Summary of Study ST002179

This data is available at the NIH Common Fund's National Metabolomics Data Repository (NMDR) website, the Metabolomics Workbench, https://www.metabolomicsworkbench.org, where it has been assigned Project ID PR001387. The data can be accessed directly via it's Project DOI: 10.21228/M8FB0C This work is supported by NIH grant, U2C- DK119886.

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This study contains a large results data set and is not available in the mwTab file. It is only available for download via FTP as data file(s) here.

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Study IDST002179
Study TitleImpact of nitisinone on the cerebrospinal fluid metabolome of a murine model of alkaptonuria
Study SummaryBackground: Nitisinone induced hypertyrosinaemia is well documented in Alkaptonuria (AKU), and there is uncertainty over whether it may contribute to a decline in cognitive function and or mood by altering neurotransmitter metabolism. The aim of this work was to evaluate the impact of nitisinone on the cerebrospinal fluid (CSF) metabolome in a murine model of AKU, with a view to providing additional insight into metabolic changes that occur following treatment with nitisinone. Methods: 17 CSF samples were collected from BALB/c Hgd-/-mice (n=8, treated with nitisinone – 4 mg/L and n=9, no treatment). Samples were diluted 1:1 with deionised water and analysed using a 1290 Infinity II liquid chromatography system coupled to a 6550 quadrupole time-of-flight mass spectrometry (Agilent, Cheadle, UK). Raw data were processed using a targeted feature extraction algorithm and an established in-house accurate mass retention time database. Matched entities (±10 ppm theoretical accurate mass and ±0.3 minutes retention time window) were filtered based on their frequency and variability. Experimental groups were compared using a moderated t-test with Benjamini-Hochberg false-discovery rate adjustment. Results: Tyrosine, acetyl-tyrosine, γ-glutamyl-tyrosine, p-hydroxyphenylacetic acid and 3-(4-hydroxyphenyl)lactic acid were shown to increase in abundance (log2 fold change 2.6-6.9, 3/5 were significant p<0.05) in the mice that received nitisinone. Several other metabolites of interest were matched but no significant differences were observed, including the aromatic amino acids phenylalanine and tryptophan, and monoamine metabolites adrenaline, 3-methoxy-4-hydroxyphenylglycol and octopamine. Conclusions: Evaluation of the CSF metabolome of a murine model of AKU showed a significant difference in the abundance of a limited number of metabolites. None of these have been reported in CSF from a murine model of AKU previously. Moreover this study confirms that some monoamine metabolites do not appear to be altered following nitisinone therapy.
Institute
University of Liverpool Institute of Life Course & Medical Sciences
Last NameDavison
First NameAndrew
Address1. Department of Clinical Biochemistry and Metabolic Medicine, Liverpool Clinical Laboratories, Liverpool University Hospitals NHS Foundation Trust, Liverpool, UK; 2. Department of Musculoskeletal and Ageing Science, Institute of Life Course and Medical Sciences, University of Liverpool, Liverpool, UK 3. School of Exercise Science, Liverpool John Moores University, Liverpool, UK
Emailandrew.davison@liverpoolft.nhs.uk
Phone0151 706 4011
Submit Date2022-05-13
Num Groups2
Total Subjects17
Raw Data AvailableYes
Raw Data File Type(s)d, mzML
Analysis Type DetailLC-MS
Release Date2022-06-08
Release Version1
Andrew Davison Andrew Davison
https://dx.doi.org/10.21228/M8FB0C
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

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Combined analysis:

Analysis ID AN003568 AN003569
Analysis type MS MS
Chromatography type Reversed phase Reversed phase
Chromatography system Agilent Infinity II Agilent Infinity II
Column Atlantis dC18 (3.0x100mm,3m,Waters,UK) Atlantis dC18 (3.0x100mm,3m,Waters,UK)
MS Type ESI ESI
MS instrument type Triple quadrupole Triple quadrupole
MS instrument name Agilent 6550 QTOF Agilent 6550 QTOF
Ion Mode POSITIVE NEGATIVE
Units area area

MS:

