Two birds with one stone: Doing metabolomics with your proteomics kit

Proteomics

Volumn 13, Issue 23-24, 2013, Pages 3371-3386

  Fischer, Roman ^a   Bowness, Paul ^b   Kessler, Benedikt M ^a  

^a UNIVERSITY OF OXFORD   (United Kingdom)

^b UNIVERSITY OF OXFORD   (United Kingdom)

Author keywords

Integration; Liquid chromatography; Mass spectrometry; Metabolomics; Technology

Indexed keywords

DIPEPTIDE; FATTY ACID; LIPID; PEPTIDE; PROSTAGLANDIN; PROTEIN; PROTEOME; STEROID; TRIPEPTIDE; VITAMIN;

BIOLOGICAL PHENOMENA AND FUNCTIONS CONCERNING THE ENTIRE ORGANISM; DATA ANALYSIS; GAS CHROMATOGRAPHY; GENOME; GENOMICS; HUMAN; HYDROPHILIC INTERACTION CHROMATOGRAPHY; IONIZATION; LIQUID CHROMATOGRAPHY; MASS SPECTROMETRY; MEASUREMENT ACCURACY; METABOLITE; METABOLOME; METABOLOMICS; NUCLEAR MAGNETIC RESONANCE; PHYSICAL CHEMISTRY; PRIORITY JOURNAL; PROTEOMICS; REVIEW; SCIENTIST; SEPARATION TECHNIQUE; WORKFLOW;

INTEGRATION; LIQUID CHROMATOGRAPHY; MASS SPECTROMETRY; METABOLOMICS; TECHNOLOGY;

ANIMALS; HUMANS; METABOLOME; METABOLOMICS; MOLECULAR WEIGHT; PROTEOMICS; SOFTWARE; TANDEM MASS SPECTROMETRY;

EID: 84890254747     PISSN: 16159853     EISSN: 16159861     Source Type: Journal    
DOI: 10.1002/pmic.201300192     Document Type: Review

References (122)

