Computational mass spectrometry for small molecules

Journal of Cheminformatics

Volumn 5, Issue 3, 2013, Pages

  Scheubert, Kerstin ^a   Hufsky, Franziska ^a,b   Böcker, Sebastian ^a  

^a FRIEDRICH SCHILLER UNIVERSITY JENA   (Germany)

^b MAX PLANCK INSTITUTE FOR CHEMICAL ECOLOGY   (Germany)

Author keywords

Fragmentation trees; Mass spectrometry; Metabolomics; Molecular formula identification; Networks; Spectral library; Structure elucidation

Indexed keywords

EID: 84877343392     PISSN: None     EISSN: 17582946     Source Type: Journal    
DOI: 10.1186/1758-2946-5-12     Document Type: Review

References (256)

1. Cui Q, Lewis IA, Hegeman AD, Anderson ME, Li J, Schulte CF, Westler WM, Eghbalnia HR, Sussman MR, Markley JL: Metabolite identification via theMadison Metabolomics Consortium Database. Nat Biotechnol 2008, 26(2):162-164. (Pubitemid 351225941)
2. Last RL, Jones AD, Shachar-Hill Y: Towards the plantmetabolome and beyond. Nat RevMol Cell Biol 2007, 8:167-174.
3. Patti GJ, Yanes O, Siuzdak G: Innovation: Metabolomics: The apogee of the omics trilogy. Nat RevMol Cell Biol 2012, 13(4):263-269.
4. Lederberg J: Topologicalmapping of organicmolecules. Proc Natl Acad Sci USA 1965, 53(1):134-139.
5. Lederberg J: How DENDRAL was conceived and born. In ACM Conf. on the History of Medical Informatics, History of Medical Informatics archive; 1987:5-19.
6. Mun IK, Mclafferty FW: Computermethods of molecular structure elucidation from unknownmass spectra. In Supercomputers in Chemistry, ACS Symposium Series, chapter 9; 1981:117-124.
7. Smith DH, Gray NA, Nourse JG, Crandell CW: The DENDRAL project: Recent advances in computer-assisted structure elucidation. Anal Chim Acta 1981, 133(4):471-497.
8. November JA: Digitizing Life: The Introduction of Computers to Biology and Medicine. PhD thesis. Princeton, USA: Princeton University; 2006.
9. Gasteiger J, Hanebeck W, Schulz KP: Prediction of mass spectra from structural information. J Chem Inf Comput Sci 1992, 32(4):264-271.
10. 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 Chromatography A 2002, 961:237-244. (Pubitemid 34761919)
11. Jeong J, Shi X, Zhang X, Kim S, Shen C: Model-based peak alignment of metabolomic profiling from comprehensive two-dimensional gas chromatography mass spectrometry. BMC Bioinformatics 2012, 13:27.
12. Lommen A, Kools HJ: MetAlign 3.0: performance enhancement by efficient use of advances in computer hardware. Metabolomics 2012, 8(4):719-726.
13. 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(3):779-787. (Pubitemid 43228585)
14. Garkani-Nejad Z, Karlovits M, Demuth W, Stimpfl T, Vycudilik W, Jalali-Heravi M, Varmuza K: Prediction of gas chromatographic retention indices of a diverse set of toxicologically relevant compounds. J Chromatogr A 2004, 1028(2):287-295. (Pubitemid 38121374)
15. Stein SE, Babushok VI, Brown RL, Linstrom PJ: Estimation of Kováts retention indices using group contributions. J Chem Inf Model 2007, 47(3):975-980. (Pubitemid 46973712)
16. Cox J, Mann M: MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification. Nat Biotechnol 2008, 26(12):1367-1372.
17. Bandeira N, Pham V, Pevzner P, Arnott D, Lill JR: Automated de novo protein sequencing ofmonoclonal antibodies. Nat Biotechnol 2008, 26(12):1336-1338.
18. Liu G, Zhang J, Larsen B, Stark C, Breitkreutz A, Lin ZY, Breitkreutz BJ, Ding Y, Colwill K, Pasculescu A, Pawson T, Wrana JL, Nesvizhskii AI, Raught B, Tyers M, Gingras AC: ProHits: Integrated software formass spectrometry-based interaction proteomics. Nat Biotechnol 2010, 28(10):1015-1017.
19. Fusaro VA, Mani DR, Mesirov JP, Carr SA: Prediction of high-responding peptides for targeted protein assays by mass spectrometry. Nat Biotechnol 2009, 27(2):190-198.
20. Elias JE, Gibbons FD, King OD, Roth FP, Gygi SP: Intensity-based protein identification by machine learning from a library of tandem mass spectra. Nat Biotechnol 2004, 22(2):214-219. (Pubitemid 38160538)
21. Mann M: Comparative analysis to guide quality improvements in proteomics. Nat Methods 2009, 6(10):717-719.
22. Böcker S: Sequencing from compomers: Using mass spectrometry for DNA de-novo sequencing of 200+ nt. J Comput Biol 2004, 11(6):1110-1134. (Pubitemid 40171216)
23. Böcker S: Simulating multiplexed SNP discovery rates using base-specific cleavage and mass spectrometry. Bioinformatics 2007, 23(2):e5 - e12. (Pubitemid 46189628)
24. Böcker S, Kehr B, Rasche F: Determination of glycan structure from tandem mass spectra. IEEE/ACM Trans Comput Biol Bioinform 2011, 8(4):976-986.
25. Goldberg D, Bern MW, Li B, Lebrilla CB: Automatic determination of O-glycan structure from fragmentation spectra. J Proteome Res 2006, 5(6):1429-1434. (Pubitemid 43865812)
26. Goldberg D, Bern MW, North SJ, Haslam SM, Dell A: Glycan family analysis for deducing N-glycan topology from single MS. Bioinformatics 2009, 25(3):365-371.
27. Baumgaertel A, Scheubert K, Pietsch B, Kempe K, Crecelius AC, Böcker S, Schubert US: Analysis of different synthetic homopolymers by the use of a new calculation software for tandemmass spectra. Rapid Commun Mass Spectrom 2011, 25(12):1765-1778.
28. Thalassinos K, Jackson AT, Williams JP, Hilton GR, Slade SE, Scrivens JH: Novel software for the assignment of peaks from tandemmass spectrometry spectra of synthetic polymers. J AmSoc Mass Spectrom 2007, 18(7):1324-1331. (Pubitemid 46963602)
29. Katajamaa M, Oresic M: Data processing formass spectrometry- basedmetabolomics. J Chromatogr A 2007, 1158(1-2):318-328.
30. Wishart DS: Current progress in computationalmetabolomics. Brief Bioinform 2007, 8(5):279-293.
31. Stein SE: Mass spectral reference libraries: An ever-expanding resource for chemical identification. Anal Chem 2012, 84(17):7274-7282.
32. Han J, Datla R, Chan S, Borchers CH: Mass spectrometry-based technologies for high-throughput metabolomics. Bioanalysis 2009, 1(9):1665-1684.
33. Kind T, Fiehn O: Advances in structure elucidation of small molecules using mass spectrometry. Bioanal Rev 2010, 2(1-4):23-60.
34. Xiao JF, Zhou B, Ressom HW: Metabolite identification and quantitation in LC-MS/MS-basedmetabolomics. Trends Analyt Chem 2012, 32:1-14.
35. Fiehn O: Extending the breadth ofmetabolite profiling by gas chromatography coupled tomass spectrometry. Trends Analyt Chem 2008, 27(3):261-269.
