Advances in structure elucidation of small molecules using mass spectrometry

Bioanalytical Reviews

Volumn 2, Issue 1, 2010, Pages 23-60

  Kind, Tobias ^a   Fiehn, Oliver ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

Fragmentation prediction; Mass spectral interpretation; Mass spectral library search; Mass spectrometry; Multistage tandem mass spectrometry; Structure elucidation; Tandem mass spectra

Indexed keywords

CHEMICAL COMPOUND; DRUG METABOLITE; ISOTOPE;

ACCURACY; ALGORITHM; ANALYTICAL PARAMETERS; ATMOSPHERIC PRESSURE; AUTOMATION; BIOTRANSFORMATION; CHEMICAL ANALYSIS; CHEMICAL BOND; CHEMICAL COMPOSITION; CHEMICAL MODIFICATION; CHEMICAL REACTION; CHEMICAL STRUCTURE; CHIRAL CHROMATOGRAPHY; COMPUTER MODEL; COMPUTER PROGRAM; DERIVATIZATION; DRUG METABOLISM; ELECTRONIC DATA INTERCHANGE; ELECTROSPRAY MASS SPECTROMETRY; HIGH PERFORMANCE LIQUID CHROMATOGRAPHY; ION CYCLOTRON RESONANCE MASS SPECTROMETRY; ION MOBILITY SPECTROMETRY; ISOTOPE LABELING; LIQUID CHROMATOGRAPHY; MASS FRAGMENTOGRAPHY; MASS SPECTROMETRY; MATHEMATICAL COMPUTING; MATRIX ASSISTED LASER DESORPTION IONIZATION TIME OF FLIGHT MASS SPECTROMETRY; MOLECULAR WEIGHT; PHARMACOLOGICAL PARAMETERS; PHYSICAL CHEMISTRY; PREDICTION; PRIORITY JOURNAL; REVIEW; ROBOTICS; STRUCTURAL BIOINFORMATICS; STRUCTURE ANALYSIS; TANDEM MASS SPECTROMETRY; TIME OF FLIGHT MASS SPECTROMETRY; X RAY CRYSTALLOGRAPHY;

EID: 78650737804     PISSN: 18672086     EISSN: 18672094     Source Type: Journal    
DOI: 10.1007/s12566-010-0015-9     Document Type: Review

References (546)

1. Brunnée C (1987) The ideal mass analyzer: fact or fiction? Int J Mass Spectrom Ion Processes 76(2): 125-237.
2. Gelpí E (2008) From large analogical instruments to small digital black boxes: 40 years of progress in mass spectrometry and its role in proteomics. Part I 1965-1984. J Mass Spectrom 43(4): 419-435.
3. Gelpí E (2009) From large analogical instruments to small digital black boxes: 40 years of progress in mass spectrometry and its role in proteomics. Part II 1985-2000. J Mass Spectrom 44(8): 1137-1161.
4. Makarov A (2000) Electrostatic axially harmonic orbital trapping: a high-performance technique of mass analysis. Anal Chem 72(6): 1156-1162.
5. Perry RH, Cooks RG, Noll RJ (2008) Orbitrap mass spectrometry: instrumentation, ion motion and applications. Mass Spectrom Rev 27(6): 661-699.
6. Gross JH (2004) Mass spectrometry: a textbook. Springer, Berlin.
7. Lattimer RP, Schulten HR (1989) Field ionization and field desorption mass spectrometry: past, present, and future. Anal Chem 61(21): 1201A-1215A.
8. Gordin A, Fialkov AB, Amirav A (2008) Classical electron ionization mass spectra in gas chromatography/mass spectrometry with supersonic molecular beams. Rapid Commun Mass Spectrom 22(17): 2660-2666.
9. Fenn JB (2003) Electrospray wings for molecular elephants (Nobel Lecture)*. Angew Chem Int Ed 42: 3871-3894.
10. Gaskell SJ (1997) Electrospray: principles and practice. J Mass Spectrom 32(7): 677-688.
11. Cech NB, Enke CG (2001) Practical implications of some recent studies in electrospray ionization fundamentals. Mass Spectrom Rev 20(6): 362-387.
12. Schmidt A, Karas M, Dulcks T (2003) Effect of different solution flow rates on analyte ion signals in nano-ESI MS, or: when does ESI turn into nano-ESI? J Am Soc Mass Spectrom 14(5): 492-500.
13. Lazar IM, Grym J, Foret F (2006) Microfabricated devices: a new sample introduction approach to mass spectrometry. Mass Spectrom Rev 25(4): 573-594.
14. Pereira-Medrano AG, Sterling A, Snijders APL, Reardon KF, Wright PC (2007) A systematic evaluation of chip-based nanoelectrospray parameters for rapid identification of proteins from a complex mixture. J Am Soc Mass Spectrom 18(9): 1714-1725.
15. Almeida R, Mosoarca C, Chirita M, Udrescu V, Dinca N, Vukeli Ž, Allen M, Zamfir AD (2008) Coupling of fully automated chip-based electrospray ionization to high-capacity ion trap mass spectrometer for ganglioside analysis. Anal Biochem 378(1): 43-52.
16. Lydic TA, Busik JV, Esselman WJ, Reid GE (2009) Complementary precursor ion and neutral loss scan mode tandem mass spectrometry for the analysis of glycerophosphatidylethanolamine lipids from whole rat retina. Anal Bioanal Chem 394(1): 267-275.
17. Wickremsinhe ER, Singh G, Ackermann BL, Gillespie TA, Chaudhary AK (2006) A review of nanoelectrospray ionization applications for drug metabolism and pharmacokinetics. Curr Drug Metab 7(8): 913-928.
18. Koulman A, Cao M, Faville M, Lane G, Mace W, Rasmussen S (2009) Semi-quantitative and structural metabolic phenotyping by direct infusion ion trap mass spectrometry and its application in genetical metabolomics. Rapid Commun Mass Spectrom: RCM 23(15): 2253-2263.
19. Kelly RT, Page JS, Marginean I, Tang K, Smith RD (2008) Nanoelectrospray emitter arrays providing interemitter electric field uniformity. Anal Chem 80(14): 5660-5665.
20. Su S, Gibson GTT, Mugo SM, Marecak DM, Oleschuk RD (2009) Microstructured photonic fibers as multichannel electrospray emitters. Anal Chem 81(17): 7281-7287.
21. Kostiainen R, Kotiaho T, Kuuranne T, Auriola S (2003) Liquid chromatography/atmospheric pressure ionization-mass spectrometry in drug metabolism studies. J Mass Spectrom 38(4): 357-372.
22. Rosenberg E (2003) The potential of organic (electrospray-and atmospheric pressure chemical ionisation) mass spectrometric techniques coupled to liquid-phase separation for speciation analysis. J Chromatogr A 1000(1-2): 841-889.
23. Hayen H, Karst U (2003) Strategies for the liquid chromatographic-mass spectrometric analysis of non-polar compounds. J Chromatogr A 1000(1-2): 549-565.
24. Covey TR, Thomson BA, Schneider BB (2009) Atmospheric pressure ion sources. Mass Spectrom Rev 28(6): 870-897.
25. Robb DB, Covey TR, Bruins AP (2000) Atmospheric pressure photoionization: an ionization method for liquid chromatography-mass spectrometry. Anal Chem 72(15): 3653-3659.
26. Marchi I, Rudaz S, Veuthey JL (2009) Atmospheric pressure photoionization for coupling liquid-chromatography to mass spectrometry: a review. Talanta 78(1): 1-18.
27. Robb DB, Blades MW (2008) State-of-the-art in atmospheric pressure photoionization for LC/MS. Anal Chim Acta 627(1): 34-49.
28. Bos SJ, van Leeuwen SM, Karst U (2006) From fundamentals to applications: recent developments in atmospheric pressure photoionization mass spectrometry. Anal Bioanal Chem 384(1): 85-99.
29. Zenobi R, Knochenmuss R (1998) Ion formation in MALDI mass spectrometry. Mass Spectrom Rev 17(5): 337-366.
30. Dreisewerd K (2003) The desorption process in MALDI. Chem Rev 103(2): 395-425.
31. Knochenmuss R, Zenobi R (2003) MALDI ionization: the role of in-plume processes. Chem Rev 103(2): 441-452.
32. Miyamoto K, Fujimaki S, Ueda Y (2009) Development of a new electron ionization/field ionization ion source for gas chromatography/time-of-flight mass spectrometry. Rapid Commun Mass Spectrom: RCM 23(20): 3350-3354.
33. Qian K, Edwards KE, Siskin M, Olmstead WN, Mennito AS, Dechert GJ, Hoosain NE (2007) Desorption and ionization of heavy petroleum molecules and measurement of molecular weight distributions. Energy Fuels 21(2): 1042-1047.
34. Schaub TM, Hendrickson CL, Qian K, Quinn JP, Marshall AG (2003) High-resolution field desorption/ionization Fourier transform ion cyclotron resonance mass analysis of nonpolar molecules. Anal Chem 75(9): 2172-2176.
35. Cody RB, Laramee JA, Durst HD (2005) Versatile new ion source for the analysis of materials in open air under ambient conditions. Anal Chem 77(8): 2297-2302.
36. Weston DJ (2010) Ambient ionization mass spectrometry: current understanding of mechanistic theory; analytical performance and application areas. Analyst 135(4): 661-668.
37. Yeping Z, Michelle L, Danlin W, Rowena M (2008) Quantification of small molecules in plasma with direct analysis in real time tandem mass spectrometry, without sample preparation and liquid chromatographic separation. Rapid Commun Mass Spectrom 22(20): 3217-3224.
38. van Berkel GJ, Pasilis SP, Ovchinnikova O (2008) Established and emerging atmospheric pressure surface sampling/ionization techniques for mass spectrometry. J Mass Spectrom 43(9): 1161-1180.
39. McDonnell LA, Heeren RMA (2007) Imaging mass spectrometry. Mass Spectrom Rev 26(4): 606-643.
40. Cornett DS, Reyzer ML, Chaurand P, Caprioli RM (2007) MALDI imaging mass spectrometry: molecular snapshots of biochemical systems. Nat Meth 4(10): 828-833.
41. Broersen A, van Liere R, Altelaar AFM, Heeren RMA, McDonnell LA (2008) Automated, feature-based image alignment for high-resolution imaging mass spectrometry of large biological samples. J Am Soc Mass Spectrom 19(6): 823-832.
42. Rubakhin SS, Jurchen JC, Monroe EB, Sweedler JV (2005) Imaging mass spectrometry: fundamentals and applications to drug discovery. Drug Discov Today 10(12): 823-837.
43. Manicke NE, Wiseman JM, Ifa DR, Cooks RG (2008) Desorption electrospray ionization (DESI) mass spectrometry and tandem mass spectrometry (MS/MS) of phospholipids and sphingolipids: ionization, adduct formation, and fragmentation. J Am Soc Mass Spectrom 19(4): 531-543.
44. Northen TR, Yanes O, Northen MT, Marrinucci D, Uritboonthai W, Apon J, Golledge SL, Nordstrom A, Siuzdak G (2007) Clathrate nanostructures for mass spectrometry. Nature 449(7165): 1033-1036.
45. Nordstrom A, Want E, Northen T, Lehtio J, Siuzdak G (2007) Multiple ionization mass spectrometry strategy used to reveal the complexity of metabolomics. Anal Chem 80(2): 421-429.
46. Kothari S, Song Q, Xia Y, Fico M, Taylor D, Amy JW, Stafford G, Cooks RG (2009) Multiplexed four-channel rectilinear ion trap mass spectrometer. Anal Chem 81(4): 1570-1579.
47. Schiewek R, Lorenz M, Giese R, Brockmann K, Benter T, Gäb S, Schmitz OJ (2008) Development of a multipurpose ion source for LC-MS and GC-API MS. Anal Bioanal Chem 392(1): 87-96.
48. Schmitt-Kopplin P, Englmann M, Rossello-Mora R, Schiewek R, Brockmann KJ, Benter T, Schmitz OJ (2008) Combining chip-ESI with APLI (cESILI) as a multimode source for analysis of complex mixtures with ultrahigh-resolution mass spectrometry. Anal Bioanal Chem 391(8): 2803-2809.
49. Byrdwell WC (2009) Dual parallel mass spectrometry for lipid and vitamin D analysis. J Chromatogr A 1217: 3992-4003.
50. Hannis JC, Muddiman DC (2000) A dual electrospray ionization source combined with hexapole accumulation to achieve high mass accuracy of biopolymers in Fourier transform ion cyclotron resonance mass spectrometry. J Am Soc Mass Spectrom 11(10): 876-883.
51. Nepomuceno AI, Muddiman DC, Bergen Iii HR, Craighead JR, Burke MJ, Caskey PE, Allan JA (2003) Dual electrospray ionization source for confident generation of accurate mass tags using liquid chromatography Fourier transform ion cyclotron resonance mass spectrometry. Anal Chem 75(14): 3411-3418.
52. Siegel MM, Tabei K, Lambert F, Candela L, Zoltan B (1998) Evaluation of a dual electrospray ionization/atmospheric pressure chemical ionization source at low flow rates (50 l/min) for the analysis of both highly and weakly polar compounds. J Am Soc Mass Spectrom 9(11): 1196-1203.
53. Liang X, Xia Y, McLuckey SA (2006) Alternately pulsed nanoelectrospray ionization/atmospheric pressure chemical ionization for ion/ion reactions in an electrodynamic ion trap. Anal Chem 78(9): 3208-3212.
54. Short LC, Hanold KA, Cai SS, Syage JA (2007) Electrospray ionization/atmospheric pressure photoionization multimode source for low-flow liquid chromatography/mass spectrometric analysis. Rapid Commun Mass Spectrom 21(10): 1561-1566.
55. Halket JM, Waterman D, Przyborowska AM, Patel RKP, Fraser PD, Bramley PM (2005) Chemical derivatization and mass spectral libraries in metabolic profiling by GC/MS and LC/MS/MS. J Exp Bot 56(410): 219-243.
56. Balogh MP (2004) Source design and the utility of multimode ionization. Spectroscopy 19(1): 52-56.
57. Fischer SM, Perkins PD (2005) Simultaneous electrospray and atmospheric pressure chemical ionization: the science behind the agilent multimode ion source. In: Agilent-Technical report.
58. Whitehouse C, White T, Willoughby R, Sheehan E (2006) Atmospheric pressure ion source for mass spectrometry. In: WO Patent WO/2006/107, 831.
59. Wang Y, Griffiths WJ (2007) Mass spectrometry for metabolite identification. In: William JG (ed) Metabolomics, metabonomics and metabolite profiling. Royal Society of Chemistry, London.
60. McLuckey SA, Wells JM (2001) Mass analysis at the advent of the 21st century. Chem Rev 101(2): 571-606.
61. Balogh MP (2004) Debating resolution and mass accuracy. LC GC N Am 22(2): 118-131.
62. Mann M, Kelleher NL (2008) Precision proteomics: the case for high resolution and high mass accuracy. Proc Natl Acad Sci 105(47): 18132.
63. Sleno L, Volmer DA, Marshall AG (2005) Assigning product ions from complex MS/MS spectra: the importance of mass uncertainty and resolving power. J Am Soc Mass Spectrom 16(2): 183-198.
64. Kellmann M, Muenster H, Zomer P, Mol H (2009) Full scan MS in comprehensive qualitative and quantitative residue analysis in food and feed matrices: how much resolving power is required? J Am Soc Mass Spectrom 20(8): 1464-1476.