1. Zhou, B., Xiao, J. F., Tuli, L., Ressom, H. W., LC-MS-based metabolomics. Mol. Biosyst. 2012, 8, 470-481.
2. Mischak, H., Ioannidis, J. P., Argiles, A., Attwood, T. K. et al., Implementation of proteomic biomarkers: making it work. Eur. J. Clin. Invest. 2012, 42, 1027-1036.
3. Mitchell, P., Proteomics retrenches. Nat. Biotechnol. 2010, 28, 665-670.
4. Chen, R., Mias, G. I., Li-Pook-Than, J., Jiang, L. et al., Personal Omics profiling reveals dynamic molecular and medical phenotypes. Cell 2012, 148, 1293-1307.
5. Sana, T. R., Roark, J. C., Li, X., Waddell, K., Fischer, S. M., Molecular formula and METLIN Personal Metabolite Database matching applied to the identification of compounds generated by LC/TOF-MS. J. Biomol. Tech. 2008, 19, 258-266.
6. Peironcely, J. E., Reijmers, T., Coulier, L., Bender, A., Hankemeier, T., Understanding and classifying metabolite space and metabolite-likeness. PLoS One 2011, 6, e28966.
7. Schrader, M., Schulz-Knappe, P., Peptidomics technologies for human body fluids. Trends Biotechnol. 2001, 19, S55-S60.
8. Schulz-Knappe, P., Schrader, M., Zucht, H. D., The peptidomics concept. Comb. Chem. High T. Scr. 2005, 8, 697-704.
9. Jost, M. M., Budde, P., Tammen, H., Hess, R. et al., The concept of functional peptidomics for the discovery of bioactive peptides in cell culture models. Comb. Chem. High T. Scr. 2005, 8, 767-773.
10. Hubatsch, I., Lazorova, L., Vahlne, A., Artursson, P., Orally active antiviral tripeptide glycyl-prolyl-glycinamide is activated by CD26 (dipeptidyl peptidase IV) before transport across the intestinal epithelium. Antimicrob. Agents Chemother. 2005, 49, 1087-1092.
11. Dunn, W. B., Broadhurst, D., Begley, P., Zelena, E. et al., Procedures for large-scale metabolic profiling of serum and plasma using gas chromatography and liquid chromatography coupled to mass spectrometry. Nat. Protoc. 2011, 6, 1060-1083.
12. Baidoo, E. E., Benke, P. I., Keasling, J. D., Mass spectrometry-based microbial metabolomics. Methods Mol. Biol. 2012, 881, 215-278.
13. Hommerson, P., Khan, A. M., de Jong, G. J., Somsen, G. W., Ionization techniques in capillary electrophoresis-mass spectrometry: principles, design, and application. Mass Spectrom. Rev. 2011, 30, 1096-1120.
14. Serkova, N. J., Brown, M. S., Quantitative analysis in magnetic resonance spectroscopy: from metabolic profiling to in vivo biomarkers. Bioanalysis 2012, 4, 321-341.
15. Lindon, J. C., Nicholson, J. K., Spectroscopic and statistical techniques for information recovery in metabonomics and metabolomics. Annu. Rev. Anal. Chem. 2008, 1, 45-69.
16. Almstetter, M. F., Oefner, P. J., Dettmer, K., Comprehensive two-dimensional gas chromatography in metabolomics. Anal. Bioanal. Chem. 2012, 402, 1993-2013.
17. Theodoridis, G. A., Gika, H. G., Want, E. J., Wilson, I. D., Liquid chromatography-mass spectrometry based global metabolite profiling: a review. Anal. Chim. Acta 2012, 711, 7-16.
18. Vuckovic, D., Current trends and challenges in sample preparation for global metabolomics using liquid chromatography-mass spectrometry. Anal. Bioanal. Chem. 2012, 403, 1523-1548.
19. Cubbon, S., Antonio, C., Wilson, J., Thomas-Oates, J., Metabolomic applications of HILIC-LC-MS. Mass Spectrom. Rev. 2010, 29, 671-684.
20. Zhang, T., Creek, D. J., Barrett, M. P., Blackburn, G., Watson, D. G., Evaluation of coupling reversed phase, aqueous normal phase, and hydrophilic interaction liquid chromatography with Orbitrap mass spectrometry for metabolomic studies of human urine. Anal. Chem. 2012, 84, 1994-2001.
21. Burgess, K., Creek, D., Dewsbury, P., Cook, K., Barrett, M. P., Semi-targeted analysis of metabolites using capillary-flow ion chromatography coupled to high-resolution mass spectrometry. Rapid Commun. Mass Spectrom. 2011, 25, 3447-3452.
22. Tolstikov, V. V., Lommen, A., Nakanishi, K., Tanaka, N., Fiehn, O., Monolithic silica-based capillary reversed-phase liquid chromatography/electrospray mass spectrometry for plant metabolomics. Anal. Chem. 2003, 75, 6737-6740.