36. Valkenborg D, Mertens I, Lemière F, Witters E, Burzykowski T: The isotopic distribution conundrum. Mass Spectrom Rev 2012, 31(1):96-109.
37. Neumann S, Böcker S: Computational mass spectrometry for metabolomics - a review. Anal Bioanal Chem 2010, 398(7):2779-2788.
38. Fernie AR, Trethewey RN, Krotzky AJ, Willmitzer L: Metabolite profiling: From diagnostics to systems biology. Nat RevMol Cell Biol 2004, 5(9):763-769. (Pubitemid 39208185)
39. Sweedler JV: Metabolomics in analytical chemistry. Anal Chem 2012, 84(14):5833.
40. Champarnaud E, Hopley C: Evaluation of the comparability of spectra generated using a tuning point protocol on twelve electrospray ionisation tandem-in-space mass spectrometers. Rapid Commun Mass Spectrom 2011, 25(8):1001-1007.
41. Bristow AWT, Webb KS, Lubben AT, Halket J: Reproducible product-ion tandem mass spectra on various liquid chromatography/mass spectrometry instruments for the development of spectral libraries. Rapid Commun Mass Spectrom 2004, 18(13):1447-1454. (Pubitemid 38868744)
42. Halket JM, Waterman D, Przyborowska AM, Patel RKP, 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(410):219-243. (Pubitemid 40181128)
43. Goodley P: Maximizing MS/MS fragmentation in the ion trap using CID voltage ramping. Technical Report 5988-0704EN, Agilent Technologies, 2007.
44. Hopley C, Bristow T, Lubben A, Simpson A, Bull E, Klagkou K, Herniman J: Langley J Towards a universal product ionmass spectral library - reproducibility of product ion spectra across eleven different mass spectrometers. Rapid Commun Mass Spectrom 2008, 22(12):1779-1786. (Pubitemid 351947742)
45. Palit M, Mallard G: Fragmentation energy index for universalization of fragmentation energy in ion trap mass spectrometers for the analysis of chemical weapon convention related chemicals by atmospheric pressure ionization-tandem mass spectrometry analysis. Anal Chem 2009, 81(7):2477-2485.
46. Knochenmuss R, Zenobi R: MALDI ionization: the role of in-plume processes. Chem Rev 2003, 103(2):441-452.
47. Kostiainen R, Kotiaho T, Kuuranne T, Auriola S: Liquid chromatography/atmospheric pressure ionization-mass spectrometry in drugmetabolism studies. JMass Spectrom 2003, 38(4):357-372. (Pubitemid 36582213)
48. Marchi I, Rudaz S, Veuthey JL: Atmospheric pressure photoionization for coupling liquid-chromatography to mass spectrometry: a review. Talanta 2009, 78(1):1-18.
49. Takáts Z, Wiseman JM, Gologan B, Cooks RG: Mass spectrometry sampling under ambient conditions with desorption electrospray ionization. Science 2004, 306(5695):471-473. (Pubitemid 39372443)
50. Horvath CG, Lipsky SR: Use of liquid ion exchange chromatography for the separation of organic compounds. Nature 1966, 211(5050):748-749.
51. MacNair JE, Lewis KC, Jorgenson JW: Ultrahigh-pressure reversed-phase liquid chromatography in packed capillary columns. Anal Chem 1997, 69(6):983-989.
52. Gao X, Zhang Q, Meng D, Isaac G, Zhao R, Fillmore TL, Chu RK, Zhou J, Tang K, Hu Z, Moore RJ, Smith RD, Katze MG, Metz TO: A reversed-phase capillary ultra-performance liquid chromatography-mass spectrometry (UPLC-MS) method for comprehensive top-down/bottom-up lipid profiling. Anal Bioanal Chem 2012, 402(9):2923-2933.
53. Zubarev R, Mann M: On the proper use of mass accuracy in proteomics. Mol Cell Proteomics 2007, 6(3):377-381. (Pubitemid 46554535)
54. Cajka T, Hajslova J, Lacina O, Mastovska K, Lehotay SJ: Rapid analysis of multiple pesticide residues in fruit-based baby food using programmed temperature vaporiser injection-low-pressure gas chromatography-high-resolution time-of-flight mass spectrometry. J Chromatogr A 2008, 1186(1-2):281-294.
55. Hernández F, Portolés T, Pitarch E, López FJ: Gas chromatography coupled to high-resolution time-of-flight mass spectrometry to analyze trace-level organic compounds in the environment, food safety and toxicology. Trends Anal Chem 2011, 30(2):388-400.
56. Hufsky F, Rempt M, Rasche F, Pohnert G, Böcker S: De novo analysis of electron impact mass spectra using fragmentation trees. Anal Chim Acta 2012, 739:67-76.
57. Bino RJ, Hall RD, Fiehn O, Kopka J, Saito K, Draper J, Nikolau BJ, Mendes P, Roessner-Tunali U, Beale MH, Trethewey RN, Lange BM, Wurtele ES, Sumner LW: Potential of metabolomics as a functional genomics tool. Trends Plant Sci 2004, 9(9):418-425. (Pubitemid 39160937)
58. Jenkins H, Hardy N, Beckmann M, Draper J, Smith AR, Taylor J, Fiehn O, Goodacre R, Bino RJ, Hall R, Kopka J, Lane GA, Lange BM, Liu JR, Mendes P, Nikolau BJ, Oliver SG, Paton NW, Rhee S, Roessner-Tunali U, Saito K, Smedsgaard J, Sumner LW, Wang T, Walsh S, Wurtele ES, Kell DB: A proposed framework for the description of plantmetabolomics experiments and their results. Nat Biotechnol 2004, 22(12):1601-1606. (Pubitemid 40039472)
59. Board Members MSI, Sansone SA, Fan T, Goodacre R, Griffin JL, Hardy NW, Kaddurah-Daouk R, Kristal BS, Lindon J, Mendes P, Morrison N, Nikolau B, Robertson D, Sumner LW, Taylor C, van der Werf M, van Ommen B, Fiehn O: Themetabolomics standards initiative. Nat Biotechnol 2007, 25(8):846-848.
60. Goodacre R, Broadhurst D, Smilde AK, Kristal BS, Baker JD, Beger R, Bessant C, Connor S, Capuani G, Craig A, Ebbels T, Kell DB, Manetti C, Newton J, Paternostro G, Somorjai R, Sjöström M, Trygg J, Wulfert F: Proposed minimum reporting standards for data analysis in metabolomics. Metabolomics 2007, 3:231-241. (Pubitemid 47470692)
61. Sumner LW, Amberg A, Barrett D, Beale M, Beger R, Daykin C, Fan T, Fiehn O, Goodacre R, Griffin JL, Hankemeier T, Hardy N, Harnly J, Higashi R, Kopka J, Lane A, Lindon JC, Marriott P, Nicholls A, Reily M, Thaden J, Viant MR: Proposed minimum reporting standards for chemical analysis. Metabolomics 2007, 3(3):211-221.
62. Horai H, Arita M, Nishioka T: Comparison of ESI-MS spectra in MassBank database. In Proc. of Conference on BioMedical Engineering and Informatics (BMEI 2008), volume 2; 2008:853-857.
63. Horai H, Arita M, Kanaya S, Nihei Y, Ikeda T, Suwa K, Ojima Y, Tanaka K, Tanaka S, Aoshima K, Oda Y, Kakazu Y, Kusano M, Tohge T, Matsuda F, Sawada Y, Hirai MY, Nakanishi H, Ikeda K, Akimoto N, Maoka T, Takahashi H, Ara T, Sakurai N, Suzuki H, Shibata D, Neumann S, Iida T, Tanaka K, Funatsu K, et al: MassBank: A public repository for sharing mass spectral data for life sciences. JMass Spectrom 2010, 45(7):703-714.