65. Marshall AG, Hendrickson CL (2008) High-resolution mass spectrometers. Annu Rev Anal Chem 1(1): 579-599.
66. Marshall AG (2000) Milestones in Fourier transform ion cyclotron resonance mass spectrometry technique development. Int J Mass Spectrom 200(1-3): 331-356.
67. Feng X, Siegel MM (2007) FTICR-MS applications for the structure determination of natural products. Anal Bioanal Chem 389(5): 1341-1363.
68. Park Y, Lebrilla CB (2005) Application of Fourier transform ion cyclotron resonance mass spectrometry to oligosaccharides. Mass Spectrom Rev 24(2): 232-264.
69. Ackermann BL, Berna MJ, Eckstein JA, Ott LW, Chaudhary AK (2008) Current applications of liquid chromatography/mass spectrometry in pharmaceutical discovery after a decade of innovation. Annu Rev Anal Chem 1: 357-396.
70. Makarov A, Denisov E, Lange O (2009) Performance evaluation of a high-field orbitrap mass analyzer. J Am Soc Mass Spectrom 20(8): 1391-1396.
71. Ow SY, Noirel J, Salim M, Evans C, Watson R, Wright PC (2010) Balancing robust quantification and identification for iTRAQ: application of UHR-ToF MS. Proteomics 10(11): 2205-2213.
72. Mondello L, Tranchida PQ, Dugo P, Dugo P (2008) Comprehensive two-dimensional gas chromatography-mass spectrometry: a review. Mass Spectrom Rev 27(2): 101.
73. Dalluge J, Beens J, Brinkman UAT (2003) Comprehensive two-dimensional gas chromatography: a powerful and versatile analytical tool. J Chromatogr A 1000(1-2): 69-108.
74. Frysinger GS, Gaines RB, Reddy CM (2002) GCxGC-a new analytical tool for environmental forensics. Environ Forensics 3(1): 27-34.
75. Bedair M, Sumner LW (2008) Current and emerging mass-spectrometry technologies for metabolomics. Trends Anal Chem 27(3): 238-250.
76. Staack RF, Hopfgartner G (2007) New analytical strategies in studying drug metabolism. Anal Bioanal Chem 388(7): 1365-1380.
77. Fjeldsted JC (2009) Accurate mass measurements with orthogonal axis time-of-flight mass spectrometry. In: Ferrer I, Thurman EM (eds) Liquid chromatography time-of-flight mass spectrometry. Wiley, New York.
78. Glish GL, Burinsky DJ (2008) Hybrid mass spectrometers for tandem mass spectrometry. J Am Soc Mass Spectrom 19(2): 161-172.
79. Stroh JG, Petucci CJ, Brecker SJ, Huang N, Lau JM (2007) Automated sub-ppm mass accuracy on an ESI-TOF for use with drug discovery compound libraries. J Am Soc Mass Spectrom 18(9): 1612-1616.
80. Kind T, Fiehn O (2006) Metabolomic database annotations via query of elemental compositions: mass accuracy is insufficient even at less than 1 ppm. BMC Bioinform 7(234): 1-10.
81. Kind T, Fiehn O (2007) Seven golden rules for heuristic filtering of molecular formulas obtained by accurate mass spectrometry. BMC Bioinform 8(1): 105.
82. Wolfender JL, Waridel P, Ndjoko K, Hobby KR, Major HJ, Hostettmann K (2000) Evaluation of Q-TOF-MS/MS and multiple stage IT-MSn for the dereplication of flavonoids and related compounds in crude plant extracts. Analusis 28(10): 895-906.
83. Jonscher KR, Yates JR (1997) The quadrupole ion trap mass spectrometer-a small solution to a big challenge. Anal Biochem 244(1): 1-15.
84. Li R, Zhou Y, Wu Z, Ding L (2006) ESI-QqTOF-MS/MS and APCI-IT-MS/MS analysis of steroid saponins from the rhizomes of Dioscorea panthaica. J Mass Spectrom 41(1): 1-22.
85. McCormack P, Jones P, Hetheridge MJ, Rowland SJ (2001) Analysis of oilfield produced waters and production chemicals by electrospray ionisation multi-stage mass spectrometry (ESI-MSn). Water Res 35(15): 3567-3578.
86. Dinan L (2006) Dereplication and partial identification of compounds. Meth Biotechnol 20: 297.
87. Lim HK, Chen J, Sensenhauser C, Cook K, Subrahmanyam V (2007) Metabolite identification by data-dependent accurate mass spectrometric analysis at resolving power of 60 000 in external calibration mode using an LTQ/Orbitrap. Rapid Commun Mass Spectrom 21(12): 1821-1832.
88. Payne AH, Glish GL (2005) Tandem mass spectrometry in quadrupole ion trap and ion cyclotron resonance mass spectrometers. Meth Enzymol 402: 109-148.
89. Cooke N (2003) Recent advances in mass spectrometry for drug discovery and development. Drug Discov 27.
90. Futrell JH (2000) Development of tandem mass spectrometry: one perspective. Int J Mass Spectrom 200(1-3): 495-508.
91. De Hoffmann E (1996) Tandem mass spectrometry: a primer. J Mass Spectrom 31(2): 129-137.
92. Dwivedi P, Wu P, Klopsch SJ, Puzon GJ, Xun L, Hill HH (2008) Metabolic profiling by ion mobility mass spectrometry (IMMS). Metabolomics 4(1): 63-80.
93. Trimpin S, Tan B, Bohrer BC, O'Dell DK, Merenbloom SI, Pazos MX, Clemmer DE, Walker JM (2009) Profiling of phospholipids and related lipid structures using multidimensional ion mobility spectrometry-mass spectrometry. Int J Mass Spectrom 287(1-3): 58-69.
94. Weston DJ, Bateman R, Wilson ID, Wood TR, Creaser C (2005) Direct analysis of pharmaceutical drug formulations using ion mobility spectrometry/quadrupole-time-of-flight mass spectrometry combined with desorption electrospray ionization. Anal Chem 77(23): 7572-7580.
95. Kertesz TM, Hall LH, Hill DW, Grant DF (2009) CE50: quantifying collision induced dissociation energy for small molecule characterization and identification. J Am Soc Mass Spectrom 20(9): 1759-1767.
96. Syrstad EA, Turecek F (2005) Toward a general mechanism of electron capture dissociation. J Am Soc Mass Spectrom 16(2): 208-224.
97. Cooper HJ, Hakansson K, Marshall AG (2005) The role of electron capture dissociation in biomolecular analysis. Mass Spectrom Rev 24(2): 201-222.
98. Zubarev RA (2004) Electron-capture dissociation tandem mass spectrometry. Curr Opin Biotechnol 15(1): 12-16.
99. Zubarev RA, Zubarev AR, Savitski MM (2008) Electron capture/transfer versus collisionally activated/induced dissociations: solo or duet? J Am Soc Mass Spectrom 19(6): 753-761.
100. Good DM, Wirtala M, McAlister GC, Coon JJ (2007) Performance characteristics of electron transfer dissociation mass spectrometry. Mol Cell Proteomics 6(11): 1942-1951.
101. Syka JEP, Coon JJ, Schroeder MJ, Shabanowitz J, Hunt DF (2004) Peptide and protein sequence analysis by electron transfer dissociation mass spectrometry. Proc Natl Acad Sci USA 101(26): 9528-9533.
102. Sleno L, Volmer DA (2004) Ion activation methods for tandem mass spectrometry. J Mass Spectrom 39(10): 1091-1112.
103. Washburn MP, Wolters D, Yates JR (2001) Large-scale analysis of the yeast proteome by multidimensional protein identification technology. Nat Biotechnol 19(3): 242-247.
104. Adahchour M, Beens J, Vreuls RJJ, Brinkman UAT (2006) Recent developments in comprehensive two-dimensional gas chromatography (GC × GC): I. Introduction and instrumental set-up. TrAC Trends Anal Chem 25(5): 438-454.
105. Marriott P, Shellie R (2002) Principles and applications of comprehensive two-dimensional gas chromatography. TrAC, Trends Anal Chem 21(9-10): 573-583.
106. Ryan D, Marriott P (2007) Comprehensive two-dimensional gas chromatography. Adv Chromatogr 46: 451.
107. Skoczynska E, Korytar P, Boer JD (2008) Maximizing chromatographic information from environmental extracts by GC×GC-ToF-MS. Environ Sci Technol 42(17): 6611-6618.
108. Gauthier GL, Grimm R (2006) Miniaturization: chip-based liquid chromatography and proteomics. Drug Discov Today Technol 3(1): 59-66.
109. Biller JE, Biemann K (1974) Reconstructed mass spectra, a novel approach for the utilization of gas chromatograph-mass spectrometer data. Anal Lett 7(7): 515-528.
110. Dromey RG, Stefik MJ, Rindfleisch TC, Duffield AM (1976) Extraction of mass spectra free of background and neighboring component contributions from gas chromatography/mass spectrometry data. Anal Chem 48(9): 1368-1375.
111. Phalp JM, Payne AW, Windig W (1995) The resolution of mixtures using data from automated probe mass spectrometry. Anal Chim Acta 318(1): 43-53.
112. Windig W, Payne AW (1997) Noise and background reduction method for component detection in chromatography/spectrometry. In: US Patent 5, 672, 869.
113. Gray ZA, Abel RH (1995) Mass spectra interpretation system including spectra extraction. In: US Patent 5, 453, 613.
114. Windig W, Phalp JM, Paynes AW (1996) A noise and background reduction method for component detection in liquid chromatography/mass spectrometry. Anal Chem 68(20): 3602-3606.
115. Zhang H, Ma L, He K, Zhu M (2008) An algorithm for thorough background subtraction from high-resolution LC/MS data: application to the detection of troglitazone metabolites in rat plasma, bile, and urine. J Mass Spectrom 43(9): 1191-1200.
116. Zhang H, Yang Y (2008) An algorithm for thorough background subtraction from high-resolution LC/MS data: application for detection of glutathione-trapped reactive metabolites. J Mass Spectrom 43(9): 1181-1190.
117. Cuyckens F, Hurkmans R, Castro-Perez JM, Leclercq L, Mortishire-Smith RJ (2009) Extracting metabolite ions out of a matrix background by combined mass defect, neutral loss and isotope filtration. Rapid Commun Mass Spectrom 23(2): 327-332.
118. Thurman EM, Ferrer I, Barcelo D (2001) Choosing between atmospheric pressure chemical ionization and electrospray ionization interfaces for the HPLC/MS analysis of pesticides. Anal Chem 73(22): 5441-5449.
119. Kauppila TJ, Wiseman JM, Ketola RA, Kotiaho T, Cooks RG, Kostiainen R (2006) Desorption electrospray ionization mass spectrometry for the analysis of pharmaceuticals and metabolites. Rapid Commun Mass Spectrom 20(3): 387-392.
120. Zhu JH, Cole RB (2000) Formation and decompositions of chloride adduct ions, [M+Cl](-), in negative ion electrospray ionization mass spectrometry. J Am Soc Mass Spectrom 11(11): 932-941.
121. Zhu JH, Cole RB (2001) Ranking of gas-phase acidities and chloride affinities of monosaccharides and linkage specificity in collision-induced decompositions of negative ion electrospray-generated chloride adducts of oligosaccharides. J Am Soc Mass Spectrom 12(11): 1193-1204.
122. Schug K, McNair HM (2002) Adduct formation in electrospray ionization. Part 1: common acidic pharmaceuticals. J Sep Sci 25(12): 760-766.
123. Ventola E, Vainiotalo P, Suman M, Dalcanale E (2006) ESI-FTICR mass spectrometric study of alcohol complexation properties of mono- and diphosphonate-bridged cavitands. J Am Soc Mass Spectrom 17(2): 213-221.
124. Zhong W, Irish PA, Martin GE (2009) Influence of differently ionized species on fragmentation pathways and energetics of a potential adenosine receptor antagonist using a triple quadrupole and a multistage LTQ-Orbitrap TM FTMS instrument. J Heterocycl Chem 46(4): 591-598.
125. Wujcik CE, Kadar EP (2008) Reduction of in-source collision-induced dissociation and thermolysis of sulopenem prodrugs for quantitative liquid chromatography/electrospray ionization mass spectrometric analysis by promoting sodium adduct formation. Rapid Commun Mass Spectrom 22(20): 3195-3206.
126. Hsu FF, Bohrer A, Turk J (1998) Formation of lithiated adducts of glycerophosphocholine lipids facilitates their identification by electrospray ionization tandem mass spectrometry. J Am Soc Mass Spectrom 9(5): 516-526.
127. Huang N, Siegel MM, Kruppa GH, Laukien FH (1999) Automation of a Fourier transform ion cyclotron resonance mass spectrometer for acquisition, analysis, and E-mailing of high-resolution exact-mass electrospray ionization mass spectral data. J Am Soc Mass Spectrom 10(11): 1166-1173.
128. Karas M, Kruger R (2003) Ion formation in MALDI: the cluster ionization mechanism. Chem Rev 103(2): 427-440.
129. Kuhl C, Tautenhahn R, Neumann S: CAMERA-rule based annotation of isotopes and adducts. http://bioconductor. org/packages/devel/bioc/html/CAMERA. html.
130. Balogh MP (2006) Spectral interpretation, part II: tools of the trade, MS-the practical art. LC GC 24: 762-769.
131. Gorlach E, Richmond R (1999) Discovery of quasi-molecular ions in electrospray spectra by automated searching for simultaneous adduct mass differences. Anal Chem 71(24): 5557-5562.
132. Horn DM, Zubarev RA, McLafferty FW (2000) Automated reduction and interpretation of high resolution electrospray mass spectra of large molecules. J Am Soc Mass Spectrom 11(4): 320-332.
133. Carvalho PC, Cociorva D, Wong CCL, Carvalho Mda G, Barbosa VC, Yates JR (2009) Charge prediction machine: tool for inferring precursor charge states of electron transfer dissociation tandem mass spectra. Anal Chem 81(5): 1996-2003.
134. Allard E, Troger RA, Arvidsson B, Sjoberg PJR (2010) Quantitative aspects of analyzing small molecules-monitoring singly or doubly charged ions? A case study of ximelagatran. Rapid Commun Mass Spectrom 24(4): 429-435.
135. Sterling HJ, Williams ER (2009) Origin of supercharging in electrospray ionization of noncovalent complexes from aqueous solution. J Am Soc Mass Spectrom 20(10): 1933-1943.
136. Jaitly N, Mayampurath A, Littlefield K, Adkins J, Anderson G, Smith R (2009) Decon2LS: an open-source software package for automated processing and visualization of high resolution mass spectrometry data. BMC Bioinform 10(1): 87.
137. Loss RD (2003) Atomic weights of the elements 2001. Pure Appl Chem 75(8): 1107-1122.
138. Brenton AG, Godfrey AR (2010) Accurate mass measurement: terminology and treatment of data. J Am Soc Mass Spectrom (in press).
139. Bristow AWT, Webb KS (2003) Intercomparison study on accurate mass measurement of small molecules in mass spectrometry. J Am Soc Mass Spectrom 14(10): 1086-1098.
140. Bereman MS, Lyndon MM, Dixon RB, Muddiman DC (2008) Mass measurement accuracy comparisons between a double-focusing magnetic sector and a time-of-flight mass analyzer. Rapid Commun Mass Spectrom 22(10): 1563-1566.
141. Makarov A, Scigelova M (2010) Coupling liquid chromatography to Orbitrap mass spectrometry. J Chromatogr A 1217(25): 3938-3945.