23. Walther, T. C., Mann, M., Mass spectrometry-based proteomics in cell biology. J. Cell Biol. 2010, 190, 491-500.
24. Fischer, R., Trudgian, D. C., Wright, C., Thomas, G. et al., Discovery of candidate serum proteomic and metabolomic biomarkers in ankylosing spondylitis. Mol. Cell. Proteomics 2012, 11, M111.013904.
25. Becker, S., Kortz, L., Helmschrodt, C., Thiery, J., Ceglarek, U., LC-MS-based metabolomics in the clinical laboratory. J. Chromatogr. B 2012, 883-884, 68-75.
26. Cox, J., Mann, M., Quantitative, high-resolution proteomics for data-driven systems biology. Annu. Rev. Biochem. 2011, 80, 273-299.
27. Wishart, D. S., Knox, C., Guo, A. C., Eisner, R. et al., HMDB: a knowledgebase for the human metabolome. Nucleic Acids Res. 2009, 37, D603-D610.
28. Wishart, D. S., Jewison, T., Guo, A. C., Wilson, M. et al., HMDB 3.0-The Human Metabolome Database in 2013. Nucleic Acids Res. 2013, 41, D801-D807.
29. Hardman, M., Makarov, A. A., Interfacing the orbitrap mass analyzer to an electrospray ion source. Anal. Chem. 2003, 75, 1699-1705.
30. Makarov, A., Denisov, E., Lange, O., Performance evaluation of a high-field Orbitrap mass analyzer. J. Am. Soc. Mass Spectrom. 2009, 20, 1391-1396.
31. Michalski, A., Damoc, E., Lange, O., Denisov, E. et al., Ultra high resolution linear ion trap Orbitrap mass spectrometer (Orbitrap Elite) facilitates top down LC MS/MS and versatile peptide fragmentation modes. Mol. Cell. Proteomics 2012, 11, O111.013698.
32. Tran, J. C., Zamdborg, L., Ahlf, D. R., Lee, J. E. et al., Mapping intact protein isoforms in discovery mode using top-down proteomics. Nature 2011, 480, 254-258.
33. Udeshi, N. D., Compton, P. D., Shabanowitz, J., Hunt, D. F., Rose, K. L., Methods for analyzing peptides and proteins on a chromatographic timescale by electron-transfer dissociation mass spectrometry. Nat. Protoc. 2008, 3, 1709-1717.
34. Siepen, J. A., Keevil, E. J., Knight, D., Hubbard, S. J., Prediction of missed cleavage sites in tryptic peptides aids protein identification in proteomics. J. Proteome Res. 2007, 6, 399-408.
35. Khanna, V., Ranganathan, S., Physiochemical property space distribution among human metabolites, drugs and toxins. BMC Bioinformatics 2009, 10(Suppl 15), S10.
36. Chalcraft, K. R., Lee, R., Mills, C., Britz-McKibbin, P., Virtual quantification of metabolites by capillary electrophoresis-electrospray ionization-mass spectrometry: predicting ionization efficiency without chemical standards. Anal. Chem. 2009, 81, 2506-2515.
37. Rosenling, T., Stoop, M. P., Smolinska, A., Muilwijk, B. et al., The impact of delayed storage on the measured proteome and metabolome of human cerebrospinal fluid. Clin. Chem. 2011, 57, 1703-1711.
38. Gika, H. G., Theodoridis, G. A., Wilson, I. D., Liquid chromatography and ultra-performance liquid chromato-graphy-mass spectrometry fingerprinting of human urine: sample stability under different handling and storage conditions for metabonomics studies. J. Chromatogr. A 2008, 1189, 314-322.
39. Dunn, W. B., Ellis, D. I., Metabolomics: current analytical platforms and methodologies. Trends Anal. Chem. 2005, 24, 285-294.
40. Zivkovic, A. M., Wiest, M. M., Nguyen, U. T., Davis, R. et al., Effects of sample handling and storage on quantitative lipid analysis in human serum. Metabolomics 2009, 5, 507-516.
41. Want, E. J., Wilson, I. D., Gika, H., Theodoridis, G. et al., Global metabolic profiling procedures for urine using UPLC-MS. Nat. Protoc. 2010, 5, 1005-1018.
42. Bottcher, C., Roepenack-Lahaye, E. V., Willscher, E., Scheel, D., Clemens, S., Evaluation of matrix effects in metabolite profiling based on capillary liquid chromatography electrospray ionization quadrupole time-of-flight mass spectrometry. Anal. Chem. 2007, 79, 1507-1513.
43. Klose, J., Protein mapping by combined isoelectric focusing and electrophoresis of mouse tissues. A novel approach to testing for induced point mutations in mammals. Humangenetik 1975, 26, 231-243.