64. Smith CA, O'Maille G, Want EJ, Qin C, Trauger SA, Brandon TR, Custodio DE, Abagyan R, Siuzdak G: METLIN: Ametabolitemass spectral database. Ther Drug Monit 2005, 27(6):747-751.
65. Tautenhahn R, Cho K, Uritboonthai W, Zhu Z, Patti GJ, Siuzdak G: An accelerated workflow for untargetedmetabolomics using the METLIN database. Nat Biotechnol 2012, 30(9):826-828.
66. Kopka J, Schauer N, Krueger S, Birkemeyer C, Usadel B, Bergmüller E, Dörmann P, Weckwerth W, Gibon Y, Stitt M, Willmitzer L, Fernie AR, Steinhauser D: GMD@CSB.DB: The Golm Metabolome Database. Bioinformatics 2005, 21(8):1635-1638. (Pubitemid 40542722)
67. Akiyama K, Chikayama E, Yuasa H, Shimada Y, Tohge T, Shinozaki K, Hirai MY, Sakurai T, Kikuchi J, Saito K: PRIMe: A web site that assembles tools for metabolomics and transcriptomics. In Silico Biol 2008, 8(3-4):339-345.
68. Neuweger H, Albaum SP, Dondrup M, Persicke M, Watt T, Niehaus K, Stoye J, Goesmann A: MeltDB: A software platform for the analysis and integration of metabolomics experiment data. Bioinformatics 2008, 24(23):2726-2732. (Pubitemid 352722615)
69. Sansone SA, Rocca-Serra P, Field D, Maguire E, Taylor C, Hofmann O, Fang H, Neumann S, Tong W, Amaral-Zettler L, Begley K, Booth T, Bougueleret L, Burns G, Chapman B, Clark T, Coleman LA, Copeland J, Das S, de Daruvar A, de Matos P, Dix I, Edmunds S, Evelo CT, Forster MJ, Gaudet P, Gilbert J, Goble C, Griffin JL, Jacob D, et al: Toward interoperable bioscience data. Nat Genet 2012, 44(2):121-126.
70. Kind T, Wohlgemuth G, Lee DY, Lu Y, Palazoglu M, Shahbaz S, Fiehn O: FiehnLib: Mass spectral and retention index libraries for metabolomics based on quadrupole and time-of-flight gas chromatography/mass spectrometry. Anal Chem 2009, 81(24):10038-10048.
71. Oberacher H, Pavlic M, Libiseller K, Schubert B, Sulyok M, Schuhmacher R, Csaszar E, Köfeler HC: On the inter-instrument and inter-laboratory transferability of a tandem mass spectral reference library: 1. Results of an Austrian multicenter study. JMass Spectrom 2009, 44(4):485-493.
72. Oberacher H, Pavlic M, Libiseller K, Schubert B, Sulyok M, Schuhmacher R, Csaszar E, Köfeler HC: On the inter-instrument and the inter-laboratory transferability of a tandemmass spectral reference library: 2. Optimization and characterization of the search algorithm. JMass Spectrom 2009, 44(4):494-502.
73. Sana TR, Roark JC, Li X, Waddell K, Fischer SM: Molecular formula and METLIN Personal Metabolite Databasematching applied to the identification of compounds generated by LC/TOF-MS. J Biomol Tech 2008, 19(4):258-266.
74. Wishart DS, Tzur D, Knox C, Eisner R, Guo AC, Young N, Cheng D, Jewell K, Arndt D, Sawhney S, Fung C, Nikolai L, Lewis M, Coutouly MA, Forsythe I, Tang P, Shrivastava S, Jeroncic K, Stothard P, Amegbey G, Block D, Hau DD, Wagner J, Miniaci J, Clements M, Gebremedhin M, Guo N, Zhang Y, Duggan GE, MacInnis GD, et al: HMDB: The human metabolome database. Nucleic Acids Res 2007, 35(suppl1):D521 - 526. (Pubitemid 46056263)
75. Wishart DS, Knox C, Guo AC, Eisner R, Young N, Gautam B, Hau DD, Psychogios N, Dong E, Bouatra S, Mandal R, Sinelnikov I, Xia J, Jia L, Cruz JA, Lim E, Sobsey CA, Shrivastava S, Huang P, Liu P, Fang L, Peng J, Fradette R, Cheng D, Tzur D, Clements M, Lewis A, Souza AD, Zuniga A, Dawe M, et al: HMDB: A knowledgebase for the human metabolome. Nucleic Acids Res 2009, 37:D603 - D610.
76. Matsuda F, Yonekura-Sakakibara K, Niida R, Kuromori T, Shinozaki K, Saito K: MS/MS spectral tag based annotation of non-targeted profile of plant secondary metabolites. Plant J 2008, 57(3):555-577.
77. Sparkman OD: Evaluating electron ionization mass spectral library search results. J AmSoc Mass Spectrom 1996, 7(4):313-318. (Pubitemid 26124976)
78. Hertz HS, Hites RA, Biemann K: Identification ofmass spectra by computer-searching a file of known spectra. Anal Chem 1971, 43(6):681-691.
79. McLafferty F, Hertel R, Villwock R: Computer identification of mass spectra: VI. Probability based matching of mass spectra: Rapid identification of specific compounds inmixtures. OrgMass Spectrom 1974, 9(7):690-702.
80. McLafferty FW, Zhang MY, Stauffer DB, Loh SY: Comparison of algorithms and databases formatching unknown mass spectra. J AmSoc Mass Spectrom 1998, 9(1):92-95. (Pubitemid 128370095)
81. Atwater BL, Stauffer DB, McLafferty FW, Peterson DW: Reliability ranking and scaling improvements to the probability based matching system for unknownmass spectra. Anal Chem 1985, 57(4):899-903.
82. Damen H, Henneberg D, Weimann B: SISCOM - a new library search system for mass spectra. Anal Chim Acta 1978, 103:289-302.
83. Sokolow S, Karnofsky J, Gustafson P: The finnigan library search programs. Finnigan Application Report 2, Finnigan Corp., 1978.
84. Stein SE, Scott DR: Optimization and testing of mass spectral library search algorithms for compound identification. J AmSoc Mass Spectrom 1994, 5(9):859-866.
85. Rasmussen GT, Isenhour TL, Marshall JC: Mass spectral library searches using ion series data compression. J Chem Inf Comput Sci 1979, 19(2):98-104. (Pubitemid 9226567)
86. Koo I, Zhang X, Kim S: Wavelet- and fourier-transform-based spectrum similarity approaches to compound identification in gas chromatography/mass spectrometry. Anal Chem 2011, 83(14):5631-5638.
87. Kim S, Koo I, Wei X, Zhang X: Amethod of finding optimal weight factors for compound identification in gas chromatography-mass spectrometry. Bioinformatics 2012, 28(8):1158-1163.
88. Stein SE: Estimating probabilities of correct identification from results ofmass spectral library searches. J AmSoc Mass Spectrom 1994, 5(4):316-323.
89. Jeong J, Shi X, Zhang X, Kim S, Shen C: An empirical bayes model using a competition score formetabolite identification in gas chromatography mass spectrometry. BMC Bioinformatics 2011, 12:392.