142. Scheppele SE, Grindstaff QG, Grigsby RD, McDonald SR, Hwang CS (1983) Computer processing of mass-spectral data. II. Assignment of formulas to experimental masses illustrating program FZM; effects of electron mass and functional form of exponential scan law on accuracy of mass measurement. Int J or Mass Spectrom Ion Phys 49(2): 179-209.
143. Ferrer I, Thurman EM (2005) Measuring the mass of an electron by LC/TOF-MS: a study of "Twin Ions". Anal Chem 77(10): 3394-3400.
144. Beier T, Häffner H, Hermanspahn N, Karshenboim SG, Kluge HJ, Quint W, Stahl S, Verdú J, Werth G (2001) New determination of the electron's mass. Phys Rev Lett 88(1): 011603.
145. Scheltema RA, Kamleh A, Wildridge D, Ebikeme C, Watson DG, Barrett MP, Jansen RC, Breitling R (2008) Increasing the mass accuracy of high-resolution LC-MS data using background ions-a case study on the LTQ-Orbitrap. Proteomics 8(22): 4647-4656.
146. Mihaleva VV, Vorst O, Maliepaard C, Verhoeven HA, de Vos RCH, Hall RD, van Ham R (2008) Accurate mass error correction in liquid chromatography time-of-flight mass spectrometry based metabolomics. Metabolomics 4(2): 171-182.
147. Southam AD, Payne TG, Cooper HJ, Arvanitis TN, Viant MR (2007) Dynamic range and mass accuracy of wide-scan direct infusion nanoelectrospray Fourier transform ion cyclotron resonance mass spectrometry-based metabolomics increased by the spectral stitching method. Anal Chem 79: 4595-4602.
148. Payne TG, Southam AD, Arvanitis TN, Viant MR (2009) A signal filtering method for improved quantification and noise discrimination in Fourier transform ion cyclotron resonance mass spectrometry-based metabolomics data. J Am Soc Mass Spectrom 20(6): 1087-1095.
149. Petyuk VA, Mayampurath AM, Monroe ME, Polpitiya AD, Purvine SO, Anderson GA, Camp DG, Smith RD (2009) DtaRefinery, a software tool for elimination of systematic errors from parent ion mass measurements in tandem mass spectra data sets. Molecular & Cellular Proteomics 9: 486-496. doi: 10. 1074/mcp. M900217-MCP200.
150. Kuehl D, Wang Y (2006) Peak shape calibration method improves the mass accuracy of mass spectrometers. BioPharm Int 19(7): 32-38, +45.
151. Gu M, Wang Y, Zhao XG, Gu ZM (2006) Accurate mass filtering of ion chromatograms for metabolite identification using a unit mass resolution liquid chromatography/mass spectrometry system. Rapid Commun Mass Spectrom 20(5): 764-770.
152. Urayama S, Zou W, Brooks K, Tolstikov V (2010) Comprehensive mass spectrometry based metabolic profiling of blood plasma reveals potent discriminatory classifiers of pancreatic cancer. Rapid Commun Mass Spectrom 24(5): 613-620.
153. Williams DK Jr, Kovach AL, Muddiman DC, Hanck KW (2009) Utilizing artificial neural networks in MATLAB to achieve parts-per-billion mass measurement accuracy with a Fourier transform ion cyclotron resonance mass spectrometer. J Am Soc Mass Spectrom 20(7): 1303-1310.
154. Savitski MM, Ivonin IA, Nielsen ML, Zubarev RA, Tsybin YO, Hakansson P (2004) Shifted-basis technique improves accuracy of peak position determination in Fourier transform mass spectrometry. J Am Soc Mass Spectrom 15(4): 457-461.
155. Yang L, Amad M, Winnik WM, Schoen AE, Schweingruber H, Mylchreest I, Rudewicz PJ (2002) Investigation of an enhanced resolution triple quadrupole mass spectrometer for high-throughput liquid chromatography/tandem mass spectrometry assays. Rapid Commun Mass Spectrom 16(21): 2060-2066.
156. Shinkawa T, Nagano K, Inomata N, Haramura M (2009) A software program for more reliable precursor ion assignation from LC-MS analysis using LTQ ultra zoom scan. J Proteomics 73(2): 357-360.
157. Budzikiewicz H, Grigsby RD (2006) Mass spectrometry and isotopes: a century of research and discussion. Mass Spectrom Rev 25(1): 146-157.
158. Hellborg R, Skog G (2008) Accelerator mass spectrometry. Mass Spectrom Rev 27(5): 398-427.
159. Tuniz C, Zoppi U, Hotchkis MAC (2004) Sherlock Holmes counts the atoms. Nucl Instrum Methods Phys Res, B Beam Interact Mater Atoms 213: 469-475.
160. Calcagnile L, Quarta G, D'Elia M (2005) High-resolution accelerator-based mass spectrometry: precision, accuracy and background. Appl Radiat Isot 62(4): 623-629.
161. Krummen M, Hilkert AW, Juchelka D, Duhr A, Schlüter HJ, Pesch R (2004) A new concept for isotope ratio monitoring liquid chromatography/mass spectrometry. Rapid Commun Mass Spectrom 18(19): 2260-2266.
162. Thurman EM, Ferrer I, Fernandez-Alba AR (2005) Matching unknown empirical formulas to chemical structure using LC/MS TOF accurate mass and database searching: example of unknown pesticides on tomato skins. J Chromatogr A 1067(1-2): 127-134.
163. Ojanpera S, Pelander A, Pelzing M, Krebs I, Vuori E, Ojanpera I (2006) Isotopic pattern and accurate mass determination in urine drug screening by liquid chromatography/time-of-flight mass spectrometry. Rapid Commun Mass Spectrom 20(7): 1161-1167.
164. Zhu P, Tong W, Alton K, Chowdhury S (2009) An accurate-mass-based spectral-averaging isotope-pattern-filtering algorithm for extraction of drug metabolites possessing a distinct isotope pattern from LC-MS data. Anal Chem 81: 5910-5917.
165. Grange AH, Genicola FA, Sovocool GW (2002) Utility of three types of mass spectrometers for determining elemental compositions of ions formed from chromatographically separated compounds. Rapid Commun Mass Spectrom 16(24): 2356-2369.
166. Grange AH, Sovocool GW (2008) Automated determination of precursor ion, product ion, and neutral loss compositions and deconvolution of composite mass spectra using ion correlation based on exact masses and relative isotopic abundances. Rapid Commun Mass Spectrom 22(15): 2375-2390.
167. Grange AH, Winnik W, Ferguson PL, Sovocool GW (2005) Using a triple-quadrupole mass spectrometer in accurate mass mode and an ion correlation program to identify compounds. Rapid Commun Mass Spectrom 19(18): 2699-2715.
168. Snider RK (2007) Efficient calculation of exact mass isotopic distributions. J Am Soc Mass Spectrom 18(8): 1511-1515.
169. Rockwood AL, Haimi P (2006) Efficient calculation of accurate masses of isotopic peaks. J Am Soc Mass Spectrom 17(3): 415-419.
170. Li L, Kresh JA, Karabacak NM, Cobb JS, Agar JN, Hong P (2008) A hierarchical algorithm for calculating the isotopic fine structures of molecules. J Am Soc Mass Spectrom 19(12): 1867-1874.
171. Olson MT, Yergey AL (2009) Calculation of the isotope cluster for polypeptides by probability grouping. J Am Soc Mass Spectrom 20(2): 295-302.
172. Rockwood AL, Kushnir MM, Nelson GJ (2003) Dissociation of individual isotopic peaks: predicting isotopic distributions of product ions in MSn. J Am Soc Mass Spectrom 14(4): 311-322.
173. Ramaley L, Herrera LC (2008) Software for the calculation of isotope patterns in tandem mass spectrometry. Rapid Commun Mass Spectrom 22(17): 2707-2714.
174. Alon T, Amirav A (2009) Isotope abundance analysis for improved sample identification with tandem mass spectrometry. Rapid Commun Mass Spectrom: RCM 23(23): 3668.
175. Williams JD, Weiner BE, Ormand JR, Brunner J, Thornquest AD Jr, Burinsky DJ (2001) Automated molecular weight assignment of electrospray ionization mass spectra. Rapid Commun Mass Spectrom 15(24): 2446-2455.
176. Hobby K, Gallagher RT, Caldwell P, Wilson ID (2009) A new approach to aid the characterisation and identification of metabolites of a model drug; partial isotope enrichment combined with novel formula elucidation software. Rapid Commun Mass Spectrom 23(2): 219-227.
177. Alon T, Amirav A (2006) Isotope abundance analysis methods and software for improved sample identification with supersonic gas chromatography/mass spectrometry. Rapid Commun Mass Spectrom 20(17): 2579-2588.
178. Rogers S, Scheltema RA, Girolami M, Breitling R (2009) Probabilistic assignment of formulas to mass peaks in metabolomics experiments. Bioinformatics 25(4): 512-518.
179. Werner E, Heilier J-F, Ducruix C, Ezan E, Junot C, Tabet J-C (2008) Mass spectrometry for the identification of the discriminating signals from metabolomics: current status and future trends. J Chromatogr B 871(2): 143-163.
180. Reemtsma T (2009) Determination of molecular formulas of natural organic matter molecules by (ultra-) high-resolution mass spectrometry. Status and needs. J Chromatogr A 1216(18): 3687-3701.
181. Koch BP, Ludwichowski KU, Kattner G, Dittmar T, Witt M (2008) Advanced characterization of marine dissolved organic matter by combining reversed-phase liquid chromatography and FT-ICR-MS. Mar Chem 111(3-4): 233-241.
182. Bocker S, Letzel MC, Liptak Z, Pervukhin A (2009) SIRIUS: decomposing isotope patterns for metabolite identification. Bioinformatics 25(2): 218.
183. Bocker S, Rasche F (2008) Towards de novo identification of metabolites by analyzing tandem mass spectra. Bioinformatics 24(16): i49.
184. Erve JCL, Gu M, Wang Y, DeMaio W, Talaat RE (2009) Spectral accuracy of molecular ions in an LTQ/Orbitrap mass spectrometer and implications for elemental composition determination. J Am Soc Mass Spectrom 20(11): 2058-2069.
185. Hegeman AD, Schulte CF, Cui Q, Lewis IA, Huttlin EL, Eghbalnia H, Harms AC, Ulrich EL, Markley JL, Sussman MR (2007) Stable isotope assisted assignment of elemental compositions for metabolomics. Anal Chem 79(18): 6912-6921.
186. Hill DW, Kertesz TM, Fontaine D, Friedman R, Grant DF (2008) Mass spectral metabonomics beyond elemental formula: chemical database querying by matching experimental with computational fragmentation spectra. Anal Chem 80(14): 5574-5582.
187. Krebs I, Yates S (2008) Fully unsupervised automatic assignment and annotation of sum formulae for product ion peaks, neutral losses in MS and Product Ion Spectra. In: ASMS 2008, MPG152. Bruker Daltonics, Billerica.
188. Rockwood AL, van Orden SL, Smith RD (1995) Rapid calculation of isotope distributions. Anal Chem 67: 2699-2704.
189. Konishi Y, Kiyota T, Draghici C, Gao J-M, Yeboah F, Acoca S, Jarussophon S, Purisima E (2006) Molecular formula analysis by an MS/MS/MS technique to expedite dereplication of natural products. Anal Chem 79(3): 1187-1197.
190. Jarussophon S, Acoca S, Gao JM, Deprez C, Kiyota T, Draghici C, Purisima E, Konishi Y (2009) Automated molecular formula determination by tandem mass spectrometry (MS/MS). Analyst 134(4): 690-700.
191. Plumb RS, Johnson KA, Rainville P, Smith BW, Wilson ID, Castro-Perez JM, Nicholson JK (2006) UPLC/MSE; a new approach for generating molecular fragment information for biomarker structure elucidation. Rapid Commun Mass Spectrom 20(13): 1989-1994.
192. Harkewicz R (2002) ESI-FTICR mass spectrometry employing data-dependent external ion selection and accumulation. J Am Soc Mass Spectrom 13(2): 144-154.
193. Wind M, Grunwald H, Gebhardt K, Illig K, Spickermann J, Nuoffer C, Roussel P, Klauer D, Fullhardt P, Schmitt-Hoffmann A (2009) Investigation of the species-dependent in vitro metabolism of BAL30630 by stable isotope labeling and isotope exchange experiments analyzed by capillary liquid chromatography coupled to mass spectrometry. J Chromatogr A 1216(18): 3946-3953.
194. Yao MM, Humphreys L, Zhu WG (2008) Rapid screening and characterization of drug metabolites using a multiple ion monitoring-dependent MS/MS acquisition method on a hybrid triple quadrupole-linear ion trap mass spectrometer. J Mass Spectrom 43(10): 1364-1375.
195. Yao M, Ma L, Duchoslav E, Zhu M (2009) Rapid screening and characterization of drug metabolites using multiple ion monitoring dependent product ion scan and postacquisition data mining on a hybrid triple quadrupole-linear ion trap mass spectrometer. Rapid Commun Mass Spectrom 23(11): 1683-1693.
196. Sang S, Lee MJ, Yang I, Buckley B, Yang CS (2008) Human urinary metabolite profile of tea polyphenols analyzed by liquid chromatography/electrospray ionization tandem mass spectrometry with data-dependent acquisition. Rapid Commun Mass Spectrom 22(10): 1567-1578.
197. Lim HK, Chen J, Cook K, Sensenhauser C, Silva J, Evans DC (2008) A generic method to detect electrophilic intermediates using isotopic pattern triggered data-dependent high-resolution accurate mass spectrometry. Rapid Commun Mass Spectrom 22(8): 1295-1311.
198. Schwartz JC, Wade AP, Enke CG, Cooks RG (1990) Systematic delineation of scan modes in multidimensional mass spectrometry. Anal Chem 62(17): 1809-1818.
199. Rochfort SJ, Trenerry VC, Imsic M, Panozzo J, Jones R (2008) Class targeted metabolomics: ESI ion trap screening methods for glucosinolates based on MSn fragmentation. Phytochemistry 69(8): 1671-1679.
200. Lloyd KG, O'Keefe DP (2004) Re-discovering surface mass spectrometry: chemical mapping from micro to macro. Appl Surf Sci 231-232: 207-216.
201. Reig N, Calaf RE, Messeguer A, Morató A, Escabros J, Gelpí E, Abian J (2007) LC-MS ion maps for the characterization of aniline derivatives of fatty acids and triglycerides in laboratory-denatured rapeseed oil. J Mass Spectrom 42(4): 527-541.
202. Pont F, Luciani B, Belmant C, Fournie JJ (2001) Characterization of phosphoantigens by high-performance anion-exchange chromatography-electrospray ionization ion trap mass spectrometry and nanoelectrospray ionization ion trap mass spectrometry. Anal Chem 73(15): 3562-3569.
203. Roussis SG (2001) Automated tandem mass spectrometry by orthogonal acceleration TOF data acquisition and simultaneous magnet scanning for the characterization of petroleum mixtures. Anal Chem 73(15): 3611-3623.
204. Germanus A (2002) Method for management of daughter ion spectra over several generations. In: US Patent 6, 362, 473.
205. Sheldon MT, Mistrik R, Croley TR (2009) Determination of ion structures in structurally related compounds using precursor ion fingerprinting. J Am Soc Mass Spectrom 20(3): 370-376.
