A comprehensive urinary metabolomic approach for identifying kidney cancer

Kind, Tobias; Tolstikov, Vladimir; Fiehn, Oliver; Weiss, Robert H.

doi:10.1016/j.ab.2007.01.028

Cited by 423 publications

(355 citation statements)

References 27 publications

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“…Here we employed a 60 m long column with a nominal maximum theoretical efficiency N max, theor 5 240 000. This column is longer than those typically used in GC-TOFMS metabolomics analysis [12], so the separation was performed at the speed optimized flow rate [13]. Using the speed optimized flow rate increases speed by 41% above the speed corresponding to the maximum column efficiency, N, with a corresponding 6% drop in N. The initial and final temperatures in the temperature program used in the present study were based on the conditions described in Ref.…”

Section: Resultsmentioning

confidence: 99%

“…Using the speed optimized flow rate increases speed by 41% above the speed corresponding to the maximum column efficiency, N, with a corresponding 6% drop in N. The initial and final temperatures in the temperature program used in the present study were based on the conditions described in Ref. [12], but here the temperature ramp was significantly shallower to achieve optimal peak capacity. We utilized a normalized temperature ramp of $101C/t M 5 41C/min.…”

Section: Resultsmentioning

confidence: 99%

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Varietal characterization of hop (Humulus lupulus L.) by GC–MS analysis of hop cone extracts

Shellie

Poynter

et al. 2009

J of Separation Science

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An approach is described for use in the varietal characterization of hop (Humulus lupulus L.) varieties. The study focuses on commercial hop varieties and was timed to coincide with the 2008 commercial hop harvest in Tasmania, Australia. Analysis of hop extracts was performed using GC-MS. A 60 m capillary column was employed to increase efficiency to permit the use of a quadrupole mass spectrometer in place of a time of flight mass spectrometer that is more commonly used for this type of analysis. A set of characterization functions were derived from discriminant analysis which were highly suitable for varietal characterization of the eight commercial varieties included in the study, namely Willamette, Victoria, Pride of Ringwood, Cascade, Southern Hallertau, Millennium, Southern Saaz, and Super Pride.

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Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

Varietal characterization of hop (Humulus lupulus L.) by GC–MS analysis of hop cone extracts

Shellie

Poynter

et al. 2009

J of Separation Science

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“…Three feasible nucleoside structures are listed in the RNA database (5-oxyacetic acid methyl ester-2-uridine, 5-carboxy-hydroxymethyl methyl ester-1504 BULLINGER ET AL. 6 -methyl-N 6 -threonylcarbamoyladenosine.© Figure© 3© exemplarily shows©the©analytical©benefit©of©higher©fragmentation steps© in© the© analysis© of© complex© ribonucleosides.© The unknown© metabolite© showed©an© almost© unspecific© fragmentation© pattern© in© the© auto-LC© IT© MS 3© runs.© Including© the information© of© the© MS 4© step© from© syringe© pump© infusion© IT MS n experiments,© it© was© possible© to© identify© the© basic© hetero© -cycle© of© the© analyzed© compound© since© the© MS 4© spectrum© was identical© to© the© MS 3© spectrum© of© the© commercially© available modified© nucleoside© N 6 -methyladenosine.© Accordingly,© the unknown© compound© could© be© identified© as© N 6 -methyl-N 6 -threonylcarbamoyladenosine© (m 6 t 6 A).© To© the© authors'© best knowledge,© this© article© describes© for© the© first© time© the© identification© of© this© hypermodified© nucleoside© in© human© urine.…”

Section: Modified Nucleosidesmentioning

confidence: 99%

“…Recently, the metabolome, represented by the end products of gene-/protein expression and the biochemical phenotype of a cell or tissue, has experienced increasing interest [5][6][7].…”

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confidence: 99%

Identification of urinary modified nucleosides and ribosylated metabolites in humans via combined ESI-FTICR MS and ESI-IT MS analysis