90. Josephs JL, Sanders M: Creation and comparison of MS/MS spectral libraries using quadrupole ion trap and triple-quadrupolemass spectrometers. Rapid Commun Mass Spectrom 2004, 18(7):743-759. (Pubitemid 38451019)
91. Milman BL: Towards a full reference library of MSn spectra. Testing of a library containing 3126 MS2 spectra of 1743 compounds. Rapid Commun Mass Spectrom 2005, 19(19):2833-2839. (Pubitemid 41383368)
92. Pavlic M, Libiseller K, Oberacher H: Combined use of ESI-QqTOF-MS and ESI-QqTOF-MS/MS with mass-spectral library search for qualitative analysis of drugs. Anal Bioanal Chem 2006, 386(1):69-82. (Pubitemid 44268051)
93. Wan KX, Vidavsky I, Gross ML: Comparing similar spectra: From similarity index to spectral contrast angle. J AmSoc Mass Spectrom 2002, 13(13):85-88. (Pubitemid 34552627)
94. Zhou B, Cheema AK, Ressom HW: SVM-based spectralmatching for metabolite identification. Conf Proc IEEE Eng Med Biol Soc 2010, 2010:756-759.
95. Hansen ME, Smedsgaard J: A new matching algorithm for high resolutionmass spectra. J AmSoc Mass Spectrom 2004, 15:1173-1180. (Pubitemid 38970061)
96. Matusita K: Decision rule, based on the distance, for the classification problem. Ann Inst Statist Math 1956, 8(1):67-77.
97. Mylonas R, Mauron Y, Masselot A, Binz PA, Budin N, Fathi M, Viette V, Hochstrasser DF, Lisacek F: X-rank: A robust algorithm for small molecule identification using tandem mass spectrometry. Anal Chem 2009, 81(18):7604-7610.
98. Gergov M, Weinmann W, Meriluoto J, Uusitalo J, Ojanperä I: Comparison of product ion spectra obtained by liquid chromatography/triple- quadrupolemass spectrometry for library search. Rapid Commun Mass Spectrom 2004, 18(10):1039-1046. (Pubitemid 38691366)
99. Issaq HJ, Van QN, Waybright TJ, Muschik GM, Veenstra TD: Analytical and statistical approaches to metabolomics research. J Sep Sci 2009, 32(13):2183-2199.
100. Böcker S, Lipták Zs: Efficientmass decomposition. In Proc. of ACM Symposium on Applied Computing (ACM SAC 2005). New York: ACM press; 2005:151-157.
101. Böcker S, Lipták Zs: A fast and simple algorithm for the Money Changing Problem. Algorithmica 2007, 48(4):413-432.
102. Böcker S, Letzel M, Lipták Zs, Pervukhin A: SIRIUS: Decomposing isotope patterns formetabolite identification. Bioinformatics 2009, 25(2):218-224.
103. Böcker S, Lipták Zs, Martin M, Pervukhin A, Sudek H: DECOMP - from interpreting mass spectrometry peaks to solving the money changing problem. Bioinformatics 2008, 24(4):591-593. (Pubitemid 351256309)
104. Kind T, Fiehn O: Seven golden rules for heuristic filtering of molecular formulas obtained by accuratemass spectrometry. BMC Bioinformatics 2007, 8:105.
105. Yergey JA: A general approach to calculating isotopic distributions formass spectrometry. Int J Mass Spectrom Ion Phys 1983, 52(2-3):337-349.
106. Rockwood AL, Van Orden, S L: Ultrahigh-speed calculation of isotope distributions. Anal Chem 1996, 68:2027-2030.
107. Rockwood AL, Haimi P: Efficient calculation of accuratemasses of isotopic peaks. J AmSoc Mass Spectrom 2006, 17(3):415-419. (Pubitemid 43290200)
108. Snider RK: Efficient calculation of exactmass isotopic distributions. J AmSoc Mass Spectrom 2007, 18(8):1511-1515. (Pubitemid 47096797)
109. Claesen J, Dittwald P, Burzykowski T, Valkenborg D: An efficient method to calculate the aggregated isotopic distribution and exact center-masses. J AmSoc Mass Spectrom 2012, 23(4):753-63.
110. Fernandez-de-Cossio Diaz J, Fernandez-de-Cossio J: Computation of isotopic peak center-mass distribution by Fourier transform. Anal Chem 2012, 84(16):7052-7056.
111. Pluskal T, Uehara T, Yanagida M: Highly accurate chemical formula prediction tool utilizing high-resolutionmass spectra, MS/MS fragmentation, heuristic rules, and isotope pattern matching. Anal Chem 2012, 84(10):4396-4403.
112. Matsuda F, Shinbo Y, Oikawa A, Hirai MY, Fiehn O, Kanaya S, Saito K: Assessment ofmetabolome annotation quality: A method for evaluating the false discovery rate of elemental composition searches. PLoS One 2009, 4(10):e7490.
113. Robertson AL, Hamming MC: MASSFORM: a computer program for the assignment of elemental compositions to high resolutionmass spectral data. BiomedMass Spectrom 1977, 4(4):203-208.
114. Dromey RG, Foyster GT: Calculation of elemental compositions from high resolutionmass spectral data. Anal Chem 1980, 52(3):394-398.
115. Fürst A, Clerc JT, Pretsch E: A computer program for the computation of themolecular formula. Chemom Intell Lab Syst 1989, 5:329-334.
116. Böcker S, Letzel M, Lipták Zs, Pervukhin A: Decomposingmetabolomic isotope patterns. In Proc. of Workshop on Algorithms in Bioinformatics (WABI 2006), volume 4175 of Lect Notes Comput Sci. Berlin: Springer; 2006:12-23.
117. Kind T, Fiehn O: Metabolomic database annotations via query of elemental compositions: Mass accuracy is insufficient even at less than 1 ppm. BMC Bioinformatics 2006, 7(1):234.
118. Wieser ME: Atomic weights of the elements 2005 (IUPAC technical report). Pure Appl Chem 2006, 78(11):2051-2066.
119. Audi G, Wapstra A, Thibault C: The AME2003 atomic mass evaluation (ii): Tables, graphs, and references. Nucl Phys A 2003, 729:129-336. (Pubitemid 37501273)
120. de Laeter JR, Böhlke JK, Biévre PD, Hidaka H, Peiser HS, Rosman KJR, Taylor PDP: Atomic weights of the elements. Review 2000 (IUPAC technical report). Pure Appl Chem 2003, 75(6):683-800.
121. Biemann K: Mass Spectrometry: Organic Chemical Applications. New York: McGraw-Hill; 1962.
122. Kubinyi H: Calculation of isotope distributions in mass spectrometry: A trivial solution for a non-trivial problem. Anal Chim Acta 1991, 247:107-119.
123. Roussis SG, Proulx R: Reduction of chemical formulas from the isotopic peak distributions of high-resolutionmass spectra. Anal Chem 2003, 75(6):1470-1482. (Pubitemid 36397182)
124. Yamamoto H, McCloskey JA: Calculations of isotopic distribution in molecules extensively labeled with heavy isotopes. Anal Chem 1977, 49(2):281-283.
125. Hsu CS: Diophantine approach to isotopic abundance calculations. Anal Chem 1984, 56(8):1356-1361.
126. Rockwood AL: Relationship of fourier transforms to isotope distribution calculations. Rapid Commun Mass Spectrom 1995, 9:103-105.