206. Mistrik R (2007) Determination of molecular structures using tandem mass spectrometry. In: U. S. 7, 197, 402.
207. Milgram KE, Barrett T, Evans AM (2008) Systems, methods, and computer-readable medium for determining composition of chemical constituents in a complex mixture. In: U. S. 12/327, 758.
208. Li Q, Yan G, Ge T (2007) A fragmentation study of podophyllotoxin and its 4′-demethyl-4b-substituted derivatives by electrospray ionization ion-trap time-of-flight tandem mass spectrometry. Rapid Commun Mass Spectrom 21(17): 2843-2852.
209. Sturt HF, Summons RE, Smith K, Elvert M, Hinrichs KU (2004) Intact polar membrane lipids in prokaryotes and sediments deciphered by high-performance liquid chromatography/electrospray ionization multistage mass spectrometry-new biomarkers for biogeochemistry and microbial ecology. Rapid Commun Mass Spectrom 18(6): 617-628.
210. Strapoc D, Picardal FW, Turich C, Schaperdoth I, Macalady JL, Lipp JS, Lin YS, Ertefai TF, Schubotz F, Hinrichs KU (2008) Methane-producing microbial community in a coal bed of the Illinois Basin. Appl Environ Microbiol 74(8): 2424.
211. Hsu FF, Turk J (2010) Electrospray ionization multiple-stage linear ion-trap mass spectrometry for structural elucidation of triacylglycerols: assignment of fatty acyl groups on the glycerol backbone and location of double bonds. J Am Soc Mass Spectrom 21(4): 657-669.
212. Hsu FF, Turk J, Rhoades ER, Russell DG, Shi Y, Groisman EA (2005) Structural characterization of cardiolipin by tandem quadrupole and multiple-stage quadrupole ion-trap mass spectrometry with electrospray ionization. J Am Soc Mass Spectrom 16(4): 491-504.
213. Serb A, Schiopu C, Flangea C, Sisu E, Zamfir AD (2009) Top-down glycolipidomics: fragmentation analysis of ganglioside oligosaccharide core and ceramidemoiety by chip-nanoelectrospray collision-induced dissociation MS2-MS6. J Mass Spectrom 44(10): 1434-1442.
214. Saad OM, Leary JA (2005) Heparin sequencing using enzymatic digestion and ESI-MSn with HOST: a heparin/HS oligosaccharide sequencing tool. Anal Chem 77(18): 5902-5911.
215. Ashline DJ, Lapadula AJ, Liu Y-H, Lin M, Grace M, Pramanik B, Reinhold VN (2007) Carbohydrate structural isomers analyzed by sequential mass spectrometry. Anal Chem 79(10): 3830-3842.
216. McLafferty FW, Hertel RH, Villwock RD (1974) Computer identification of mass spectra: VI. Probability based matching of mass spectra: rapid identification of specific compounds in mixtures. Org Mass Spectrom 9(7): 690-702.
217. Stein SE, Scott DR (1994) Optimization and testing of mass spectral library search algorithms for compound identification. J Am Soc Mass Spectrom 5(9): 859-866.
218. David Sparkman O (1996) Evaluating electron ionization mass spectral library search results. J Am Soc Mass Spectrom 7(4): 313-318.
219. Horai H, Arita M, Nishioka T (2008) Comparison of ESI-MS spectra in MassBank database. 2008 International Conference on BioMedical Engineering and Informatics 853-857.
220. Horai H, Arita M, Kanaya S, Nihei Y, Ikeda T, Suwa K, Ojima Y, Tanaka K, Tanaka S, Aoshima K (2010) MassBank: a public repository for sharing mass spectral data for life sciences. J Mass Spectrom 45(7): 703-714.
221. Akiyama K, Chikayama E, Yuasa H, Shimada Y, Tohge T, Shinozaki K, Hirai MY, Sakurai T, Kikuchi J, Saito K (2008) PRIMe: a Web site that assembles tools for metabolomics and transcriptomics. In Silico Biol 8(3): 339-345.
222. Sawada Y, Akiyama K, Sakata A, Kuwahara A, Otsuki H, Sakurai T, Saito K, Hirai MY (2009) Widely targeted metabolomics based on large-scale MS/MS data for elucidating metabolite accumulation patterns in plants. Plant Cell Physiol 50(1): 37.
223. Matsuda F, Hirai MY, Sasaki E, Akiyama K, Yonekura-Sakakibara K, Provart NJ, Sakurai T, Shimada Y, Saito K (2010) AtMetExpress development: a phytochemical atlas of Arabidopsis development. Plant Physiol 152(2): 566-578.
224. Dresen S, Gergov M, Politi L, Halter C, Weinmann W (2009) ESI-MS/MS library of 1, 253 compounds for application in forensic and clinical toxicology. Analytical and Bioanalytical Chemistry 395: 2521-2526.
225. Schreiber A, Efer J, Engewald W (2000) Application of spectral libraries for high-performance liquid chromatography-atmospheric pressure ionisation mass spectrometry to the analysis of pesticide and explosive residues in environmental samples. J Chromatogr A 869(1-2): 411-425.
226. Mueller CA, Weinmann W, Dresen S, Schreiber A, Gergov M (2005) Development of a multi-target screening analysis for 301 drugs using a QTrap liquid chromatography/tandem mass spectrometry system and automated library searching. Rapid Commun Mass Spectrom 19(10): 1332-1338.
227. Fredenhagen A, Derrien C, Gassmann E (2005) An MS/MS library on an ion-trap instrument for efficient dereplication of natural products. Different fragmentation patterns for [M+H] + and [M+Na] + Ions†. J Nat Prod 68(3): 385-391.
228. Anthony WTB, Kenneth SW, Anneke TL, John H (2004) Reproducible product-ion tandem mass spectra on various liquid chromatography/mass spectrometry instruments for the development of spectral libraries. Rapid Commun Mass Spectrom 18(13): 1447-1454.
229. Milman BL (2005) Towards a full reference library of MSn spectra. Testing of a library containing 3126 MS2 spectra of 1743 compounds. Rapid Commun Mass Spectrom 19(19): 2833-2839.
230. Hopley C, Bristow T, Lubben A, Simpson A, Bull E, Klagkou K, Herniman J, Langley J (2008) Towards a universal product ion mass spectral library-reproducibility of product ion spectra across eleven different mass spectrometers. Rapid Commun Mass Spectrom 22(12): 1779-1786.
231. Palit M, Mallard G (2009) 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 81(7): 2477-2485.
232. Oberacher H, Pavlic M, Libiseller K, Schubert B, Sulyok M, Schuhmacher R, Csaszar E, Köfeler HC (2009) On the inter-instrument and inter-laboratory transferability of a tandem mass spectral reference library: 1. Results of an Austrian multicenter study. J Mass Spectrom 44: 485-493.
233. Pavlic M, Libiseller K, Oberacher H (2006) Combined use of ESI-QqTOF-MS and ESI-QqTOF-MS/MS with mass-spectral library search for qualitative analysis of drugs. Anal Bioanal Chem 386(1): 69-82.
234. Oberacher H, Pavlic M, Libiseller K, Schubert B, Sulyok M, Schuhmacher R, Csaszar E, Köfeler HC (2009) On the inter-instrument and the inter-laboratory transferability of a tandem mass spectral reference library: 2. Optimization and characterization of the search algorithm. J Mass Spectrom 44(4): 494-502.
235. Hansen ME, Smedsgaard J (2004) A new matching algorithm for high resolution mass spectra. J Am Soc Mass Spectrom 15(8): 1173-1180.
236. Kandasamy K, Pandey A, Molina H (2009) Evaluation of several MS/MS search algorithms for analysis of spectra derived from electron transfer dissociation experiments. Anal Chem 81(17): 7170-7180.
237. Kapp EA, Schütz F, Connolly LM, Chakel JA, Meza JE, Miller CA, Fenyo D, Eng JK, Adkins JN, Omenn GS et al (2005) An evaluation, comparison, and accurate benchmarking of several publicly available MS/MS search algorithms: sensitivity and specificity analysis. Proteomics 5(13): 3475-3490.
238. Wan KX, Vidavsky I, Gross ML (2002) Comparing similar spectra: from similarity index to spectral contrast angle. J Am Soc Mass Spectrom 13(1): 85-88.
239. McLafferty FW, Zhang M-Y, Stauffer DB, Loh SY (1998) Comparison of algorithms and databases for matching unknown mass spectra. J Am Soc Mass Spectrom 9(1): 92-95.
240. Gergov M, Weinmann W, Meriluoto J, Uusitalo J, Ojanpera I (2004) Comparison of product ion spectra obtained by liquid chromatography/triple-quadrupole mass spectrometry for library search. Rapid Commun Mass Spectrom 18(10): 1039-1046.
241. Mylonas R, Mauron Y, Masselot A, Binz PA, Budin N, Fathi M, Viette V, Hochstrasser DF, Lisacek F (2009) X-Rank: a robust algorithm for small molecule identification using tandem mass spectrometry. Anal Chem 81(18): 7604-7610.
242. Samudrala R, Levitt M (2000) Decoys 'R'Us: a database of incorrect conformations to improve protein structure prediction. PRS 9(07): 1399-1401.
243. Choi H, Nesvizhskii AI (2007) False discovery rates and related statistical concepts in mass spectrometry-based proteomics. J Proteome Res 7(01): 47-50.
244. Kim S, Gupta N, Pevzner PA (2008) Spectral probabilities and generating functions of tandem mass spectra: a strike against decoy databases. J Proteome Res 7(8): 3354-3363.
245. Elias JE, Gygi SP (2007) Target-decoy search strategy for increased confidence in large-scale protein identifications by mass spectrometry. Nat Meth 4(3): 207-214.
246. Anabel SF, Michael K, Stefan WT, Gerold K (2002) Identification of anhydroecgonine methyl ester N-oxide, a new metabolite of anhydroecgonine methyl ester, using electrospray mass spectrometry. J Mass Spectrom 37(5): 525-532.
247. Zhu XY, Sato T (2007) The distinction of underivatized monosaccharides using electrospray ionization ion trap mass spectrometry. Rapid Commun Mass Spectrom 21(2): 191-198.
248. Chen G, Pramanik BN, Bartner PL, Saksena AK, Gross ML (2002) Multiple-stage mass spectrometric analysis of complex oligosaccharide antibiotics (everninomicins) in a quadrupole ion trap. J Am Soc Mass Spectrom 13(11): 1313-1321.
249. Delaney J, Vouros P (2001) Liquid chromatography ion trap mass spectrometric analysis of oligosaccharides using permethylated derivatives. Rapid Commun Mass Spectrom 15(5): 325-334.
250. Kameyama A, Kikuchi N, Nakaya S, Ito H, Sato T, Shikanai T, Takahashi Y, Takahashi K, Narimatsu H (2005) A strategy for identification of oligosaccharide structures using observational multistage mass spectral library. Anal Chem 77(15): 4719-4725.
251. McLafferty FW, Turecek F (1993) Interpretation of mass spectra. University Science Books, Mill Valley.
252. Watson JT, Sparkman OD (2007) Introduction to mass spectrometry: instrumentation, applications, and strategies for data interpretation. Wiley, Chichester.
253. Smith RM (2004) Understanding mass spectra: a basic approach. Wiley-Interscience, Chichester.
254. Karsten L, Hans-Martin S, Johan KT, Karl JJ, Manfred E, Alfred P, Herbert T, Arnd I (2007) Even-electron ions: a systematic study of the neutral species lost in the dissociation of quasi-molecular ions. J Mass Spectrom 42(8): 1024-1044.
255. Cai Y, Mo Z, Rannulu NS, Guan B, Kannupal S, Gibba BC, Cole RB (2010) Characterization of an exception to the 'even-electron rule' upon low-energy collision induced decomposition in negative ion electrospray tandem mass spectrometry. J Mass Spectrom 45(3): 235-240.
256. Thurman EM, Ferrer I, Pozo OJ, Sancho JV, Hernandez F (2007) The even-electron rule in electrospray mass spectra of pesticides. Rapid Commun Mass Spectrom 21(23): 3855-3868.
257. Badertscher M, Bischofberger K, Munk ME, Pretsch E (2001) A novel formalism to characterize the degree of unsaturation of organic molecules. J Chem Inf Comput Sci 41(4): 889-893.
258. Baigorri R, Zamarreño AM, Fuentes M, Gonzalez-Gaitano G, Garcia-Mina JM, Almendros G, Gonzalez-Vila FJ (2008) Multivariate statistical analysis of mass spectra as a tool for the classification of the main humic substances according to their structural and conformational features. J Agric Food Chem 56(14): 5480-5487.
259. Meija J (2006) Mathematical tools in analytical mass spectrometry. Anal Bioanal Chem 385(3): 486-499.
260. Hertkorn N, Ruecker C, Meringer M, Gugisch R, Frommberger M, Perdue EM, Witt M, Schmitt-Kopplin P (2007) High-precision frequency measurements: indispensable tools at the core of the molecular-level analysis of complex systems. Anal Bioanal Chem 389(5): 1311-1327.
261. Cooks RG (1969) Bond formation upon electron-impact. Org Mass Spectrom 2(5): 481.
262. Borth S, Hänsel W, Rösner P, Junge T (2000) Synthesis of 2, 3- and 3, 4-methylenedioxyphenylalkylamines and their regioisomeric differentiation by mass spectral analysis using GC-MS-MS. Forensic Sci Int 114(3): 139-153.
263. Watson JT, Sparkman OD (2008) Chemical ionization. In: Introduction to mass spectrometry: instrumentation, applications and strategies for data interpretation, 4th edition. Wiley, New York, pp 449-484.
264. Richard AJ (2002) Ion chemistry and fragmentation. In: Rossi DT, Sinz MW (eds) Mass spectrometry in drug discovery. CRC, Boca Raton, p 85.
265. Hill AW, Mortishire-Smith RJ (2005) Automated assignment of high-resolution collisionally activated dissociation mass spectra using a systematic bond disconnection approach. Rapid Commun Mass Spectrom 19(21): 3111-3118.
266. Heinonen M, Rantanen A, Mielikäinen T, Kokkonen J, Kiuru J, Ketola RA, Rousu J (2008) FiD: a software for ab initio structural identification of product ions from tandem mass spectrometric data. Rapid Commun Mass Spectrom 22(19): 3043-3052.
267. Heinonen M, Rantanen A, Mielikäinen T, Pitkänen E, Kokkonen J, Rousu J (2006) Ab Initio prediction of molecular fragments from tandem mass spectrometry data. Proceedings of German Conference on Bioinformatics (GCB 2006), Lecture Notes in Informatics 83: 40-53.
268. Goodley P (2007) Maximizing MS/MS Fragmentation in the Ion Trap Using CID Voltage Ramping. In: Agilent Report 5988-0704EN.
269. Levsen K, Schiebel HM, Terlouw JK, Jobst KJ, Elend M, Preiß A, Thiele H, Ingendoh A (2007) Even-electron ions: a systematic study of the neutral species lost in the dissociation of quasi-molecular ions. J Mass Spectrom 42(8): 1024-1044.
270. Holcapek M, Jirasko R, Lísa M (2010) Basic rules for the interpretation of atmospheric pressure ionization mass spectra of small molecules. J Chromatogr 1217(25): 3908-3921.
271. Brodbelt JS (2000) Probing molecular recognition by mass spectrometry. Int J Mass Spectrom 200(1): 57-69.
272. Yao ZP, Wan TSM, Kwong KP, Che CT (2000) Chiral analysis by electrospray ionization mass spectrometry/mass spectrometry. 1. Chiral recognition of 19 common amino acids. Anal Chem 72(21): 5383-5393.
