics 2006, 5:423-432. 10.1074/ mcp.M500133-MCP200 16269421
38. Wolski WE Lalowski M Martus P Herwig R Giavalisco P Gobom J Sickmann A Lehrach H Reinert K Transformation and other factors of the peptide mass spectrometry pairwise peak-list comparison process BMC Bioinformatics 2005, 6:285. 1343595 16318636 10.1186/1471-2105-6-285
39. Reiner E Abbey LE Moran TF Papamichalis P Schafer RW Characterization of normal human cells by pyrolysis gas chromatography mass spectrometry Biomed Mass Spectrom 1979, 6:491-498. 10.1002/bms.1200061107 394768