127. Rockwood AL, Van Orden, S L, Smith RD: Rapid calculation of isotope distributions. Anal Chem 1995, 67:2699-2704.
128. Rockwood AL, Orden SLV, Smith RD: Ultrahigh resolution isotope distribution calculations. Rapid Commun Mass Spectrom 1996, 10:54-59. (Pubitemid 126784563)
129. Li L, Kresh JA, Karabacak NM, Cobb JS, Agar JN, Hong P: A hierarchical algorithm for calculating the isotopic fine structures of molecules. J AmSoc Mass Spectrom 2008, 19(12):1867-1874.
130. Li L, Karabacak NM, Cobb JS, Wang Q, Hong P, Agar JN: Memory-efficient calculation of the isotopicmass states of a molecule. Rapid Commun Mass Spectrom 2010, 24(18):2689-2696.
131. Olson MT, Yergey AL: Calculation of the isotope cluster for polypeptides by probability grouping. J AmSoc Mass Spectrom 2009, 20(2):295-302.
132. Böcker S: Comment on "An efficient method to calculate the aggregated isotopic distribution and exact center-masses" by Claesen et al. J AmSoc Mass Spectrom 2012, 23(10):1826-1827.
133. Fernandez-de-Cossio J: Computation of the isotopic distribution in two dimensions. Anal Chem 2010, 82(15):6726-6729.
134. Claesen J, Dittwald P, Burzykowski T, Valkenborg D: Reply to the comment on: "An efficientmethod to calculate the aggregated isotopic distribution and exact center-masses" by Claesen et al. J AmSoc Mass Spectrom 2012, 23(10):1828-1829.
135. Stoll N, Schmidt E, Thurow K: Isotope pattern evaluation for the reduction of elemental compositions assigned to high-resolution mass spectral data from electrospray ionization fourier transform ion cyclotron resonancemass spectrometry. J AmSoc Mass Spectrom 2006, 17(12):1692-1699. (Pubitemid 44809949)
136. Tong H, Bell D, Tabei K, Siegel MM: Automated datamassaging, interpretation, and e-mailingmodules for high throughput open access mass spectrometry. J AmSoc Mass Spectrom 1999, 10(11):1174-1187. (Pubitemid 34498674)
137. Alon T, Amirav A: Isotope abundance analysis methods and software for improved sample identification with supersonic gas chromatography/mass spectrometry. Rapid Commun Mass Spectrom 2006, 20(17):2579-2588. (Pubitemid 44320213)
138. Ipsen A, Want EJ, Ebbels TMD: Construction of confidence regions for isotopic abundance patterns in LC/MS data sets for rigorous determination of molecular formulas. Anal Chem 2010, 82(17):7319-7328.
139. Rodgers RP, Blumer EN, Hendrickson CL, Marshall AG: Stable isotope incorporation triples the uppermass limit for determination of elemental composition by accuratemassmeasurement. J AmSoc Mass Spectrom 2000, 11(10):835-840. (Pubitemid 34532577)
140. Hegeman AD, Schulte CF, Cui Q, Lewis IA, Huttlin EL, Eghbalnia H, Harms AC, Ulrich EL, Markley JL, Sussman MR: Stable isotope assisted assignment of elemental compositions for metabolomics. Anal Chem 2007, 79(1):6912-6921. (Pubitemid 47438668)
141. Giavalisco P, Li Y, Matthes A, Eckhardt A, Hubberten HM, Hesse H, Segu S, Hummel J, Köhl K, Willmitzer L: Elemental formula annotation of polar and lipophilic metabolites using 13C, 15N and 34S isotope labelling, in combination with high-resolutionmass spectrometry. Plant J 2011, 68(2):364-376.
142. Baran R, Bowen BP, Bouskill NJ, Brodie EL, Yannone SM, Northen TR: Metabolite identification in Synechococcus sp. PCC 7002 using untargeted stable isotope assistedmetabolite profiling. Anal Chem 2010, 82(21):9034-9042.
143. Jarussophon S, Acoca S, Gao JM, Deprez C, Kiyota T, Draghici C, Purisima E, Konishi Y: Automatedmolecular formula determination by tandem mass spectrometry (MS/MS). Analyst 2009, 134(4):690-700.
144. Konishi Y, Kiyota T, Draghici C, Gao JM, Yeboah F, Acoca S, Jarussophon S, Purisima E: Molecular formula analysis by an MS/MS/MS technique to expedite dereplication of natural products. Anal Chem 2007, 79(3):1187-1197.
145. Rojas-Chertó M, Kasper PT, Willighagen EL, Vreeken RJ, Hankemeier T, Reijmers TH: Elemental composition determination based on MSn. Bioinformatics 2011, 27:2376-2383.
146. Zurek G, Krebs I, Götz S, Scheible H, Laufer S, Kammerer B, Albrecht W: A software solution automatically assigns formulae for construction of fragmentation pathways accelerating drug elucidation with ESI-TOF. LCGC Eur Appl Book 2008, 7:31-33.
147. Böcker S, Rasche F: Towards de novo identification of metabolites by analyzing tandemmass spectra. Bioinformatics 2008, 24:I49 - I55.
148. Rasche F, Svatoš A, Maddula RK, Böttcher C, Böcker S: Computing fragmentation trees from tandem mass spectrometry data. Anal Chem 2011, 83(4):1243-1251.
149. Singleton KE, Cooks RG, Wood KV: Utilization of natural isotopic abundance ratios in tandemmass spectrometry. Anal Chem 1983, 55(4):762-764. (Pubitemid 13527396)
150. Rockwood AL, Kushnir MM, Nelson GJ: Dissociation of individual isotopic peaks: Predicting isotopic distributions of product ions in MSn. J AmSoc Mass Spectrom 2003, 14:311-322. (Pubitemid 36876032)
151. Ramaley L, Herrera LC: Software for the calculation of isotope patterns in tandem mass spectrometry. Rapid Commun Mass Spectrom 2008, 22(17):2707-2714.
152. Rogers S, Scheltema RA, Girolami M, Breitling R: Probabilistic assignment of formulas tomass peaks in metabolomics experiments. Bioinformatics 2009, 25(4):512-518.
153. Stein SE: Chemical substructure identification by mass spectral library searching. J AmSoc Mass Spectrom 1995, 6(8):644-655.
154. Demuth W, Karlovits M, Varmuza K: Spectral similarity versus structural similarity: Mass spectrometry. Anal Chim Acta 2004, 516(1-2):75-85. (Pubitemid 38813100)
155. Sheldon MT, Mistrik R, Croley TR: Determination of ion structures in structurally related compounds using precursor ion fingerprinting. J AmSoc Mass Spectrom 2009, 20(3):370-376.
156. Werner E, Heilier JF, Ducruix C, Ezan E, Junot C, Tabet JC: Mass spectrometry for the identification of the discriminating signals from metabolomics: Current status and future trends. J Chromatogr B 2008, 871(2):143-163.
157. Venkataraghavan R, McLafferty FW, van Lear GE: Computer-aided interpretation of mass spectra. OrgMass Spectrom 1969, 2(1):1-15.
158. Kwok KS, Venkataraghavan R, McLafferty FW: Computer-aided interpretation of mass spectra. III. Self-training interpretive and retrieval system. J AmChemSoc 1973, 95(13):4185-4194.
159. Scott DR: Pattern recognition/expert system for mass spectra of volatile toxic and other organic compounds. Anal Chim Acta 1992, 265:43-54.