273. Splitter JS, Turecek F, Luftmann H (1994) Applications of mass spectrometry to organic stereochemistry. VCH, New York.
274. Xianmei Cai AV, Dass C (2003) Conformational analysis of proteins and peptides. Curr Org Chem 7(18): 1841-1854.
275. Kaltashov IA, Eyles SJ (2002) Studies of biomolecular conformations and conformational dynamics by mass spectrometry. Mass Spectrom Rev 21(1): 37-71.
276. Knapman TW, Berryman JT, Campuzano I, Harris SA, Ashcroft AE (2009) Considerations in experimental and theoretical collision cross-section measurements of small molecules using travelling wave ion mobility spectrometry-mass spectrometry. Int J Mass Spectrom (in press).
277. Valentine SJ, Clemmer DE (2009) Treatise on the measurement of molecular masses with ion mobility spectrometry. Anal Chem 81(14): 5876-5880.
278. Ramanathan R, Comezoglu SN, Humphreys WG (2009) Metabolite identification strategies and procedures. CRC, Boca Raton, 1420092200.
279. Lynch T, Price A (2007) The effect of cytochrome P 450 metabolism on drug response, interactions, and adverse effects. Am Fam Physician 76(3): 391-396.
280. Levsen K, Schiebel H-M, Behnke B, Dötzer R, Dreher W, Elend M, Thiele H (2005) Structure elucidation of phase II metabolites by tandem mass spectrometry: an overview. J Chromatogr A 1067(1-2): 55-72.
281. Anari MR, Baillie TA (2005) Bridging cheminformatic metabolite prediction and tandem mass spectrometry. Drug Discov Today 10(10): 711-717.
282. Pelkonen O, Tolonen A, Korjamo T, Turpeinen M, Raunio H (2009) From known knowns to known unknowns: predicting in vivo drug metabolites. Bioanalysis 1(2): 393-414.
283. Ekins S, Andreyev S, Ryabov A, Kirillov E, Rakhmatulin EA, Bugrim A, Nikolskaya T (2005) Computational prediction of human drug metabolism. Expert Opin Drug Metab Toxicol 1(2): 303-324.
284. Marchant CA, Briggs KA, Long A (2008) In silico tools for sharing data and knowledge on toxicity and metabolism: Derek for windows, meteor, and vitic. Toxicol Mech Methods 18(2-3): 177-187.
285. Wen B, Fitch WL (2009) Analytical strategies for the screening and evaluation of chemically reactive drug metabolites. Expert Opin Drug Metab Toxicol 5(1): 39-55.
286. Anari MR, Sanchez RI, Bakhtiar R, Franklin RB, Baillie TA (2003) Integration of knowledge-based metabolic predictions with liquid chromatography data-dependent tandem mass spectrometry for drug metabolism studies: application to studies on the biotransformation of indinavir. Anal Chem 76(3): 823-832.
287. Mortishire-Smith RJ, O'Connor D, Castro-Perez JM, Kirby J (2005) Accelerated throughput metabolic route screening in early drug discovery using high-resolution liquid chromatography/quadrupole time-of-flight mass spectrometry and automated data analysis. Rapid Commun Mass Spectrom 19(18): 2659-2670.
288. Zhu M, Ma L, Zhang D, Ray K, Zhao W, Humphreys WG, Skiles G, Sanders M, Zhang H (2006) Detection and characterization of metabolites in biological matrices using mass defect filtering of liquid chromatography/high resolution mass spectrometry data. Drug Metab Dispos 34(10): 1722.
289. Mortishire-Smith RJ, Castro-Perez JM, Yu K, Shockcor JP, Goshawk J, Hartshorn MJ, Hill A (2009) Generic dealkylation: a tool for increasing the hit-rate of metabolite rationalization, and automatic customization of mass defect filters. Rapid Commun Mass Spectrom 23(7): 939-948.
290. Zhang H, Zhu M, Ray KL, Ma L, Zhang D (2008) Mass defect profiles of biological matrices and the general applicability of mass defect filtering for metabolite detection. Rapid Commun Mass Spectrom 22(13): 2082-2088.
291. Bateman KP, Castro-Perez J, Wrona M, Shockcor JP, Yu K, Oballa R, Nicoll-Griffith DA (2007) MSE with mass defect filtering for in vitro and in vivo metabolite identification. Rapid Commun Mass Spectrom 21(9): 1485-1496.
292. Stranz DD, Miao S, Campbell S, Maydwell G, Ekins S (2008) Combined computational metabolite prediction and automated structure-based analysis of mass spectrometric data. Toxicol Mech Methods 18(2-3): 243-250.
293. Leclercq L, Mortishire-Smith RJ, Huisman M, Cuyckens F, Hartshorn MJ, Hill A (2009) IsoScore: automated localization of biotransformations by mass spectrometry using product ion scoring of virtual regioisomers. Rapid Commun Mass Spectrom 23(1): 39-50.
294. Hopfgartner G, Husser C, Zell M (2003) Rapid screening and characterization of drug metabolites using a new quadrupole-linear ion trap mass spectrometer. J Mass Spectrom 38(2): 138-150.
295. Duan Y, Ma X, Zou W, Wang C, Behbahan IS, Ahuja TP, Tolstikov V, Zern MA (2010) Differentiation and characterization of metabolically functioning hepatocytes from human embryonic stem cells. Stem Cells 28(4): 674-686.
296. Bell SC, Gayton-Ely M, Nida CM (2009) Bioassays for bomb-makers: proof of concept. Anal Bioanal Chem 395(2): 401-409.
297. Gorman GS, Coward L, Kerstner-Wood C, Freeman L, Hebert CD, Kapetanovic IM (2009) In-vitro and in-vivo metabolic studies of the candidate chemopreventative pentamethylchromanol using liquid chromatography/tandem mass spectrometry. J Pharm Pharmacol 61(10): 1309-1318.
298. Chen Y, Liu HF, Liu L, Nguyen K, Jones EB, Fretland AJ (2010) The in vitro metabolism of bupropion revisited: concentration dependent involvement of cytochrome P450 2C19. Xenobiotica 40(8): 536-546.
299. Wind M, Gebhardt K, Grunwald H, Spickermann J, Donzelli M, Kellenberger L, Muller M, Fullhardt P, Schmitt-Hoffmann A, Schleimer M (2007) Elucidation of the in vitro metabolic profile of stable isotope labeled BAL19403 by accurate mass capillary liquid chromatography/quadrupole time-of-flight mass spectrometry and isotope exchange. Rapid Commun Mass Spectrom 21(7): 1093-1099.
300. Liu DQ, Hop C (2005) Strategies for characterization of drug metabolites using liquid chromatography-tandem mass spectrometry in conjunction with chemical derivatization and on-line H/D exchange approaches. J Pharm Biomed Anal 37(1): 1-18.
301. Kiffe M, Graf D, Trunzer M (2007) Two-dimensional liquid chromatography/mass spectrometry set-up for structural elucidation of metabolites in complex biological matrices. Rapid Commun Mass Spectrom 21(6): 961-970.
302. Nassar A-EF, Talaat RE (2004) Strategies for dealing with metabolite elucidation in drug discovery and development. Drug Discov Today 9(7): 317-327.
303. Ong SE, Blagoev B, Kratchmarova I, Kristensen DB, Steen H, Pandey A, Mann M (2002) Stable isotope labeling by amino acids in cell culture, SILAC, as a simple and accurate approach to expression proteomics. Mol Cell Proteomics 1(5): 376.
304. Ramos-Fernandez A, Lopez-Ferrer D, Vazquez J (2007) Improved method for differential expression proteomics using trypsin-catalyzed 18O labeling with a correction for labeling efficiency. Mol Cell Proteomics 6(7): 1274-1286.
305. Li X-J, Zhang H, Ranish JA, Aebersold R (2003) Automated statistical analysis of protein abundance ratios from data generated by stable-isotope dilution and tandem mass spectrometry. Anal Chem 75(23): 6648-6657.
306. Beynon RJ, Pratt JM (2005) Metabolic labeling of proteins for proteomics. Mol Cell Proteomics 4(7): 857.
307. Wang YK, Ma Z, Quinn DF, Fu EW (2001) Inverse 18O labeling mass spectrometry for the rapid identification of marker/target proteins. Anal Chem 73(15): 3742-3750.
308. Birkemeyer C, Luedemann A, Wagner C, Erban A, Kopka J (2005) Metabolome analysis: the potential of in vivo labeling with stable isotopes for metabolite profiling. Trends Biotechnol 23(1): 28-33.
309. Giavalisco P, Hummel J, Lisec J, Inostroza AC, Catchpole G, Willmitzer L (2008) High-resolution direct infusion-based mass spectrometry in combination with whole 13C metabolome isotope labeling allows unambiguous assignment of chemical sum formulas. Anal Chem 80(24): 9417-9425.
310. Garcia DE, Baidoo EE, Benke PI, Pingitore F, Tang YJ, Villa S, Keasling JD (2008) Separation and mass spectrometry in microbial metabolomics. Curr Opin Microbiol 11(3): 233-239.
311. Lane AN, Fan TWM, Higashi RM (2008) Isotopomer-based metabolomic analysis by NMR and mass spectrometry. Methods Cell Biol 84: 541-588.
312. Emmerling M, Dauner M, Ponti A, Fiaux J, Hochuli M, Szyperski T, Wuthrich K, Bailey JE, Sauer U (2002) Metabolic flux responses to pyruvate kinase knockout in Escherichia coli. J Bacteriol 184(1): 152-164.
313. Christensen B, Nielsen J (1999) Isotopomer analysis using GC-MS. Metab Eng 1(4): 282-290.
314. Wittmann C, Heinzle E (1999) Mass spectrometry for metabolic flux analysis. Biotechnol Bioeng 62(6): 739-750.
315. Feldberg L, Venger I, Malitsky S, Rogachev I, Aharoni A (2009) Dual Labeling of Metabolites for Metabolome Analysis (DLEMMA): a new approach for the identification and relative quantification of metabolites by means of dual isotope labeling and liquid chromatography-mass spectrometry. Anal Chem 81(22): 9257-9266.
316. Liu Y, Wang M, Xue M, Li Y, Li X, Ruan J, Liu K (2008) Structural elucidation of in vivo metabolites of penehyclidine in rats by the method of liquid chromatography-mass spectrometry, gas chromatography-mass spectrometry and isotope ion cluster. J Chromatogr B Anal Technol Biomed Life Sci 873(1): 41-50.
317. Kuhn F, Oehme M, Romero F, Abou-Mansour E, Tabacchi R (2003) Differentiation of isomeric flavone/isoflavone aglycones by MS2 ion trap mass spectrometry and a double neutral loss of CO. Rapid Commun Mass Spectrom 17(17): 1941-1949.
318. Wickens JR, Sleeman R, Keely BJ (2006) Atmospheric pressure ionisation mass spectrometric fragmentation pathways of noscapine and papaverine revealed by multistage mass spectrometry and in-source deuterium labelling. Rapid Commun Mass Spectrom 20(3): 473-480.
319. Taylor EW, Jia W, Mark B, Dollinger GD (2002) Accelerating the drug optimization process: identification, structure elucidation, and quantification of in vivo metabolites using stable isotopes with LC/MSn and the chemiluminescent nitrogen detector. Anal Chem 74(13): 3232-3238.
320. Ohashi N, Furuuchi S, Yoshikawa M (1998) Usefulness of the hydrogen-deuterium exchange method in the study of drug metabolism using liquid chromatography-tandem mass spectrometry. J Pharm Biomed Anal 18(3): 325-334.
321. Lehane M, Sáez MJF, Magdalena AB, Cañás IR, Sierra MD, Hamilton B, Furey A, James KJ (2004) Liquid chromatography-multiple tandem mass spectrometry for the determination of ten azaspiracids, including hydroxyl analogues in shellfish. J Chromatogr A 1024(1-2): 63-70.
322. Liu DQ, Wu L, Sun M, MacGregor PA (2007) On-line H/D exchange LC-MS strategy for structural elucidation of pharmaceutical impurities. J Pharm Biomed Anal 44(2): 320-329.
323. Keller BO, Sui J, Young AB, Whittal RM (2008) Interferences and contaminants encountered in modern mass spectrometry. Anal Chim Acta 627(1): 71-81.
324. Little JL (1999) Artifacts in trimethylsilyl derivatization reactions and ways to avoid them. J Chromatogr A 844(1-2): 1-22.
325. Xu F, Zou L, Ong CN (2009) Multiorigination of chromatographic peaks in derivatized GC/MS metabolomics: a confounder that influences metabolic pathway interpretation. J Proteome Res 8(12): 5657-5665.
326. Gfrerer M, Lankmayr E (2005) DDT degradation during enhanced solid-liquid extractions A consideration. J Chromatogr A 1072(1): 117-125.
327. Fiehn O, Wohlgemuth G, Scholz M, Kind T, Lee DY, Lu Y, Moon S, Nikolau B (2008) Quality control for plant metabolomics: reporting MSI-compliant studies. Plant J 53(4): 691-704.
328. Clark HA, Jurs PC (1981) Simulation of mass spectral intensities by regression analysis of calculated structural characteristics. Anal Chim Acta 132: 75-88.
329. Zhou C, Bowler LD, Feng J (2008) A machine learning approach to explore the spectra intensity pattern of peptides using tandem mass spectrometry data. BMC Bioinform 9(1): 325.
330. Timm W, Scherbart A, Böcker S, Kohlbacher O, Nattkemper TW (2008) Peak intensity prediction in MALDI-TOF mass spectrometry: a machine learning study to support quantitative proteomics. BMC Bioinform 9(1): 443.
331. Hochstrasser DF, Appel RD (2002) Peptide mass fingerprinting peak intensity prediction: extracting knowledge from spectra. Proteomics 2: 1374-1391.
332. Zhang H, Singh S, Reinhold VN (2005) Congruent strategies for carbohydrate sequencing. 2. FragLib: an MSn spectral library. Anal Chem 77(19): 6263-6270.
333. Kameyama A, Nakaya S, Ito H, Kikuchi N, Angata T, Nakamura M, Ishida HK, Narimatsu H (2006) Strategy for simulation of CID spectra of N-linked oligosaccharides toward glycomics. J Proteome Res 5(4): 808-814.
334. Chen T, Kao MY, Tepel M, Rush J, Church GM (2001) A dynamic programming approach to de novo peptide sequencing via tandem mass spectrometry. J Comput Biol 8(3): 325-337.
335. Katerina K, Frank P, Mark H, Andy O, Alistair F, Langley GJ (2003) Approaches towards the automated interpretation and prediction of electrospray tandem mass spectra of non-peptidic combinatorial compounds. Rapid Commun Mass Spectrom 17(11): 1163-1168.
336. Jalali-Heravi M, Fatemi MH (2000) Simulation of mass spectra of noncyclic alkanes and alkenes using artificial neural network. Anal Chim Acta 415(1-2): 95-103.
337. Chen H, Fan B, Xia H, Petitjean M, Yuan S, Panaye A, Doucet JP (2003) MASSIS: a mass spectrum simulation system 1. Principle and method. Eur J Mass Spectrom (Chichester, England) 9(3): 175.
338. Chen H, Fan B, Petitjean M, Panaye A, Doucet JP, Li F, Xia H, Yuan S (2003) MASSIS: a mass spectrum simulation system. 2: procedures and performance. Eur J Mass Spectrom (Chichester, England) 9(5): 445.