44. Hustoft, H. K., Reubsaet, L., Greibrokk, T., Lundanes, E., Malerod, H., Critical assessment of accelerating trypsination methods. J. Pharm. Biomed. Anal. 2011, 56, 1069-1078.
45. Wisniewski, J. R., Zougman, A., Nagaraj, N., Mann, M., Universal sample preparation method for proteome analysis. Nat. Methods 2009, 6, 359-362.
46. Kang, S. U., Fuchs, K., Sieghart, W., Pollak, A. et al., Gel-based mass spectrometric analysis of a strongly hydrophobic GABAA-receptor subunit containing four transmembrane domains. Nat. Protoc. 2009, 4, 1093-1102.
47. Wang, B., Malik, R., Nigg, E. A., Korner, R., Evaluation of the low-specificity protease elastase for large-scale phosphoproteome analysis. Anal. Chem. 2008, 80, 9526-9533.
48. Shevchenko, A., Tomas, H., Havlis, J., Olsen, J. V., Mann, M., In-gel digestion for mass spectrometric characterization of proteins and proteomes. Nat. Protoc. 2006, 1, 2856-2860.
49. Friedman, D. B., Andacht, T. M., Bunger, M. K., Chien, A. S. et al., The ABRF Proteomics Research Group studies: educational exercises for qualitative and quantitative proteomic analyses. Proteomics 2011, 11, 1371-1381.
50. Simpson, H., Berthemy, A., Buhrman, D., Burton, R. et al., High throughput liquid chromatography mass spectrometry bioanalysis using 96-well disk solid phase extraction plate for the sample preparation. Rapid Commun. Mass Spectrom. 1998, 12, 75-82.
51. Wessel, D., Flugge, U. I., A method for the quantitative recovery of protein in dilute solution in the presence of detergents and lipids. Anal. Biochem. 1984, 138, 141-143.
52. Michopoulos, F., Lai, L., Gika, H., Theodoridis, G., Wilson, I., UPLC-MS-based analysis of human plasma for metabonomics using solvent precipitation or solid phase extraction. J. Proteome Res. 2009, 8, 2114-2121.
53. Lorenz, M. A., Burant, C. F., Kennedy, R. T., Reducing time and increasing sensitivity in sample preparation for adherent mammalian cell metabolomics. Anal. Chem. 2011, 83, 3406-3414.
54. Bruce, S. J., Tavazzi, I., Parisod, V., Rezzi, S. et al., Investigation of human blood plasma sample preparation for performing metabolomics using ultrahigh performance liquid chromatography/mass spectrometry. Anal. Chem. 2009, 81, 3285-3296.
55. Geiger, T., Wehner, A., Schaab, C., Cox, J., Mann, M., Comparative proteomic analysis of eleven common cell lines reveals ubiquitous but varying expression of most proteins. Mol. Cell. Proteomics 2012, 11, M111.014050.
56. Cutillas, P. R., Principles of nanoflow liquid chromatography and applications to proteomics. Curr. Nanosci. 2005, 1, 65-71.
57. Schmidt, A., Karas, M., Dulcks, T., 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. 2003, 14, 492-500.
58. Griffiths, W. J., Liu, S., Yang, Y., Purdy, R. H., Sjovall, J., Nano-electrospray tandem mass spectrometry for the analysis of neurosteroid sulphates. Rapid Commun. Mass Spectrom. 1999, 13, 1595-1610.
59. Mizuno, H., Tsuyama, N., Date, S., Harada, T., Masujima, T., Live single-cell metabolomics of tryptophan and histidine metabolites in a rat basophil leukemia cell. Anal. Sci. 2008, 24, 1525-1527.
60. Michopoulos, F., Theodoridis, G., Smith, C. J., Wilson, I. D., Metabolite profiles from dried biofluid spots for metabonomic studies using UPLC combined with oaToF-MS. J. Proteome Res. 2010, 9, 3328-3334.
61. Lu, W., Bennett, B. D., Rabinowitz, J. D., Analytical strategies for LC-MS-based targeted metabolomics. J. Chromatogr. B 2008, 871, 236-242.
62. Ombrone, D., Salvatore, F., Ruoppolo, M., Quantitative liquid chromatography coupled with tandem mass spectrometry analysis of urinary acylglycines: application to the diagnosis of inborn errors of metabolism. Anal. Biochem. 2011, 417, 122-128.
63. t-Kindt, R., Scheltema, R. A., Jankevics, A., Brunker, K. et al., Metabolomics to unveil and understand phenotypic diversity between pathogen populations. PLoS Neglect Trop. D 2010, 4, e904.
64. Bajad, S. U., Lu, W., Kimball, E. H., Yuan, J. et al., Separation and quantitation of water soluble cellular metabolites by hydrophilic interaction chromatography-tandem mass spectrometry. J. Chromatogr. A 2006, 1125, 76-88.