160. Scott DR: Rapid and accuratemethod for estimating molecular weights of organic compounds from low resolutionmass spectra. Chemometr Intell Lab 1992, 16(3):193-202. (Pubitemid 23012552)
161. Scott DR, Levitsky A, Stein SE: Large scale evaluation of a pattern recognition/expert system for mass spectralmolecular weight estimation. Anal Chim Acta 1993, 278:137-147. (Pubitemid 23161069)
162. Henneberg D, Weimann B, Zalfen U: Computer-aided interpretation of mass spectra using databases with spectra and structures. I. Structure searches. OrgMass Spectrom 1993, 28:198-206.
163. Varmuza K, Werther W: Mass spectral classifiers for supporting systematic structure elucidation. J Chem Inf Comp Sci 1996, 36(2):323-333. (Pubitemid 126591186)
164. Schymanski EL, Meinert C, Meringer M, Brack W: The use of MS classifiers and structure generation to assist in the identification of unknowns in effect-directed analysis. Anal Chim Acta 2008, 615(2):136-147.
165. Xiong Q, Zhang Y, Li M: Computer-assisted prediction of pesticide substructure using mass spectra. Anal Chim Acta 2007, 593(2):199-206. (Pubitemid 46817521)
166. Zhang L, Liang Y, Chen A: Selection of neutral losses and characteristic ions for mass spectral classifier. Analyst 2009, 134(8):1717-1724.
167. Hummel J, Strehmel N, Selbig J, Walther D, Kopka J: Decision tree supported substructure prediction ofmetabolites from GC-MS profiles. Metabolomics 2010, 6(2):322-333.
168. Tsugawa H, Tsujimoto Y, Arita M, Bamba T, Fukusaki E: GC/MS based metabolomics: Development of a datamining system for metabolite identification by using soft independentmodeling of class analogy (SIMCA). BMC Bioinformatics 2011, 12:131.
169. Heinonen M, Shen H, Zamboni N, Rousu J: Metabolite identification andmolecular fingerprint prediction via machine learning. Bioinformatics 2012, 28(18):2333-2341.
170. Kerber A, Laue R, Moser D: Ein Strukturgenerator für molekulare Graphen. Anal Chim Acta 1990, 235:221-228.
171. Benecke C, Grund R, Hohberger R, Kerber A, Laue R, Wieland T: MOLGEN+, a generator of connectivity isomers and stereoisomers formolecular structure elucidation. Anal Chim Acta 1995, 314:141-147.
172. Kerber A, Laue R, Meringer M, Rücker C: Molecules in silico: The generation of structural formulae and its applications. J Comput Chem Japan 2004, 3(3):85-96.
173. Molchanova MS, Shcherbukhin VV, Zefirov NS: Computer generation of molecular structures by the SMOG program. J Chem Inf Comput Sci 1996, 36(4):888-899. (Pubitemid 126581743)
174. Fontana P, Pretsch E: Automatic spectra interpretation, structure generation, and ranking. J Chem Inf Comput Sci 2002, 42(3):614-619. (Pubitemid 35355270)
175. Gray NAB, Buchs A, Smith DH, Djerassi C: Computer assisted structural interpretation of mass spectral data. Helv Chim Acta 1981, 64(2):458-470.
176. Faulon JL: Stochastic generator of chemical structure: (1) Application to the structure elucidation of largemolecules. J Chem Inf Comput Sci 1994, 34:1204-1218.
177. Peironcely JE, Rojas-Chertó M, Fichera D, Reijmers T, Coulier L, Faulon JL, Hankemeier T: OMG: open molecule generator. J Cheminform 2012, 4(1):21.
178. Hill DW, Kertesz TM, Fontaine D, Friedman R, Grant DF: Mass spectral metabonomics beyond elemental formula: Chemical database querying by matching experimental with computational fragmentation spectra. Anal Chem 2008, 80(14):5574-5582.
179. Wolf S, Schmidt S, Müller-Hannemann M, Neumann S: In silico fragmentation for computer assisted identification of metabolite mass spectra. BMC Bioinformatics 2010, 11:148.
180. Kangas LJ, Metz TO, Isaac G, Schrom BT, Ginovska-Pangovska B, Wang L, Tan L, Lewis RR, Miller JH: In silico identification software (ISIS): A machine learning approach to tandem mass spectral identification of lipids. Bioinformatics 2012, 28(13):1705-1713.
181. Kameyama A, Nakaya S, Ito H, Kikuchi N, Angata T, Nakamura M, Ishida HK, Narimatsu H: Strategy for simulation of CID spectra of N-linked oligosaccharides toward glycomics. J Proteome Res 2006, 5(4):808-814.
182. Zhang H, Singh S, Reinhold VN: Congruent strategies for carbohydrate sequencing. 2. FragLib: An MSn spectral library. Anal Chem 2005, 77(19):6263-6270. (Pubitemid 41436961)
183. Chen T, Kao MY, Tepel M, Rush J, Church GM: A dynamic programming approach to de novo peptide sequencing via tandem mass spectrometry: Society for Industrial and Applied Mathematics; 2000.
184. Dančík V, Addona TA, Clauser KR, Vath JE, Pevzner PA: De novo peptide sequencing via tandem mass spectrometry: A graph-theoretical approach. In Proc. of Research in Computational Molecular Biology (RECOMB 1999):135-144.
185. Taylor JA, Johnson RS: Sequence database searches via de novo peptide sequencing by tandemmass spectrometry. Rapid Commun Mass Spectrom 1997, 11:1067-1075. (Pubitemid 27269545)
186. Jalali-Heravi M, Fatemi M: Simulation of mass spectra of noncyclic alkanes and alkenes using artificial neural network. Anal Chim Acta 2000, 415(1-2):95-103. (Pubitemid 30249165)
187. Cooks RG: Bond formation upon electron-impact. OrgMass Spectrom 1969, 2(5):481-519.
188. Bandu ML, Watkins KR, Bretthauer ML, Moore CA, Desaire H: Prediction of MS/MS data. 1. A focus on pharmaceuticals containing carboxylic acids. Anal Chem 2004, 76(6):1746-1753. (Pubitemid 38338424)
189. Klagkou K, Pullen F, HarrisonM, Organ A, Firth A, Langley GJ: Approaches towards the automated interpretation and prediction of electrospray tandem mass spectra of non-peptidic combinatorial compounds. Rapid Commun Mass Spectrom 2003, 17(11):1163-1168. (Pubitemid 36648661)
190. Gray NAB, Carhart RE, Lavanchy A, Smith DH, Varkony T, Buchanan BG, White WC, Creary L: Computerized mass spectrum prediction and ranking. Anal Chem 1980, 52(7):1095-1102. (Pubitemid 11425200)
191. Clark HA, Jurs PC: Simulation of mass spectral intensities by regression analysis of calculated structural characteristics. Anal Chim Acta 1981, 132:75-88.
192. Chen H, Fan B, Xia H, Petitjean M, Yuan S, Panaye A, Doucet JP: MASSIS: Amass spectrum simulation system 1. Principle and method. Eur J Mass Spectrom (Chichester, Eng) 2003, 9(3):175-186. (Pubitemid 37117077)
193. Chen H, Fan B, Petitjean M, Panaye A, Doucet JP, Li F, Xia H, Yuan S: MASSIS: amass spectrum simulation system. 2: Procedures and performance. Eur J Mass Spectrom (Chichester, Eng) 2003, 9(5):445-457. (Pubitemid 37548534)
194. Fan B, Chen H, Petitjean M, Panaye A, Doucet JP, Xia H, Yuan S: New strategy ofmass spectrum simulation based on reduced and concentrated knowledge databases. Spectrosc Lett 2005, 38(2):145-170. (Pubitemid 40416795)
195. Schymanski EL, Meringer M, Brack W: Matching structures to mass spectra using fragmentation patterns: Are the results as good as they look? Anal Chem 2009, 81(9):3608-3617.