339. Fan B, Chen H, Petitjean M, Panaye A, Doucet JP, Xia H, Yuan S (2005) New strategy of mass spectrum simulation based on reduced and concentrated knowledge databases. Spectrosc Lett 38(2): 145-170.
340. Bandu ML, Watkins KR, Bretthauer ML, Moore CA, Desaire H (2004) Prediction of MS/MS Data. 1. A focus on pharmaceuticals containing carboxylic acids. Anal Chem 76(6): 1746-1753.
341. Wolf S, Schmidt S, Mueller-Hannemann M, Neumann S (2010) In silico fragmentation for computer assisted identification of metabolite mass spectra. BMC Bioinformatics 11: 148.
342. Schymanski EL, Meringer M, Brack W (2009) Matching structures to mass spectra using fragmentation patterns: are the results as good as they look? Anal Chem 81(9): 3608-3617.
343. Pelander A, Tyrkkö E, Ojanperä I (2009) In silico methods for predicting metabolism and mass fragmentation applied to quetiapine in liquid chromatography/time-of-flight mass spectrometry urine drug screening. Rapid Commun Mass Spectrom 23(4): 506-514.
344. Lukka PB, Kestell P, Paxton JW, Baguley BC (2008) Development and validation of a liquid chromatography-mass spectrometry (LC-MS) assay for the determination of the anti-cancer agent N-[2-(dimethylamino) ethyl]-2, 6-dimethyl-1-oxo-1, 2-dihydrobenzo [b]-1, 6-naphthyridine-4-carboxamide (SN 28049). J Chromatogr B 875(2): 368-372.
345. Eash MA, Gohlke RS (1962) Mass spectrometric analysis. A small computer program for the analysis of mass spectra. Anal Chem 34(6): 713.
346. Biemann K, McMurray W (1966) Computer-aided interpretation of high resolution mass spectra (high resolution mass spectrometry in computer-aided interpretation). Tetrahedron Lett 88(11): 2597-2598.
347. Lederberg J (1987) How DENDRAL was conceived and born. ACM, pp. 5-19.
348. Scheurell M, Franke S, Shah RM, Hühnerfuss H (2009) Occurrence of diclofenac and its metabolites in surface water and effluent samples from Karachi, Pakistan. Chemosphere 77(6): 870-876.
349. Stein SE (1995) Chemical substructure identification by mass spectral library searching. J Am Soc Mass Spectrom 6(8): 644-655.
350. Kerber A, Meringer M, RÜCker C (2006) CASE via MS: ranking structure candidates by mass spectra. Croat Chem Acta 79(3): 449-464.
351. Schymanski EL, Meinert C, Meringer M, Brack W (2008) The use of MS classifiers and structure generation to assist in the identification of unknowns in effect-directed analysis. Anal Chim Acta 615(2): 136-147.
352. Varmuza K, Werther W (1996) Mass spectral classifiers for supporting systematic structure elucidation. J Chem Inf Comput Sci 36(2): 323-333.
353. Zhang L, Liang Y, Chen A (2009) Selection of neutral losses and characteristic ions for mass spectral classifier. Analyst 134(8): 1717-1724.
354. Xiong Q, Zhang Y, Li M (2007) Computer-assisted prediction of pesticide substructure using mass spectra. Anal Chim Acta 593(2): 199-206.
355. Hummel J, Strehmel N, Selbig J, Walther D, Kopka J (2010) Decision tree supported substructure prediction of metabolites from GC-MS profiles. Metabolomics 6(2): 322-333.
356. Mitch A, Phelps DMR, Jeffrey SJ, Katherine LF, Katie AA, John CB, Thomas SL, Michael RG, James TD (2008) Development and validation of a sensitive liquid chromatography/mass spectrometry method for quantitation of flavopiridol in plasma enables accurate estimation of pharmacokinetic parameters with a clinically active dosing schedule. J Chromatogr B Anal Technol Biomed Life Sci 868(1-2): 110.
357. Diana J, Govaerts C, Hoogmartens J, van Schepdael A, Adams E (2006) Characterization of impurities in dirithromycin by liquid chromatography/ion trap mass spectrometry. J Chromatogr A 1125(1): 52-66.
358. Zou W, Tolstikov VV (2009) Pattern recognition and pathway analysis with genetic algorithms in mass spectrometry based metabolomics. Algorithms 2(2): 638.
359. Vafiadi C, Topakas E, Bakx EJ, Schols HA, Christakopoulos P (2007) Structural characterisation by ESI-MS of feruloylated arabino-oligosaccharides synthesised by chemoenzymatic esterification. Molecules 12(7): 1367-1375.
360. Li L, Low MY, Ge X, Bloodworth BC, Koh HL (2009) Isolation and structural elucidation of dapoxetine as an adulterant in a health supplement used for sexual performance enhancement. J Pharm Biomed Anal 50(5): 724-728.
361. Adams PE (2003) Metabolite characterization in drug discovery utilizing robotic liquid-handling, quadruple time-of-flight mass spectrometry and in-silico prediction. Curr Drug Metab 4(4): 259-271.
362. Wu R, McMahon TB (2009) Structures, energetics, and dynamics of gas phase ions studied by FTICR and HPMS. Mass Spectrom Rev 28(4): 546-585.
363. Holmes JL, Aubry C, Mayer PM (2006) Assigning structures to ions in mass spectrometry. CRC, Boca Raton, 9780849319501.
364. Luo YR (2007) Comprehensive handbook of chemical bond energies. CRC, Boca Raton, 9780849373664.
365. Bouchoux G (2007) Gas-phase basicities of polyfunctional molecules. Part 1: Theory and methods. Mass Spectrom Rev 26(6): 775-835.
366. Zhang J, Ha T-K, Knochenmuss R, Zenobi R (2002) Theoretical calculation of gas-phase sodium binding energies of common MALDI matrices. J Phys Chem A 106(28): 6610-6617.
367. Chen ECM, Chen ES (2000) Negative ion mass spectra, electron affinities, gas phase acidities, bond dissociation energies, and negative ion states of cytosine and thymine. J Phys Chem B 104(32): 7835-7844.
368. Wolken JK, Turecek F (2000) Proton affinity of uracil. A computational study of protonation sites. J Am Soc Mass Spectrom 11(12): 1065-1071.
369. Bourcier S, Hoppilliard Y (2009) Use of diagnostic neutral losses for structural information on unknown aromatic metabolites: an experimental and theoretical study. Rapid Commun Mass Spectrom 23(1): 93-103.
370. Heaton AL, Armentrout PB (2008) Experimental and theoretical studies of sodium cation interactions with d-arabinose, xylose, glucose, and galactose. J Phys Chem A 112(41): 10156-10167.
371. Nourse BD, Cooks RG (1991) Proton affinity determinations using the kinetic method in an ion trap mass spectrometer. Int J Mass Spectrom Ion Processes 106: 249-272.
372. Cooks RG, Wong PSH (1998) Kinetic method of making thermochemical determinations: advances and applications. Acc Chem Res 31(7): 379-386.
373. Alexander A, Sophie H, Teresa P, Frank SP, Patricia W, Jo-Anne R (2009) Can density functional theory (DFT) be used as an aid to a deeper understanding of tandem mass spectrometric fragmentation pathways? Rapid Commun Mass Spectrom 23(17): 2619-2627.
374. Jeilani YA, Cardelino BH, Ibeanusi VM (2010) Positive chemical ionization triple-quadrupole mass spectrometry and ab initio computational studies of the multi-pathway fragmentation of phthalates. J Mass Spectrom 45(6): 678-685.
375. Schug KA, Maier NM, Lindner W (2006) Chiral recognition mass spectrometry: remarkable effects observed from the relative ion abundances of ternary diastereomeric complexes using electrospray ionization. Chem Commun (4): 414-416.
376. Glotzer SC, Kim S, Cummings PT, Deshmukh A, Head-Gordon M, Karniadakis G, Petzold L, Sagui C, Shinozuka M (2010) International assessment of research and development in simulation-based engineering and science. www. wtec. org.
377. Mitrevski BS, Kouremenos KA, Marriott PJ (2009) Accelerating analysis for metabolomics, drugs and their metabolites in biological samples using multidimensional gas chromatography. Bioanalysis 1(2): 367-391.
378. Stein SE (1999) An integrated method for spectrum extraction and compound identification from gas chromatography/mass spectrometry data. J Am Soc Mass Spectrom 10(8): 770-781.
379. Lee S, Mandrake L, Bornstein B, Bue B (2009) Quantification of trace chemicals using vehicle cabin atmosphere monitor. Aerospace Conference 2009 IEEE. doi: 10. 1109/AERO. 2009. 4839630.
380. Mandrake L, Lee S, Bornstein B, Bue B (2009) Adapting AMDIS for autonomous spectral identification of hazardous compounds for ISS monitoring. Aerospace Conference 2009 IEEE. doi: 10. 1109/AERO. 2009. 4839578.
381. Kind T: Structure elucidation of small molecules. http://fiehnlab. ucdavis. edu/staff/kind/Metabolomics/Structure_Elucidation/.
382. Cuadros-Inostroza A, Caldana C, Redestig H, Kusano M, Lisec J, Pena-Cortes H, Willmitzer L, Hannah MA (2009) TargetSearch-a bioconductor package for the efficient preprocessing of GC-MS metabolite profiling data. BMC Bioinform 10(1): 428.
383. Renard BY, Kirchner M, Steen H, Steen JAJ, Hamprecht FA (2008) NITPICK: peak identification for mass spectrometry data. BMC Bioinformatics 9: 355.
384. Lu H, Liang Y, Dunn WB, Shen H, Kell DB (2008) Comparative evaluation of software for deconvolution of metabolomics data based on GC-TOF-MS. TrAC, Trends Anal Chem 27(3): 215-227.
385. Luedemann A, Strassburg K, Erban A, Kopka J (2008) TagFinder for the quantitative analysis of gas chromatography-mass spectrometry (GC-MS)-based metabolite profiling experiments. Bioinformatics 24(5): 732.
386. Fiehn O (2008) Extending the breadth of metabolite profiling by gas chromatography coupled to mass spectrometry. Trends Anal Chem 27(3): 261-269.
387. Ebada SS, Edrada RA, Lin W, Proksch P (2008) Methods for isolation, purification and structural elucidation of bioactive secondary metabolites from marine invertebrates. Nat Protocols 3(12): 1820-1831.
388. Nojima S, Apperson C, Schal C (2008) A simple, convenient, and efficient preparative GC system that uses a short megabore capillary column as a trap. J Chem Ecol 34(3): 418-428.
389. Sauer PE, Eglinton TI, Hayes JM, Schimmelmann A, Sessions AL (2001) Compound-specific D/H ratios of lipid biomarkers from sediments as a proxy for environmental and climatic conditions. Geochim Cosmochim Acta 65(2): 213-222.
390. Sutton PA, Lewis CA, Rowland SJ (2005) Isolation of individual hydrocarbons from the unresolved complex hydrocarbon mixture of a biodegraded crude oil using preparative capillary gas chromatography. Org Geochem 36(6): 963-970.
391. Sinninghe Damsté JS, Baas M, Geenevasen JAJ, Kenig F (2005) Structural identification of sedimentary C21 and C22 highly branched isoprenoid alkanes. Org Geochem 36(4): 511-517.
392. Zhang A, Amalin D, Shirali S, Serrano MS, Franqui RA, Oliver JE, Klun JA, Aldrich JR, Meyerdirk DE, Lapointe SL (2004) Sex pheromone of the pink hibiscus mealybug, Maconellicoccus hirsutus, contains an unusual cyclobutanoid monoterpene. Proc Natl Acad Sci USA 101(26): 9601.
393. Dickens JC, Oliver JE, Hollister B, Davis JC, Klun JA (2002) Breaking a paradigm: male-produced aggregation pheromone for the Colorado potato beetle. J Exp Biol 205(13): 1925.
394. Wang Y, Lu X, Xu GW (2008) Simultaneous separation of hydrophilic and hydrophobic compounds by using an online HILIC-RPLC system with two detectors. J Sep Sci 31(9): 1564-1572.
395. Francois I, Sandra K, Sandra P (2009) Comprehensive liquid chromatography: fundamental aspects and practical considerations-A review. Anal Chim Acta 641(1-2): 14-31.
396. Shellie RA, Haddad PR (2006) Comprehensive two-dimensional liquid chromatography. Anal Bioanal Chem 386(3): 405-415.
397. Okamoto M, Yamashita K, Nakai K (2006) On-line sample enrichment system coupled to electrospray ionization time-of-flight mass spectrometry (ESI-TOF-MS). J Pharm Biomed Anal 41(3): 707-713.
398. Steiner F, Mahsunah A, Arnold F, Piecha T, Huber CG (2007) Automated semipreparative purification with mass spectrometric fraction collection trigger: modeling and experimental evaluation of a setup employing passive splitting. J Sep Sci 30(10): 1496-1508.
399. Drexler DM, Tiller PR (1998) 'Intelligent' fraction collection to improve structural characterization by mass spectrometry. Rapid Commun Mass Spectrom 12(13): 895-900.
400. Dear GJ, Plumb RS, Sweatman BC, Ismail IM, Ayrton J (1999) Tandem mass spectrometry linked fraction collection for the isolation of drug metabolites from biological matrices. Rapid Commun Mass Spectrom 13(10): 886-894.
401. Plumb RS, Ayrton J, Dear GJ, Sweatman BC, Ismail IM (1999) The use of preparative high performance liquid chromatography with tandem mass spectrometric directed fraction collection for the isolation and characterisation of drug metabolites in urine by nuclear magnetic resonance spectroscopy and liquid chromatography/sequential mass spectrometry. Rapid Commun Mass Spectrom 13(10): 845-854.
402. de Vlieger JSB, Kolkman AJ, Ampt KAM, Commandeur JNM, Vermeulen NPE, Kool J, Wijmenga SS, Niessen WMA, Irth H, Honing M (2010) Determination and identification of estrogenic compounds generated with biosynthetic enzymes using hyphenated screening assays, high resolution mass spectrometry and off-line NMR. Journal of Chromatography B: Analytical Technologies in the Biomedical and Life Sciences 878(7-8): 667-674.
403. Alexander AJ, Xu F, Bernard C (2006) The design of a multi-dimensional LC-SPE-NMR system (LC2-SPE-NMR) for complex mixture analysis. Magn Reson Chem 44(1): 1-6.
404. Corcoran O, Spraul M (2003) LC-NMR-MS in drug discovery. Drug Discov Today 8(14): 624-631.
405. Christophoridou S, Dais P, Tseng LH, Spraul M (2005) Separation and identification of phenolic compounds in olive oil by coupling high-performance liquid chromatography with postcolumn solid-phase extraction to nuclear magnetic resonance spectroscopy (LC-SPE-NMR). J Agric Food Chem 53(12): 4667-4679.
406. Tatsis EC, Boeren S, Exarchou V, Troganis AN, Vervoort J, Gerothanassis IP (2007) Identification of the major constituents of Hypericum perforatum by LC/SPE/NMR and/or LC/MS. Phytochemistry 68(3): 383-393.
407. Exarchou V, Godejohann M, van Beek TA, Gerothanassis IP, Vervoort J (2003) LC-UV-solid-phase extraction-NMR-MS combined with a cryogenic flow probe and its application to the identification of compounds present in Greek oregano. Anal Chem 75(22): 6288-6294.