65. Buszewski, B., Noga, S., Hydrophilic interaction liquid chromatography (HILIC)-a powerful separation technique. Anal. Bioanal. Chem. 2012, 402, 231-247.
66. Duarte, I. F., Legido-Quigley, C., Parker, D. A., Swann, J. R. et al., Identification of metabolites in human hepatic bile using 800 MHz 1H NMR spectroscopy, HPLC-NMR/MS and UPLC-MS. Mol. Biosyst. 2009, 5, 180-190.
67. Nakayama, F., Nakagaki, M., Quantitative determination of bile acids in bile with reversed-phase high-performance liquid chromatography. J. Chromatogr. 1980, 183, 287-293.
68. Ikegami, T., Horie, K., Saad, N., Hosoya, K. et al., Highly efficient analysis of underivatized carbohydrates using monolithic-silica-based capillary hydrophilic interaction (HILIC) HPLC. Anal. Bioanal. Chem. 2008, 391, 2533-2542.
69. Peng, M., Liu, L., Jiang, M., Liang, C. et al., Measurement of free carnitine and acylcarnitines in plasma by HILIC-ESI-MS/MS without derivatization. J. Chromatogr. B 2013, 932C, 12-18.
70. Kumar, A., Hart, J. P., McCalley, D. V., Determination of catecholamines in urine using hydrophilic interaction chromatography with electrochemical detection. J. Chromatogr. A 2011, 1218, 3854-3861.
71. Schwertner, H. A., Valtier, S., Bebarta, V. S., Liquid chromatographic mass spectrometric (LC/MS/MS) determination of plasma hydroxocobalamin and cyanocobalamin concentrations after hydroxocobalamin antidote treatment for cyanide poisoning. J. Chromatogr. B 2012, 905, 10-16.
72. Mayer, W. J., McCarthy, J. P., Greenberg, M. S., The determination of oxalic acid in urine by high performance liquid chromatography with electrochemical detection. J. Chromatogr. Sci. 1979, 17, 656-660.
73. Kitanovski, Z., Grgic, I., Veber, M., Characterization of carboxylic acids in atmospheric aerosols using hydrophilic interaction liquid chromatography tandem mass spectrometry. J. Chromatogr. A 2011, 1218, 4417-4425.
74. Tsuzuki, W., Ushida, K., Preparative separation of cis- and trans-isomers of unsaturated fatty acid methyl esters contained in edible oils by reversed-phase high-performance liquid chromatography. Lipids 2009, 44, 373-379.
75. t-Kindt, R., Jankevics, A., Scheltema, R. A., Zheng, L. et al., Towards an unbiased metabolic profiling of protozoan parasites: optimisation of a Leishmania sampling protocol for HILIC-orbitrap analysis. Anal. Bioanal. Chem. 2010, 398, 2059-2069.
76. Tyrefors, N., Hyllbrant, B., Ekman, L., Johansson, M., Langstrom, B., Determination of morphine, morphine-3-glucuronide and morphine-6-glucuronide in human serum by solid-phase extraction and liquid chromatography-mass spectrometry with electrospray ionisation. J. Chromatogr. A 1996, 729, 279-285.
77. Kolmonen, M., Leinonen, A., Kuuranne, T., Pelander, A., Ojanpera, I., Hydrophilic interaction liquid chromatography and accurate mass measurement for quantification and confirmation of morphine, codeine and their glucuronide conjugates in human urine. J. Chromatogr. B 2010, 878, 2959-2966.
78. Plattner, R. D., Spencer, G. F., Kleiman, R., Triglyceride separation by reverse phase high-performance liquid-chromatography. J. Am. Oil Chem. Soc. 1977, 54, 511-515.
79. Zheng, L. A., T'Kind, R., Decuypere, S., von Freyend, S. J. et al., Profiling of lipids in Leishmania donovani using hydrophilic interaction chromatography in combination with Fourier transform mass spectrometry. Rapid Commun. Mass Spectrom. 2010, 24, 2074-2082.
80. Nour, V., Trandafir, I., Ionica, M. E., HPLC organic acid analysis in different citrus juices under reversed phase conditions. Not. Bot. Horti Agrobo. 2010, 38, 44-48.
81. Huang, Y., Tian, Y., Zhang, Z. J., Peng, C., A HILIC-MS/MS method for the simultaneous determination of seven organic acids in rat urine as biomarkers of exposure to realgar. J. Chromatogr. B 2012, 905, 37-42.