196. Kerber A, Laue R, Meringer M, Varmuza K: MOLGEN-MS: Evaluation of low resolution electron impactmass spectra with MS classification and exhaustive structure generation. AdvMass Spectrom 2001, 15:939-940.
197. Kerber A, Meringer M, Rücker C: CASE via MS: Ranking structure candidates by mass spectra. Croat Chem Acta 2006, 79(3):449-464.
198. Pelander A, Tyrkkö E, Ojanperä I: In silico methods for predicting metabolism andmass fragmentation applied to quetiapine in liquid chromatography/time-of-flightmass spectrometry urine drug screening. Rapid Commun Mass Spectrom 2009, 23(4):506-514.
199. Kumari S, Stevens D, Kind T, Denkert C, Fiehn O: Applying in-silico retention index andmass spectra matching for identification of unknownmetabolites in accuratemass GC-TOFmass spectrometry. Anal Chem 2011, 83(15):5895-5902.
200. Sweeney DL: Smallmolecules asmathematical partitions. Anal Chem 2003, 75(20):5362-5373.
201. Hill AW, Mortishire-Smith RJ: Automated assignment of high-resolution collisionally activated dissociationmass spectra using a systematic bond disconnection approach. Rapid Commun Mass Spectrom 2005, 19:3111-3118. (Pubitemid 41540740)
202. Heinonen M, Rantanen A, Mielikäinen T, Pitkänen E, Kokkonen J, Rousu J: Ab initio prediction of molecular fragments from tandem mass spectrometry data. In Proc. of German Conference on Bioinformatics (GCB 2006), volume P-83 of Lecture Notes in Informatics:40-53.
203. Heinonen M, Rantanen A, Mielikäinen T, Kokkonen J, Kiuru J, Ketola RA, Rousu J: FiD: A software for ab initio structural identification of product ions from tandem mass spectrometric data. Rapid Commun Mass Spectrom 2008, 22(19):3043-3052.
204. Böcker S, Rasche F, Steijger T: Annotating fragmentation patterns. In Proc. of Workshop on Algorithms in Bioinformatics (WABI 2009), volume 5724 of Lect Notes Comput Sci. Berlin: Springer; 2009:13-24.
205. Schymanski EL, Gallampois CMJ, Krauss M, Meringer M, Neumann S, Schulze T, Wolf S, Brack W: Consensus structure elucidation combining GC/EI-MS, structure generation and calculated properties. Anal Chem 2012, 84(7):3287-3295.
206. Gerlich M, Neumann S: MetFusion: Integration of compound identification strategies. JMass Spectrom 2013, 48(3):291-8.
207. Menikarachchi LC, Cawley S, Hill DW, Hall LM, Hall L, Lai S, Wilder J, Grant DF: MolFind: A software package enabling HPLC/MS-based identification of unknown chemical structures. Anal Chem 2012, 84(21):9388-9394.
208. Ridder L, van der Hooft JJJ, Verhoeven S, de Vos RCH, van Schaik R, Vervoort J: Substructure-based annotation of high-resolution multistage MSn spectral trees. Rapid Commun Mass Spectrom 2012, 26(20):2461-2471.
209. Ludwig M, Hufsky F, Elshamy S, Böcker S: Finding characteristic substructures formetabolite classes. In Proc. of German Conference on Bioinformatics (GCB 2012), volume 26 of OpenAccess Series in Informatics (OASIcs); 2012:23-38. Schloss Dagstuhl-Leibniz-Zentrum fuer Informatik.
210. Bode HB, Müller R: The impact of bacterial genomics on natural product research. Angew Chem Int Ed Engl 2005, 44:6828-6846. (Pubitemid 41546526)
211. Bandeira N, Ng J, Meluzzi D, Linington RG, Dorrestein P, Pevzner PA: De novo sequencing of nonribosomal peptides. In Proc. of Research in Computational Molecular Biology (RECOMB 2008), volume 4955 of Lect Notes Bioinform. Berlin: Springer; 2008:181-195.
212. Liu WT, Ng J, Meluzzi D, Bandeira N, Gutierrez M, Simmons TL, Schultz AW, Linington RG, Moore BS, Gerwick WH, Pevzner PA, Dorrestein PC: Interpretation of tandem mass spectra obtained from cyclic nonribosomal peptides. Anal Chem 2009, 81:4200-4209.
213. Ng J, Bandeira N, Liu WT, Ghassemian M, Simmons TL, Gerwick WH, Linington R, Dorrestein PC, Pevzner PA: Dereplication and de novo sequencing of nonribosomal peptides. Nat Methods 2009, 6(8):596-599.
214. Mohimani H, Yang YL, Liu WT, Hsieh PW, Dorrestein PC, Pevzner PA: Sequencing cyclic peptides bymultistage mass spectrometry. Proteomics 2011, 11(18):3642-3650.
215. Rojas-Chertó M, Peironcely JE, Kasper PT, van der Hooft JJJ, de Vos RCH, Vreeken RJ, Hankemeier T, Reijmers TH: Metabolite identification using automated comparison of high-resolutionmultistage mass spectral trees. Anal Chem 2012, 84(13):5524-5534.
216. Kasper PT, Rojas-Chertó M, Mistrik R, Reijmers T, Hankemeier T, Vreeken RJ: Fragmentation trees for the structural characterisation of metabolites. Rapid Commun Mass Spectrom 2012, 26(19):2275-2286.
217. Rauf I, Rasche F, Nicolas F, Böcker S: Findingmaximum colorful subtrees in practice. In Proc. of Research in Computational Molecular Biology (RECOMB 2012), volume 7262 of Lect Notes Comput Sci. Berlin: Springer; 2012:213-223.
218. Hufsky F, Böcker S: Comparing fragmentation trees from electron impact mass spectra with annotated fragmentation pathways. In Proc. of German Conference on Bioinformatics (GCB 2012), volume 26 of OpenAccess Series in Informatics (OASIcs); 2012:12-22. Schloss Dagstuhl-Leibniz-Zentrum fuer Informatik.
219. Scheubert K, Hufsky F, Rasche F, Böcker S: Computing fragmentation trees from metabolite multiple mass spectrometry data. In Proc. of Research in Computational Molecular Biology (RECOMB 2011), volume 6577 of Lect Notes Comput Sci. Berlin: Springer; 2011:377-391.
220. Scheubert K, Hufsky F, Rasche F, Böcker S: Computing fragmentation trees from metabolite multiple mass spectrometry data. J Comput Biol 2011, 18(11):1383-1397.
221. Rasche F, Scheubert K, Hufsky F, Zichner T, Kai M, Svatoš A, Böcker S: Identifying the unknowns by aligning fragmentation trees. Anal Chem 2012, 84(7):3417-3426.
222. Hufsky F, Dührkop K, Rasche F, Chimani M, Böcker S: Fast alignment of fragmentation trees. Bioinformatics 2012, 28:i265 - i273.
223. Rarey M, Dixon JS: Feature trees: A newmolecular similaritymeasure based on treematching. J Comput AidedMol Des 1998, 12(5):471-490.
224. Fiehn O, Kopka J, Dörmann P, Altmann T, Trethewey RN, Willmitzer L: Metabolite profiling for plant functional genomics. Nat Biotechnol 2000, 18(11):1157-1161.