408. Seger C, Godejohann M, Tseng LH, Spraul M, Girtler A, Sturm S, Stuppner H (2005) LC-DAD-MS/SPE-NMR hyphenation. A tool for the analysis of pharmaceutically used plant extracts: identification of isobaric iridoid glycoside regioisomers from Harpagophytum procumbens. Anal Chem 77(3): 878-885.
409. Bringmann G, Wohlfarth M, Rischer H, Schlauer J, Brun R (2002) Extract screening by HPLC coupled to MS-MS, NMR, and CD: a dimeric and three monomeric naphthylisoquinoline alkaloids from Ancistrocladus griffithii. Phytochemistry 61(2): 195-204.
410. Lin Y, Schiavo S, Orjala J, Vouros P, Kautz R (2008) Microscale LC-MS-NMR platform applied to the identification of active cyanobacterial metabolites. Anal Chem 80(21): 8045-8054.
411. Schlotterbeck G, Ceccarelli SM (2009) LC-SPE-NMR-MS: a total analysis system for bioanalysis. Bioanalysis 1(3): 549-559.
412. Castro A, Moco S, Coll J, Vervoort J (2010) LC-MS-SPE-NMR for the isolation and characterization of neo-clerodane diterpenoids from Teucrium luteum subsp flavovirens. J Nat Products 73(5): 962-965.
413. Sorensen D, Raditsis A, Trimble LA, Blackwell BA, Sumarah MW, Miller JD (2007) Isolation and structure elucidation by LC-MS-SPE/NMR: PR toxin- and cuspidatol-related eremophilane sesquiterpenes from Penicillium roqueforti. J Nat Prod 70(1): 121-123.
414. Miliauskas G, van Beek TA, De Waard P, Venskutonis RP, Sudhölter EJR (2005) Identification of radical scavenging compounds in Rhaponticum carthamoides by means of LC-DAD-SPE-NMR. J Nat Prod 68(2): 168-172.
415. Kind T, Leamy T, Leary JA, Fiehn O (2009) Software platform virtualization in chemistry research and university teaching. J Cheminformatics 1(1): 18.
416. Dua S, Blanksby SJ, Bowie JH (2000) Electron capture of tetracyanoethylene oxide in the gas phase. Rearrangement of the parent radical anion to form [(NC)3C]-. A joint experimental and ab initio study. Int J Mass Spectrom 194(2-3): 165-170.
417. Hofmeister GE, Zhou Z, Leary JA (1991) Linkage position determination in lithium-cationized disaccharides-tandem mass-spectrometry and semiempirical calculations. J Am Chem Soc 113(16): 5964-5970.
418. Rodgers MT, Armentrout PB (1999) Absolute alkali metal ion binding affinities of several azoles determined by threshold collision-induced dissociation. Int J Mass Spectrom 187: 359-380.
419. Fell LM, Francis JT, Holmes JL, Terlouw JK (1997) The intriguing behaviour of (ionized) oxalacetic acid investigated by tandem mass spectrometry. Int J Mass Spectrom 165: 179-194.
420. Milletti F, Storchi L, Sforna G, Cross S, Cruciani G (2009) Tautomer enumeration and stability prediction for virtual screening on large chemical databases. J Chem Inf Model 49(1): 68-75.
421. Ge GB, Zhang R, Ai CZ, He YQ, Zhang YY, Liu XB, Yang L, Wang ZT, Yang L (2009) Stereochemical differentiation of C-7 hydroxyltaxane isomers by electrospray ionization mass spectrometry. Rapid Commun Mass Spectrom: RCM 23(3): 425-432.
422. Hayen H, Michels A, Franzke J (2009) Dielectric barrier discharge ionization for liquid chromatography/mass spectrometry. Anal Chem 81(24): 10239-10245.
423. Lee AC, Crippen GM (2009) Predicting pKa. J Chem Inf Model 49(9): 2013-2033.
424. Sanz-Nebot V, Toro I, Barbosa J (2001) Prediction of retention behaviour and evaluation of pKa values of peptides and quinolones in liquid chromatography. J Chromatogr A 933(1-2): 45-56.
425. Marvin Calculator Plugins-resonance structures, tautomer, stereoisomer, pKa, logP calculation. http://www. chemaxon. com/.
426. Bioclipse cheminformatics platform; [http://www. bioclipse. net/].
427. Molchanova MS, Shcherbukhin VV, Zefirov NS (1996) Computer generation of molecular structures by the SMOG program. J Chem Inf Comput Sci 36(4): 888-899.
428. Fontana P, Pretsch E (2002) Automatic spectra interpretation, structure generation, and ranking. J Chem Inf Comput Sci 42(3): 614-619.
429. Faulon J-L, Visco DP, Roe D (2005) Enumerating molecules. In: Kenny B, Lipkowitz RLTRC (eds) Reviews in computational chemistry. Wiley, New York, pp 209-286.
430. Hawkins DM (2003) The problem of overfitting. J Chem Inf Comput Sci 44(1): 1-12.
431. Heberger K (2007) Quantitative structure-(chromatographic) retention relationships. J Chromatogr A 1158(1-2): 273-305.
432. Kaliszan R (2007) QSRR: quantitative structure-(chromatographic) retention relationships. Chem Rev 107(7): 3212-3246.
433. Karelson M, Lobanov VS, Katritzky AR (1996) Quantum-chemical descriptors in QSAR/QSPR studies. Chem Rev 96(3): 1027-1044.
434. Albaugh DR, Hall LM, Hill DW, Kertesz TM, Parham M, Hall LH, Grant DF (2009) Prediction of HPLC retention index using artificial neural networks and IGroup E-state indices. J Chem Inf Model 49(4): 788-799.
435. Hill DW, Kind AJ (1994) Reversed-phase solvent-gradient HPLC retention indexes of drugs. J Anal Toxicol 18(5): 233-242.
436. Babushok VI, Linstrom PJ, Reed JJ, Zenkevich IG, Brown RL, Mallard WG, Stein SE (2007) Development of a database of gas chromatographic retention properties of organic compounds. J Chromatogr A 1157(1-2): 414-421.
437. Zenkevich IG, Babushok VI, Linstrom PJ, White E, Stein SE (2009) Application of histograms in evaluation of large collections of gas chromatographic retention indices. J Chromatogr A 1216(38): 6651-6661.
438. Stein SE, Babushok VI, Brown RL, Linstrom PJ (2007) Estimation of Kovats retention indices using group contributions. J Chem Inf Model 47(3): 975-980.
439. Baker JK, Ma C-Y (1979) Retention index scale for liquid-liquid chromatography. J Chromatogr A 169: 107-115.
440. Smith RM (1982) Alkylarylketones as a retention index scale in liquid chromatography. J Chromatogr A 236(2): 313-320.
441. Bogusz M, Wu M (1991) Standardized HPLC/DAD system, based on retention indices and spectral library, applicable for systematic toxicological screening. J Anal Toxicol 15(4): 188-197.
442. Krokhin OV, Spicer V (2009) Peptide retention standards and hydrophobicity indexes in reversed-phase high-performance liquid chromatography of peptides. Anal Chem 81(22): 9522-9530.
443. Zaikin V, Halket JM (2009) A handbook of derivatives for mass spectrometry. IM, West Sussex, 1901019098.
444. Fernandes-Whaley M, Muhlberger F, Whaley A, Adam T, Zimmermann R, Rohwer E, Walte A (2005) On-line derivatization for resonance-enhanced multiphoton ionization time-of-flight mass spectrometry: detection of aliphatic aldehydes and amines via reactive coupling of aromatic photo ionization labels. Anal Chem 77(1): 1-10.
445. Eggink M, Wijtmans M, Ekkebus R, Lingeman H, de Esch IJP, Kool J, Niessen WMA, Irth H (2008) Development of a selective ESI-MS derivatization reagent: synthesis and optimization for the analysis of aldehydes in biological mixtures. Anal Chem 80(23): 9042-9051.
446. Hong H, Wang Y (2007) Derivatization with girard reagent T combined with LC- MS/MS for the sensitive detection of 5-Formyl-2-deoxyuridine in cellular DNA. Anal Chem 79(1): 322-326.
447. Yang WC, Mirzaei H, Liu X, Regnier FE (2006) Enhancement of amino acid detection and quantification by electrospray ionization mass spectrometry. Anal Chem 78(13): 4702-4708.
448. Segura J, Ventura R, Jurado C (1998) Derivatization procedures for gas chromatographic-mass spectrometric determination of xenobiotics in biological samples, with special attention to drugs of abuse and doping agents. J Chromatogr B Biomed Sci Appl 713(1): 61-90.
449. Ternes TA, Andersen H, Gilberg D, Bonerz M (2002) Determination of estrogens in sludge and sediments by liquid extraction and GC/MS/MS. Anal Chem 74(14): 3498-3504.
450. Ternes TA (2001) Analytical methods for the determination of pharmaceuticals in aqueous environmental samples. TrAC, Trends Anal Chem 20(8): 419-434.
451. Sacher F, Lange FT, Brauch HJ, Blankenhorn I (2001) Pharmaceuticals in groundwaters: analytical methods and results of a monitoring program in Baden-Württemberg, Germany. J Chromatogr A 938(1-2): 199-210.
452. Molnár-Perl I, Horváth K (1997) Simultaneous quantitation of mono-, di-and trisaccharides as their TMS ether oxime derivatives by GC-MS: I. In model solutions. Chromatographia 45(1): 321-327.
453. Horvath K, Molnár-Perl I (1997) Simultaneous quantitation of mono-, di-and trisaccharides by GC-MS of their TMS ether oxime derivatives: II. In honey. Chromatographia 45(1): 328-335.
454. Zampolli MG, Basaglia G, Dondi F, Sternberg R, Szopa C, Pietrogrande MC (2007) Gas chromatography-mass spectrometry analysis of amino acid enantiomers as methyl chloroformate derivatives: application to space analysis. J Chromatogr A 1150(1-2): 162-172.
455. Kaspar H, Dettmer K, Chan Q, Daniels S, Nimkar S, Daviglus ML, Stamler J, Elliott P, Oefner PJ (2009) Urinary amino acid analysis: a comparison of iTRAQ-LC-MS/MS, GC-MS, and amino acid analyzer. J Chromatogr B Anal Technol Biomed Life Sci 877(20-21): 1838-1846.
456. Kiousi P, Angelis YS, Lyris E, Koupparis M, Calokerinos AC, Atta-Politou J, Georgakopoulos CG (2009) Two-step silylation procedure for the unified analysis of 190 doping control substances in human urine samples by GC-MS. Bioanalysis 1(7): 1209-1224.
457. Somuramasami J, Winger BE, Gillespie TA, Kenttämaa HI (2009) Identification and counting of carbonyl and hydroxyl functionalities in protonated bifunctional analytes by using solution derivatization prior to mass spectrometric analysis via ion-molecule reactions. J Am Soc Mass Spectrom 21(5): 773-784.
458. Hummel J, Selbig J, Walther D, Kopka J (2007) The Golm Metabolome Database: a database for GC-MS based metabolite profiling. Topics in Current Genetics 18: 75.
459. Kind T, Wohlgemuth G, Lu Y, Palazoglu M, Shahbaz S, Fiehn O (2009) FiehnLib: mass spectral and retention index libraries for metabolomics based on quadrupole and time-of-flight gas chromatography/mass spectrometry. Anal Chem 81(24): 10038-10048.
460. Guo K, Li L (2009) Differential 12C-/13C-isotope dansylation labeling and fast liquid chromatography/mass spectrometry for absolute and relative quantification of the metabolome. Anal Chem 81(10): 3919-3932.
461. Wang Y, Xiao J, Suzek TO, Zhang J, Wang J, Bryant SH (2009) PubChem: a public information system for analyzing bioactivities of small molecules. Nucleic Acids Res 37(Web Server issue): W623.
462. Williams AJ (2008) A perspective of publicly accessible/open-access chemistry databases. Drug Discov Today 13(11-12): 495-501.
463. Kanehisa M, Araki M, Goto S, Hattori M, Hirakawa M, Itoh M, Katayama T, Kawashima S, Okuda S, Tokimatsu T (2008) KEGG for linking genomes to life and the environment. Nucleic Acids Res 36(Database issue): D480.
464. Wishart DS, Knox C, Guo AC, Eisner R, Young N, Gautam B, Hau DD, Psychogios N, Dong E, Bouatra S (2008) HMDB: a knowledgebase for the human metabolome. Nucleic Acids Res 37: D603-D610.
465. Degtyarenko K, de Matos P, Ennis M, Hastings J, Zbinden M, McNaught A, Alcantara R, Darsow M, Guedj M, Ashburner M (2008) ChEBI: a database and ontology for chemical entities of biological interest. Nucleic Acids Res 36(Database issue): D344.
466. Wishart DS (2008) DrugBank and its relevance to pharmacogenomics. Pharmacogenomics 9(8): 1155-1162.
467. Draper J, Enot DP, Parker D, Beckmann M, Snowdon S, Lin W, Zubair H (2009) Metabolite signal identification in accurate mass metabolomics data with MZedDB, an interactive m/z annotation tool utilising predicted ionisation behaviour 'rules'. BMC Bioinformatics 10(1): 227.
468. Nicklaus MC, Filippov IV, Sitzmann M, Ihlenfeldt W-D, Oellien F, Bienfait B, Voigt JH, Sun G (2010) Chemical structure lookup service. http://cactus. nci. nih. gov/.
469. Brown M, Dunn WB, Dobson P, Patel Y, Winder CL, Francis-McIntyre S, Begley P, Carroll K, Broadhurst D, Tseng A (2009) Mass spectrometry tools and metabolite-specific databases for molecular identification in metabolomics. Analyst 134(7): 1322-1332.
470. Villas-Bôas SG, Mas S, Akesson M, Smedsgaard J, Nielsen J (2005) Mass spectrometry in metabolome analysis. Mass Spectrom Rev 24(5): 613-646.
471. Dettmer K, Aronov PA, Hammock BD (2007) Mass spectrometry-based metabolomics. Mass Spectrom Rev 26(1): 51.
472. Haleem JI, Que NV, Timothy JW, Gary MM, Timothy DV (2009) Analytical and statistical approaches to metabolomics research. J Sep Sci 32(13): 2183-2199.
473. Wishart DS (2009) Computational strategies for metabolite identification in metabolomics. Bioanalysis 1(9): 1579-1596.
474. Kertesz TM, Hill DW, Albaugh DR, Hall LH, Hall LM, Grant DF (2009) Database searching for structural identification of metabolites in complex biofluids for mass spectrometry-based metabonomics. Bioanalysis 1(9): 1627-1643.
475. Ma S, Zhu M (2009) Recent advances in applications of liquid chromatography-tandem mass spectrometry to the analysis of reactive drug metabolites. Chem-Biol Interact 179(1): 25-37.
476. Calza P, Medana C, Carbone F, Giancotti V, Baiocchi C (2008) Characterization of intermediate compounds formed upon photoinduced degradation of quinolones by high-performance liquid chromatography/high-resolution multiple-stage mass spectrometry. Rapid Commun Mass Spectrom 22(10): 1533-1552.
477. Li Q, Yan G, Ge T (2008) A fragmentation study of two compounds related to 4′-demethylepipodophyllotoxin in negative ion electrospray ionization by MSn ion-trap time-of-flight mass spectrometry. Rapid Commun Mass Spectrom 22(3): 373-378.
478. Gallart-Ayala H, Moyano E, Galceran MT (2007) Liquid chromatography/multi-stage mass spectrometry of bisphenol A and its halogenated derivatives. Rapid Commun Mass Spectrom 21(24): 4039-4048.