Bullinger

Fux

Nicholson

et al. 2008

J. Am. Soc. Mass Spectrom.

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The physiological response of the human body to several diseases can be reflected by the metabolite pattern in biological fluids. Cancer, like other diseases accompanied by metabolic disorders, causes characteristic effects on cell turnover rate, activity of modifying enzymes, and RNA/DNA modifications. This results in an altered excretion of modified nucleosides and biochemically related compounds. In the course of our metabolic profiling project, we screened 24-h urine of patients suffering from lung, rectal, or head and neck cancer for previously unknown ribosylated metabolites. Therefore, we developed a sample preparation procedure based on boronate affinity chromatography followed by additional prepurification with preparative TLC. The isolated metabolites were analyzed by ion trap mass spectrometry (IT MS) and Fourier transform ion cyclotron resonance mass spectrometry (FTICR MS). IT MS was applied for LC-auto MS 3 screening runs and Msn(n = 4-6) syringe pump infusion experiments, yielding characteristic fragmentation patterns. FTICR MS measurements enabled the calculation of corresponding molecular formulae based on accurate mass determination (mass accuracy: 1-5 ppm for external and sub-ppm values for internal calibration).We were able to identify 22 metabolites deriving from cellular RNA metabolism and related metabolic pathways like histidine metabolism, purine biosynthesis, methionine/polyamine cycle, and nicotinate/nicotinamide metabolism. The compounds l-ribosyl-3-hydroxypyridinium, 1-ribosyl-pyridinium, and 3-ribosyl-1-methyl-Lhistidinium as well as a series of ribosylated histamines, conjugated to carboxylic acids at the N'

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“…[7][8][9][10][11][12] Pasikanti et al 13 reported a method for GC-MS profiling of human urine where 150 putative metabolites were detected and 144 of them were assigned a name by using retention indices and mass spectral matching scores with the NIST library. However, GC-MS is limited to analysing non-polar and volatile compounds.…”

Section: Introductionmentioning

confidence: 99%

Evaluation of Coupling Reversed Phase, Aqueous Normal Phase, and Hydrophilic Interaction Liquid Chromatography with Orbitrap Mass Spectrometry for Metabolomic Studies of Human Urine

et al. 2012

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In this study, we assessed three liquid chromatographic platforms: reversed phase (RP), aqueous normal phase (ANP) and hydrophilic interaction (HILIC) for the analysis of polar metabolite standard mixtures and for their coverage of urinary metabolites. The two zwitterionic HILIC columns showed high-quality chromatographic performance for metabolite standards, improved separation for isomers and the greatest coverage of polar metabolites in urine. In contrast, on the reversed phase column most metabolites eluted very rapidly with little or no separation. Using an Exactive Orbitrap mass spectrometer with a HILIC liquid chromatographic platform approximately 800 metabolites with repeatable peak areas (RSD ≤ 25%) could be putatively identified in human urine, by elemental composition assignment within a 3 ppm mass error.The ability of the methodology for the verification of non-molecular ions, which arise from adduct formation, and the possibility of distinguishing isomers could also be demonstrated. Careful examination of the raw data and the use of masses for predicted metabolites produced an extension of the metabolite list for human urine.

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A comprehensive urinary metabolomic approach for identifying kidney cancer

Cited by 423 publications

References 27 publications

Varietal characterization of hop (Humulus lupulus L.) by GC–MS analysis of hop cone extracts

Varietal characterization of hop (Humulus lupulus L.) by GC–MS analysis of hop cone extracts

Identification of urinary modified nucleosides and ribosylated metabolites in humans via combined ESI-FTICR MS and ESI-IT MS analysis

Evaluation of Coupling Reversed Phase, Aqueous Normal Phase, and Hydrophilic Interaction Liquid Chromatography with Orbitrap Mass Spectrometry for Metabolomic Studies of Human Urine

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