82. Yanes, E. G., Lovett, D. P., High-throughput bioanalytical method for analysis of synthetic cannabinoid metabolites in urine using salting-out sample preparation and LC-MS/MS. J. Chromatogr. B 2012, 909, 42-50.
83. Liao, J. C., Hoffman, N. E., Barboriak, J. J., Roth, D. A., High-performance liquid chromatography of pyruvic and alpha-ketoglutaric acids and its application to urine samples. Clin. Chem. 1977, 23, 802-805.
84. Montenegro, P., Valente, I. M., Goncalves, L. M., Rodrigues, J. A., Barros, A. A., Single determination of alpha-ketoglutaric acid and pyruvic acid in beer by HPLC with UV detection. Anal. Methods 2011, 3, 1207-1212.
85. Lin, W. S., Huang, M. Q., Xue, X. H., Bertelsen, K. et al., A highly sensitive and selective method for the determination of leukotriene B-4 (LTB4) in ex vivo stimulated human plasma by ultra fast liquid chromatography-tandem mass spectrometry. J. Chromatogr. B 2013, 925, 54-62.
86. Self, W. T., Tsai, L., Stadtman, T. C., Synthesis and characterization of selenotrisulfide-derivatives of lipoic acid and lipoamide. Proc. Natl. Acad. Sci. USA 2000, 97, 12481-12486.
87. Marrubini, G., Mendoza, B. E. C., Massolini, G., Separation of purine and pyrimidine bases and nucleosides by hydrophilic interaction chromatography. J. Sep. Sci. 2010, 33, 803-816.
88. Aebersold, R., Mann, M., Mass spectrometry-based proteomics. Nature 2003, 422, 198-207.
89. Boersema, P. J., Mohammed, S., Heck, A. J. R., Hydrophilic interaction liquid chromatography (HILIC) in proteomics. Anal. Bioanal. Chem. 2008, 391, 151-159.
90. Brouwers, J. F. H. M., Gadella, B. M., van Golde, L. M. G., Tielens, A. G. M., Quantitative analysis of phosphatidylcholine molecular species using HPLC and light scattering detection. J. Lipid Res. 1998, 39, 344-353.
91. Zhu, C., Dane, A., Spijksma, G., Wang, M. et al., An efficient hydrophilic interaction liquid chromatography separation of 7 phospholipid classes based on a diol column. J. Chromatogr. A 2012, 1220, 26-34.
92. Gika, H., Theodoridis, G., Mattivi, F., Vrhovsek, U., Pappa-Louisi, A., Hydrophilic interaction ultra performance liquid chromatography retention prediction under gradient elution. Anal. Bioanal. Chem. 2012, 404, 701-709.
93. Whelan, T. J., Gray, M. J., Slonecker, P. J., Shalliker, R. A., Wilson, M. A., Study of the selectivity of reversed-phase columns for the separation of polycarboxylic acids and polyphenol compounds. J. Chromatogr. A 2005, 1097, 148-156.
94. Gouda, A., Fateen, E., Nazim, W., Porphyrins profile by high performance liquid chromatography/electrospray ionization tandem mass spectrometry for the diagnosis of porphyria. J. Inherit. Metab. Dis. 2012, 35, S161-S161.
95. Masoodi, M., Nicolaou, A., Lipidomic analysis of twenty-seven prostanoids and isoprostanes by liquid chromatography/electrospray tandem mass spectrometry. Rapid Commun. Mass Spectrom. 2006, 20, 3023-3029.
96. Montalvo, B. C., Villar, C. I., Hornillos, R. C., Diez, L. P., Determination of pterins in urine by high-performance liquid chromatography on C18 columns conditioned with cetyltrimethylammonium bromide. J. Chromatogr. 1988, 458, 217-223.
97. Shi, Z. G., Wu, Y. B., Luo, Y. B., Feng, Y. Q., Analysis of pterins in urine by HILIC. Chromatographia 2010, 71, 761-768.
98. Pasakova, I., Gladziszova, M., Charvatova, J., Stariat, J. et al., Use of different stationary phases for separation of isoniazid, its metabolites and vitamin B6 forms. J. Sep. Sci. 2011, 34, 1357-1365.
99. Krcmova, L., Urbanek, L., Solichova, D., Kasparova, M. et al., HPLC method for simultaneous determination of retinoids and tocopherols in human serum for monitoring of anticancer therapy. J. Sep. Sci. 2009, 32, 2804-2811.
100. Sullards, M. C., Liu, Y., Chen, Y., Merrill, A. H., Jr., Analysis of mammalian sphingolipids by liquid chromatography tandem mass spectrometry (LC-MS/MS) and tissue imaging mass spectrometry (TIMS). Biochim. Biophys. Acta 2011, 1811, 838-853.
101. Scherer, M., Leuthauser-Jaschinski, K., Ecker, J., Schmitz, G., Liebisch, G., A rapid and quantitative LC-MS/MS method to profile sphingolipids. J. Lipid Res. 2010, 51, 2001-2011.