479. Yan G, Li Q, Tan H, Ge T (2007) Electrospray ionization ion-trap time-of-flight tandem mass spectrometry of two furofurans: sesamin and gmelinol. Rapid Commun Mass Spectrom 21(22): 3613-3620.
480. Piccinelli AL, Campone L, Dal Piaz F, Cuesta-Rubio O, Rastrelli L (2009) Fragmentation pathways of polycyclic polyisoprenylated benzophenones and degradation profile of nemorosone by multiple-stage tandem mass spectrometry. J Am Soc Mass Spectrom 20(9): 1688-1698.
481. Kovácik V, Bekesová S, Tvaroska I, Kovác P (2006) Positive Electrospray ion trap multistage mass spectrometric fragmentation of synthetic analogs of saccharide part of lipopolysaccharides of vibrio cholerae O: 1. J Am Soc Mass Spectrom 17(6): 749-756.
482. Kirk JM, Tarbin J, Keely BJ (2006) Analysis of androgenic steroid Girard P hydrazones using multistage tandem mass spectrometry. Rapid Commun Mass Spectrom 20(8): 1247-1252.
483. Schmidt J, Boettcher C, Kuhnt C, Kutchan TM, Zenk MH (2007) Poppy alkaloid profiling by electrospray tandem mass spectrometry and electrospray FT-ICR mass spectrometry after [ring-13C6]-tyramine feeding. Phytochemistry 68(2): 189-202.
484. Cataldi TRI, Lelario F, Bufo SA (2005) Analysis of tomato glycoalkaloids by liquid chromatography coupled with electrospray ionization tandem mass spectrometry. Rapid Commun Mass Spectrom 19(21): 3103-3110.
485. Dudley E, Tuytten R, Bond A, Lemière F, Brenton AG, Esmans EL, Newton RP (2005) Study of the mass spectrometric fragmentation of pseudouridine: comparison of fragmentation data obtained by matrix-assisted laser desorption/ionisation post-source decay, electrospray ion trap multistage mass spectrometry, and by a method utilising electrospray quadrupole time-of-flight tandem mass spectrometry and in-source fragmentation. Rapid Commun Mass Spectrom 19(21): 3075-3085.
486. Vrkic AK, O'Hair RAJ, Foote S (2000) Fragmentation reactions of all 64 deprotonated trinucleotide and 16 mixed base tetranucleotide anions via tandem mass spectrometry in an ion trap. Aust J Chem 53(4): 307-320.
487. Vukics V, Guttman A (2010) Structural characterization of flavonoid glycosides by multi-stage mass spectrometry. Mass Spectrom Rev 29: 1-16.
488. Cuyckens F, Claeys M (2004) Mass spectrometry in the structural analysis of flavonoids. J Mass Spectrom 39(1): 1-15.
489. de Rijke E, Out P, Niessen WMA, Ariese F, Gooijer C, Brinkman UAT (2006) Analytical separation and detection methods for flavonoids. J Chromatogr A 1112(1-2): 31-63.
490. Portet B, Fabre N, Rozenberg R, Habib-Jiwan J-L, Moulis C, Quetin-Leclercq J (2008) Analysis of minor flavonoids in Piper hostmannianum var. berbicense using liquid chromatography coupled with atmospheric pressure chemical ionization mass spectrometry. J Chromatogr A 1210(1): 45-54.
491. Nakabayashi R, Kusano M, Kobayashi M, Tohge T, Yonekura-Sakakibara K, Kogure N, Yamazaki M, Kitajima M, Saito K, Takayama H (2009) Metabolomics-oriented isolation and structure elucidation of 37 compounds including two anthocyanins from Arabidopsis thaliana. Phytochemistry 70(8): 1017-1029.
492. Prakash C, Shaffer CL, Nedderman A (2007) Analytical strategies for identifying drug metabolites. Mass Spectrom Rev 26(3): 340-369.
493. Tozuka Z, Kaneko H, Shiraga T, Mitani Y, Beppu M, Terashita S, Kawamura A, Kagayama A (2003) Strategy for structural elucidation of drugs and drug metabolites using (MS) n fragmentation in an electrospray ion trap. J Mass Spectrom 38(8): 793-808.
494. Trunzer M, Faller B, Zimmerlin A (2008) Metabolic soft spot identification and compound optimization in early discovery phases using metasite and LC-MS/MS validation. J Med Chem 52(2): 329-335.
495. Pan C, Liu F, Ji Q, Wang W, Drinkwater D, Vivilecchia R (2006) The use of LC/MS, GC/MS, and LC/NMR hyphenated techniques to identify a drug degradation product in pharmaceutical development. J Pharm Biomed Anal 40(3): 581-590.
496. Zhang J, Schubothe K, Li B, Russell S, Lebrilla CB (2004) Infrared multiphoton dissociation of O-linked mucin-type oligosaccharides. Anal Chem 77(1): 208-214.
497. Chen Y, Monshouwer M, Fitch WL (2007) Analytical tools and approaches for metabolite identification in early drug discovery. Pharm Res 24(2): 248-257.
498. Habicht SC, Vinueza NR, Duan P, Fu M, Kenttämaa HI (2010) Data-dependent neutral gain MS3: toward automated identification of the N-oxide functional group in drug metabolites. J Am Soc Mass Spectrom 21(4): 559-563.
499. Elyashberg ME, Williams AJ, Martin GE (2008) Computer-assisted structure verification and elucidation tools in NMR-based structure elucidation. Prog Nucl Magn Reson Spectrosc 53(1-2): 1-104.
500. Cheng KW, Wong CC, Wang M, He QY, Chen F (2009) Identification and characterization of molecular targets of natural products by mass spectrometry. Mass Spectrom Rev 29(1): 126-155.
501. Wilson ID, Brinkman UAT (2003) Hyphenation and hypernation: the practice and prospects of multiple hyphenation. J Chromatogr A 1000(1-2): 325-356.
502. Laniewski K, Vagero M, Forsberg E, Forngren T, Hagman G (2004) Complementary use of gas chromatography-mass spectrometry, gas chromatography-atomic emission detection and nuclear magnetic resonance for identification of pharmaceutically related impurities of unknown structures. J Chromatogr A 1027(1-2): 93-102.
503. Schiller J, Süß R, Arnhold J, Fuchs B, Leßig J, Müller M, Petkovic M, Spalteholz H, Zschörnig O, Arnold K (2004) Matrix-assisted laser desorption and ionization time-of-flight (MALDI-TOF) mass spectrometry in lipid and phospholipid research. Prog Lipid Res 43(5): 449-488.
504. Pulfer M, Murphy RC (2003) Electrospray mass spectrometry of phospholipids. Mass Spectrom Rev 22(5): 332-364.
505. Han X, Gross RW (2005) Shotgun lipidomics: electrospray ionization mass spectrometric analysis and quantitation of cellular lipidomes directly from crude extracts of biological samples. Mass Spectrom Rev 24(3): 367-412.
506. Souady J, Dadimov D, Kirsch S, Bindila L, Peter-Katalinic J, Vakhrushev SY (2010) Software utilities for the interpretation of mass spectrometric data of glycoconjugates: application to glycosphingolipids of human serum. Rapid Commun Mass Spectrom 24(7): 1039-1048.
507. Byrdwell WC, Neff WE (2002) Dual parallel electrospray ionization and atmospheric pressure chemical ionization mass spectrometry (MS), MS/MS and MS/MS/MS for the analysis of triacylglycerols and triacylglycerol oxidation products. Rapid Commun Mass Spectrom 16(4): 300-319.
508. Forrester JS, Milne SB, Ivanova PT, Brown HA (2004) Computational lipidomics: a multiplexed analysis of dynamic changes in membrane lipid composition during signal transduction. Mol Pharmacol 65(4): 813-821.
509. Yang K, Cheng H, Gross RW, Han X (2009) Automated lipid identification and quantification by multidimensional mass spectrometry-based shotgun lipidomics. Anal Chem 81(11): 4356-4368.
510. Schwudke D, Oegema J, Burton L, Entchev E, Hannich JT, Ejsing CS, Kurzchalia T, Shevchenko A (2006) Lipid profiling by multiple precursor and neutral loss scanning driven by the data-dependent acquisition. Anal Chem 78(2): 585-595.
511. Pittenauer E, Allmaier G (2009) The renaissance of high-energy CID for structural elucidation of complex lipids: MALDI-TOF/RTOF-MS of alkali cationized triacylglycerols. J Am Soc Mass Spectrom 20(6): 1037-1047.
512. Song H, Hsu FF, Ladenson J, Turk J (2007) Algorithm for processing raw mass spectrometric data to identify and quantitate complex lipid molecular species in mixtures by data-dependent scanning and fragment ion database searching. J Am Soc Mass Spectrom 18(10): 1848-1858.
513. Ibanez M, Sancho JV, Pozo Ó, Niessen W, Hernandez F (2005) Use of quadrupole time-of-flight mass spectrometry in the elucidation of unknown compounds present in environmental water. Rapid Commun Mass Spectrom 19(2): 169-178.
514. Schymanski EL, Bataineh M, Goss KU, Brack W (2009) Integrated analytical and computer tools for structure elucidation in effect-directed analysis. TrAC, Trends Anal Chem 28(5): 550-561.
515. Niessen WMA (2009) Group-specific fragmentation of pesticides and related compounds in liquid chromatography-tandem mass spectrometry. J Chromatogr A 1217(25): 4061-4070.
516. Krauss M, Singer H, Hollender J (2010) LC-high resolution MS in environmental analysis: from target screening to the identification of unknowns. Analytical and Bioanalytical Chemistry 397(3): 943-951.
517. Smyth WF (2005) Recent applications of capillary electrophoresis-electrospray ionisation-mass spectrometry in drug analysis. Electrophoresis 26(7-8): 1334-1357.
518. Klampfl CW (2006) Recent advances in the application of capillary electrophoresis with mass spectrometric detection. Electrophoresis 27(1): 3-34.
519. Buckingham S (2003) Bioinformatics: programmed for success. Nature 425(6954): 209-215.
520. Rudnick PA, Clauser KR, Kilpatrick LE, Tchekhovskoi DV, Neta P, Blonder N, Billheimer DD, Blackman RK, Bunk DM, Cardasis HL (2009) Performance metrics for liquid chromatography-tandem mass spectrometry systems in proteomic analyses and evaluation by the CPTAC network. Molecular & Cellular Proteomics M900223.
521. Kind T, Scholz M, Fiehn O (2009) How large is the metabolome? A critical analysis of data exchange practices in chemistry. PLoS ONE 4(5): e5440.
522. Bradley JC, Lancashire RJ, Lang A, Williams AJ (2009) The spectral game: leveraging Open Data and crowdsourcing for education. J Cheminformatics 1(1): 9.
523. Go EP (2009) Database resources in metabolomics: an overview. Journal of Neuroimmune Pharmacology 5: 18-30.
524. Han J, Datla R, Chan S, Borchers CH (2009) Mass spectrometry-based technologies for high-throughput metabolomics. Mass Spectrometry 1(9): 1665-1684.
525. Downing J, Murray-Rust P, Tonge AP, Morgan P, Rzepa HS, Cotterill F, Day N, Harvey MJ (2008) SPECTRa: the deposition and validation of primary chemistry research data in digital repositories. J Chem Inf Model 48(8): 1571.
526. Neuweger H, Albaum SP, Dondrup M, Persicke M, Watt T, Niehaus K, Stoye J, Goesmann A (2008) MeltDB: a software platform for the analysis and integration of metabolomics experiment data. Bioinformatics 24(23): 2726.
527. Scholz M, Fiehn O (2007) SetupX-a public study design database for metabolomic projects. Pac Symp Biocomput 2007: 169-180.
528. Mendes P, Mendes P, Lewis IA, Lewis IA (2008) Metabolite identification via the Madison Metabolomics Consortium Database. Nat Biotechnol 26(2): 162-164.
529. Smith CA, Maille GO, Want EJ, Qin C, Trauger SA, Brandon TR, Custodio DE, Abagyan R, Siuzdak G (2005) METLIN: a metabolite mass spectral database. Ther Drug Monit 27(6): 747.
530. Sana TR, Roark JC, Li X, Waddell K, Fischer SM (2008) Molecular formula and METLIN Personal Metabolite Database matching applied to the identification of compounds generated by LC/TOF-MS. Journal of Biomolecular Techniques: JBT 19(4): 258-266.
531. Shinbo Y, Nakamura Y, Altaf-Ul-Amin M, Asahi H, Kurokawa K, Arita M, Saito K, Ohta D, Shibata D, Kanaya S (2006) KNApSAcK: a comprehensive species-metabolite relationship database. Plant Metabolomics 57: 165-181.
532. Matsuda F, Yonekura-Sakakibara K, Niida R, Kuromori T, Shinozaki K, Saito K (2009) MS/MS spectral tag-based annotation of non-targeted profile of plant secondary metabolites. Plant J 57(3): 555.
533. Hamacher M, Stephan C, Meyer HE, Eisenacher M (2009) Data handling and processing in proteomics. Expert Rev Proteomics 6(3): 217-219.
534. Rodriguez H (2008) International summit on proteomics data release and sharing policy. J Proteome Res 7(11): 4609.
535. Jennifer AM, Ian PS, Conrad B (2007) Public proteomic MS repositories and pipelines: available tools and biological applications. Proteomics 7(16): 2769-2786.
536. Falkner JA, Andrews PC (2007) Tranche: secure decentralized data storage for the proteomics community. J Biomol Tech 18(1): 3.
537. Falkner JA, Falkner JW, Andrews PC (2007) ProteomeCommons. org IO Framework: reading and writing multiple proteomics data formats. Bioinformatics 23(2): 262.
538. Pedrioli PGA, Eng JK, Hubley R, Vogelzang M, Deutsch EW, Raught B, Pratt B, Nilsson E, Angeletti RH, Apweiler R (2004) A common open representation of mass spectrometry data and its application to proteomics research. Nat Biotechnol 22(11): 1459-1466.
539. Eric D (2008) mzML: a single, unifying data format for mass spectrometer output. Proteomics 8(14): 2776-2777.
540. Droit A, Fillon J, Morissette J, Poirier GG (2006) Bioinformatic standards for proteomics-oriented mass spectrometry. Curr Proteomics 3(2): 119-128.
541. Deutsch EW, Lam H, Aebersold R (2008) Data analysis and bioinformatics tools for tandem mass spectrometry in proteomics. Physiol Genomics 33(1): 18.
542. Davis G, Rew R, Hartnett E, Caron J, Emmerson S, Davies H (2010) netCDF exchange format description and software. http://www. unidata. ucar. edu/software/netcdf/.
543. Lampen P, Hillig H, Davies AN, Linscheid M (1994) JCAMP-DX for mass spectrometry. Appl Spectrosc 48(12): 1545-1552.
544. Murray-Rust P (2008) Open data in science. Ser Rev 34(1): 52-64.
545. McLafferty FW, Stauffer DA, Loh SY, Wesdemiotis C (1999) Unknown identification using reference mass spectra. Quality evaluation of databases. J Am Soc Mass Spectrom 10(12): 1229-1240.
546. Ausloos P, Clifton CL, Lias SG, Mikaya AI, Stein SE, Tchekhovskoi DV, Sparkman OD, Zaikin V, Zhu D (1999) The critical evaluation of a comprehensive mass spectral library. J Am Soc Mass Spectrom 10(4): 287-299.