MS ID:MS003325
Analysis ID:AN003568
Instrument Name:Agilent 6550 QTOF
Instrument Type:Triple quadrupole
MS Type:ESI
MS Comments:Quadrupole time-of-flight mass spectrometry (QTOF-MS) conditions An Agilent 6550 QTOF-MS equipped with a dual jet stream electrospray ionisation source was operated in 2GHz mode, over the mass range of 50-1700, in negative and positive polarities. A reference mass correction solution was continually infused at a flow rate of 0.5 mL/min via an external isocratic pump (Agilent, UK) for constant mass correction (see Preparation of reference mass correction solution). Capillary and fragmentor voltages were 4000 V and 380 V, respectively. Desolvation gas temperature was 200 °C with flow rate at 15 L/min. The sheath gas temperature was 300 °C with flow rate at 12 L/min and nebulizer pressure was 40 psi and nozzle voltage 1000 V. Data acquisition rate was 3 spectra/s. Preparation of reference mass correction solution Reference mass correction solution was prepared in 95:5 methanol:water containing 5 mmol/L purine (CAS No. 120-73-0), 100 mmol/L trifluoroacetic acid ammonium salt (TFA, CAS No. 3336-58-1) and 2.5 mmol/L hexakis(1H, 1H, 3H-tetrafluoropropoxy)phosphazine (HP-0921, CAS No. 58943-98-9) (Agilent, Cheadle, UK). Reference ions monitored were: purine (m/z 121.0509) and HP-0921 (m/z 922.0098) (positive polarity) and TFA (m/z 112.9856), purine (m/z 119.0363) and HP-0921 (HP-0921 + formate adduct: m/z 966.0007) (negative polarity). Data acquisition and handling parameters Data were acquired using Acquisition (Build 06.00, Agilent, Cheadle, UK). Quality checks and processing of raw data files (Agilent ‘.d’ files) were performed with Qualitative Analysis software (Build 07.00, Agilent, Cheadle, UK). Extracted ion chromatograms of reference masses were performed to check mass accuracy remained <5 ppm throughout the run and that the reference ion signal did not drop out during the chromatographic run. In addition, to check chromatographic reproducibility binary pump pressure curves for injections across each analytical sequence were overlaid. Mass accuracy and chromatographic reproducibility were acceptable for all experiments performed. Acquired profiling sample data were mined for signals against an established in-house AMRT database of compounds (contains theoretical accurate mass, measured retention time, and empirical formula for 469 intermediary metabolites, MW 72-785) using ‘targeted feature extraction’ with Profinder software (Build 08.00, Agilent, Cheadle, UK). Targeted feature extraction uses the molecular formulae from the AMRT database to extract and group spectral signals (i.e. adducts, isotopes and multimers) that correspond to individual database compounds. Feature extraction employed a window of theoretical accurate mass ±10 ppm and database retention time ±0.3 min. Allowed species were: H+, Na+ and NH4+ (positive polarity) and H- and CHO2- (negative polarity). Dimers were allowed for both polarities. Charge state range was 1-2. Data files were then exported from Profinder as ‘.CEF’ files as a whole batch for each profiling experiment and imported to Mass Profiler Professional (MPP) software for statistical analysis (Build 14.5, Agilent, Cheadle, UK).
Ion Mode:POSITIVE
  
MS ID:MS003326
Analysis ID:AN003569
Instrument Name:Agilent 6550 QTOF
Instrument Type:Triple quadrupole
MS Type:ESI
MS Comments:Quadrupole time-of-flight mass spectrometry (QTOF-MS) conditions An Agilent 6550 QTOF-MS equipped with a dual jet stream electrospray ionisation source was operated in 2GHz mode, over the mass range of 50-1700, in negative and positive polarities. A reference mass correction solution was continually infused at a flow rate of 0.5 mL/min via an external isocratic pump (Agilent, UK) for constant mass correction (see Preparation of reference mass correction solution). Capillary and fragmentor voltages were 4000 V and 380 V, respectively. Desolvation gas temperature was 200 °C with flow rate at 15 L/min. The sheath gas temperature was 300 °C with flow rate at 12 L/min and nebulizer pressure was 40 psi and nozzle voltage 1000 V. Data acquisition rate was 3 spectra/s. Preparation of reference mass correction solution Reference mass correction solution was prepared in 95:5 methanol:water containing 5 mmol/L purine (CAS No. 120-73-0), 100 mmol/L trifluoroacetic acid ammonium salt (TFA, CAS No. 3336-58-1) and 2.5 mmol/L hexakis(1H, 1H, 3H-tetrafluoropropoxy)phosphazine (HP-0921, CAS No. 58943-98-9) (Agilent, Cheadle, UK). Reference ions monitored were: purine (m/z 121.0509) and HP-0921 (m/z 922.0098) (positive polarity) and TFA (m/z 112.9856), purine (m/z 119.0363) and HP-0921 (HP-0921 + formate adduct: m/z 966.0007) (negative polarity). Data acquisition and handling parameters Data were acquired using Acquisition (Build 06.00, Agilent, Cheadle, UK). Quality checks and processing of raw data files (Agilent ‘.d’ files) were performed with Qualitative Analysis software (Build 07.00, Agilent, Cheadle, UK). Extracted ion chromatograms of reference masses were performed to check mass accuracy remained <5 ppm throughout the run and that the reference ion signal did not drop out during the chromatographic run. In addition, to check chromatographic reproducibility binary pump pressure curves for injections across each analytical sequence were overlaid. Mass accuracy and chromatographic reproducibility were acceptable for all experiments performed. Acquired profiling sample data were mined for signals against an established in-house AMRT database of compounds (contains theoretical accurate mass, measured retention time, and empirical formula for 469 intermediary metabolites, MW 72-785) using ‘targeted feature extraction’ with Profinder software (Build 08.00, Agilent, Cheadle, UK). Targeted feature extraction uses the molecular formulae from the AMRT database to extract and group spectral signals (i.e. adducts, isotopes and multimers) that correspond to individual database compounds. Feature extraction employed a window of theoretical accurate mass ±10 ppm and database retention time ±0.3 min. Allowed species were: H+, Na+ and NH4+ (positive polarity) and H- and CHO2- (negative polarity). Dimers were allowed for both polarities. Charge state range was 1-2. Data files were then exported from Profinder as ‘.CEF’ files as a whole batch for each profiling experiment and imported to Mass Profiler Professional (MPP) software for statistical analysis (Build 14.5, Agilent, Cheadle, UK).
Ion Mode:NEGATIVE
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