225. Arkin A, Shen P, Ross J: A test case of correlation metric construction of a reaction pathway from measurements. Science 1997, 277(5330):1275-1279. (Pubitemid 27449073)
226. Kose F, Weckwerth W, Linke T, Fiehn O: Visualizing plant metabolomic correlation networks using clique-metabolitematrices. Bioinformatics 2001, 17(12):1198-1208. (Pubitemid 33735346)
227. Steuer R, Kurths J, Fiehn O, Weckwerth W: Observing and interpreting correlations inmetabolomic networks. Bioinformatics 2003, 19(8):1019-1026. (Pubitemid 36675824)
228. Krumsiek J, Suhre K, Illig T, Adamski J, Theis FJ: Gaussian graphical modeling reconstructs pathway reactions from high-throughput metabolomics data. BMC Syst Biol 2011, 5:21.
229. Breitling R, Ritchie S, Goodenowe D, Stewart ML, Barrett MP: Ab initio prediction of metabolic networks using Fourier transform mass spectrometry data. Metabolomics 2006, 2(3):155-164. (Pubitemid 44473574)
230. Watrous J, Roach P, Alexandrov T, Heath BS, Yang JY, Kersten RD, van der Voort M, Pogliano K, Gross H, Raaijmakers JM, Moore BS, Laskin J, Bandeira N, Dorrestein PC: Mass spectralmolecular networking of livingmicrobial colonies. Proc Natl Acad Sci USA 2012, 109(26):E1743 - E1752.
231. Stein SE: An integrated method for spectrum extraction and compound identification from gas chromatography/mass spectrometry data. J AmSoc Mass Spectrom 1999, 10(8):770-781. (Pubitemid 34506228)
232. 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.
233. Luedemann A, Strassburg K, Erban A, Kopka J: TagFinder for the quantitative analysis of gas chromatography-mass spectrometry (GC-MS)-basedmetabolite profiling experiments. Bioinformatics 2008, 24(5):732-737. (Pubitemid 351321224)
234. Luedemann A, von Malotky L, Erban A, Kopka J: TagFinder: Preprocessing software for the fingerprinting and the profiling of gas chromatography-mass spectrometry based metabolome analyses. MethodsMol Biol 2012, 860:255-286.
235. Hiller K, Hangebrauk J, Jäger C, Spura J, Schreiber K, Schomburg D: MetaboliteDetector: Comprehensive analysis tool for targeted and nontargeted GC/MS basedmetabolome analysis. Anal Chem 2009, 81(9):3429-3439.
236. Cuadros-Inostroza A, Caldana C, Redestig H, Kusano M, Lisec J, Peña-Cortés H, Willmitzer L, Hannah MA: TargetSearch-a Bioconductor package for the efficient preprocessing of GC-MS metabolite profiling data. BMC Bioinformatics 2009, 10:428.
237. Aggio R, Villas-B ̂ oas SG, Ruggiero K: Metab: An R package for high-throughput analysis of metabolomics data generated by GC-MS. Bioinformatics 2011, 27(16):2316-2318.
238. O'Callaghan S, Desouza DP, Isaac A, Wang Q, Hodkinson L, Olshansky M, Erwin T, Appelbe B, Tull DL, Roessner U, Bacic A, McConville MJ, Likic VA: PyMS: A Python toolkit for processing of gas chromatography-mass spectrometry (GC-MS) data. Application and comparative study of selected tools. BMC Bioinformatics 2012, 13(1):115.
239. Ni Y, Qiu Y, Jiang W, Suttlemyre K, Su M, Zhang W, Jia W, Du X: ADAP-GC 2.0: Deconvolution of coelutingmetabolites from GC/TOF-MS data formetabolomics studies. Anal Chem 2012, 84(15):6619-6629.
240. Castillo S, Mattila I, Miettinen J, Orešič M, Hyötyläinen T: Data analysis tool for comprehensive two-dimensional gas chromatography/time-of-flightmass spectrometry. Anal Chem 2011, 83(8):3058-3067.
241. Benton HP, Wong DM, Trauger SA, Siuzdak G: XCMS2: Processing tandem mass spectrometry data for metabolite identification and structural characterization. Anal Chem 2008, 80(16):6382-6389.
242. Benton HP, Want EJ, Ebbels TMD: Correction ofmass calibration gaps in liquid chromatography-mass spectrometrymetabolomics data. Bioinformatics 2010, 26(19):2488-2489.
243. Tautenhahn R, Patti GJ, Rinehart D, Siuzdak G: XCMS Online: A web-based platform to process untargeted metabolomic datas. Anal Chem 2012, 84(11):5035-5039.
244. Alonso A, Julià A, Beltran A, Vinaixa M, Díaz M, Ibañez L, Correig X, Marsal S: AStream: An R package for annotating LC/MS metabolomic data. Bioinformatics 2011, 27(9):1339-1340.
245. Wei X, Sun W, Shi X, Koo I, Wang B, Zhang J, Yin X, Tang Y, Bogdanov B, Kim S, Zhou Z, McClain C, Zhang X: MetSign: A computational platform for high-resolutionmass spectrometry-based metabolomics. Anal Chem 2011, 83(20):7668-7675.
246. 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 2012, 84(1):283-289.
247. Bueschl C, Kluger B, Berthiller F, Lirk G, Winkler S, Krska R, Schuhmacher R: MetExtract: A new software tool for the automated comprehensive extraction of metabolite-derived LC/MS signals inmetabolomics research. Bioinformatics 2012, 28(5):736-738.
248. Creek DJ, Jankevics A, Burgess KEV, Breitling R, Barrett MP: IDEOM: An Excel interface for analysis of LC-MS basedmetabolomics data. Bioinformatics 2012.
249. Scheltema RA, Jankevics A, Jansen RC, Swertz MA, Breitling R: PeakML/mzMatch: A file format, Java library, R library, and tool-chain formass spectrometry data analysis. Anal Chem 2011, 83(7):2786-2793.
250. Brown M, Wedge DC, Goodacre R, Kell DB, Baker PN, Kenny LC, Mamas MA, Neyses L, Dunn WB: Automated workflows for accurate mass-based putative metabolite identification in LC/MS-derived metabolomic datasets. Bioinformatics 2011, 27(8):1108-1112.
251. Brodsky L, Moussaieff A, Shahaf N, Aharoni A, Rogachev I: Evaluation of peak picking quality in LC-MSmetabolomics data. Anal Chem 2010, 82(22):9177-9187.
252. Katajamaa M, Miettinen J, Oresic M: MZmine: Toolbox for processing and visualization of mass spectrometry based molecular profile data. Bioinformatics 2006, 22(5):634-636. (Pubitemid 43372832)
253. Pluskal T, Castillo S, Villar-Briones A, Oresic M: MZmine 2: Modular framework for processing, visualizing, and analyzingmass spectrometry- basedmolecular profile data. BMC Bioinformatics 2010, 11:395.
254. Broeckling CD, Reddy IR, Duran AL, Zhao X, Sumner LW: MET-IDEA: Data extraction tool formass spectrometry-basedmetabolomics. Anal Chem 2006, 78(13):4334-4341.
255. Lommen A: MetAlign: Interface-driven, versatilemetabolomics tool for hyphenated full-scan mass spectrometry data preprocessing. Anal Chem 2009, 81(8):3079-3086.
256. Lipkus AH, Yuan Q, Lucas KA, Funk SA, Bartelt WF, Schenck RJ, Trippe AJ: Structural diversity of organic chemistry: A scaffold analysis of the CAS registry. J Org Chem2008, 73(12):4443-4451. (Pubitemid 351842458)