102. Chen, Z., Li, J., Zhang, J., Xing, X. et al., Simultaneous determination of hair cortisol, cortisone and DHEAS with liquid chromatography-electrospray ionization-tandem mass spectrometry in negative mode. J. Chromatogr. B 2013, 929, 187-194.
103. Antonio, C., Larson, T., Gilday, A., Graham, I. et al., Hydrophilic interaction chromatography/electrospray mass spectrometry analysis of carbohydrate-related metabolites from Arabidopsis thaliana leaf tissue. Rapid Commun. Mass Spectrom. 2008, 22, 1399-1407.
104. Yang, S., Sadilek, M., Lidstrom, M. E., Streamlined pentafluorophenylpropyl column liquid chromatography-tandem quadrupole mass spectrometry and global C-13-labeled internal standards improve performance for quantitative metabolomics in bacteria. J. Chromatogr. A 2010, 1217, 7401-7410.
105. Imbert, L., Gaudin, M., Libong, D., Touboul, D. et al., Comparison of electrospray ionization, atmospheric pressure chemical ionization and atmospheric pressure photoionization for a lipidomic analysis of Leishmania donovani. J. Chromatogr. A 2012, 1242, 75-83.
106. Takats, Z., Wiseman, J. M., Gologan, B., Cooks, R. G., Mass spectrometry sampling under ambient conditions with desorption electrospray ionization. Science 2004, 306, 471-473.
107. Cody, R. B., Laramee, J. A., Durst, H. D., Versatile new ion source for the analysis of materials in open air under ambient conditions. Anal. Chem. 2005, 77, 2297-2302.
108. Haapala, M., Pol, J., Saarela, V., Arvola, V. et al., Desorption atmospheric pressure photoionization. Anal. Chem. 2007, 79, 7867-7872.
109. Nemes, P., Vertes, A., Laser ablation electrospray ionization for atmospheric pressure, in vivo, and imaging mass spectrometry. Anal. Chem. 2007, 79, 8098-8106.
110. Harris, G. A., Nyadong, L., Fernandez, F. M., Recent developments in ambient ionization techniques for analytical mass spectrometry. Analyst 2008, 133, 1297-1301.
111. Yates, J. R., Ruse, C. I., Nakorchevsky, A., Proteomics by mass spectrometry: approaches, advances, and applications. Annu. Rev. Biomed. Eng. 2009, 11, 49-79.
112. Bensimon, A., Heck, A. J., Aebersold, R., Mass spectro-metry-based proteomics and network biology. Annu. Rev. Biochem. 2012, 81, 379-405.
113. Cox, J., Mann, M., Computational principles of determining and improving mass precision and accuracy for proteome measurements in an Orbitrap. J. Am. Soc. Mass Spectrom. 2009, 20, 1477-1485.
114. Oppermann, M., Damoc, N. E., Crone, C., Moehring, T. et al., High precision measurement and fragmentation analysis for metabolite identification. Methods Mol. Biol. 2012, 860, 145-156.
115. Psychogios, N., Hau, D. D., Peng, J., Guo, A. C. et al., The human serum metabolome. PLoS One 2011, 6, e16957.
116. Perkins, D. N., Pappin, D. J., Creasy, D. M., Cottrell, J. S., Probability-based protein identification by searching sequence databases using mass spectrometry data. Electrophoresis 1999, 20, 3551-3567.
117. Cox, J., Mann, M., MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification. Nat. Biotechnol. 2008, 26, 1367-1372.
118. Nesvizhskii, A. I., A survey of computational methods and error rate estimation procedures for peptide and protein identification in shotgun proteomics. J. Proteomics 2010, 73, 2092-2123.
119. Trudgian, D. C., Thomas, B., McGowan, S. J., Kessler, B. M. et al., CPFP: a central proteomics facilities pipeline. Bioinformatics 2010, 26, 1131-1132.
120. Miladinovic, S. M., Kozhinov, A. N., Gorshkov, M. V., Tsybin, Y. O., On the utility of isotopic fine structure mass spectrometry in protein identification. Anal. Chem. 2012, 84, 4042-4051.
121. Wolf, S., Schmidt, S., Muller-Hannemann, M., Neumann, S., In silico fragmentation for computer assisted identification of metabolite mass spectra. BMC Bioinformatics 2010, 11, 148.
122. Hutchens, T. W., Yip, T. T., New desorption strategies for the mass-spectrometric analysis of macromolecules. Rapid Commun. Mass Spectrom. 1993, 7, 576-580.