Summary of Study ST001251

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 PR000838. The data can be accessed directly via it's Project DOI: 10.21228/M8C671 This work is supported by NIH grant, U2C- DK119886.

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Study IDST001251
Study TitleThe effects of a training program encompassing cold exposure, breathing exercises, and meditation on plasma metabomics during experimental human endotoxemia
Study TypeExperimental human endotoxemia study
Study SummaryStudy to investigate the effects of a training program encompassing cold exposure, breathing exercises, and meditation on plasma metabolomic during experimental human endotoxemia.
Institute
Radboud University Medical Centre
DepartmentIntensive Care Medicine
LaboratoryMetabolomic Discoveries (acquired by Metabolon in September 2017)
Last NameKox
First NameMatthijs
AddressIntensive Care Medicine (710), Geert Grooteplein 10
Emailmatthijs.kox@radboudumc.nl
Phone243653881
Submit Date2019-09-16
Num Groups2
Total Subjects24
Num Males24
Analysis Type DetailLC-MS
Release Date2019-10-04
Release Version1
Matthijs Kox Matthijs Kox
https://dx.doi.org/10.21228/M8C671
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

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Combined analysis:

Analysis ID AN002077
Analysis type MS
Chromatography type Reversed phase
Chromatography system Agilent 1290
Column Discovery HS F5-3 (15cm x 2.1 mm,3um) Supelco,Sigma Aldrich)
MS Type ESI
MS instrument type QTOF
MS instrument name Agilent 6540 QTOF
Ion Mode UNSPECIFIED
Units relative abundance

MS:

MS ID:MS001928
Analysis ID:AN002077
Instrument Name:Agilent 6540 QTOF
Instrument Type:QTOF
MS Type:ESI
MS Comments:The 6540 QTOF/MS Detector (Agilent) operated in both positive and negative ESI mode in a detection range of 50 to 1700 m/z at 2 GHz in extended dynamic range. The DualAJS ESI source was set to the following parameters: Gas temperature 200 °C, drying gas 8 L/min, nebulizer 35 psig, sheath gas temp: 350 °C, sheath gas flow 11 L/min, VCAp 3500 V and nozzle voltage of 0 V. Online calibration of the instrument was performed throughout the data acquisition using Agilent ES-TOF Reference Mass Solution Kit. Chromatograms were generated by the LC-MS instrument in .d format. Raw data were converted into mzXML and chromatogram peaks were extracted using XCMS v1.42.0 (https://pubs.acs.org/doi/10.1021/ac051437y), which was optimized using the IPO R package (https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-015-0562-8) with the following settings: peakwidth=c(10, 70), ppm= 20, snthresh=10, mzdiff=0.0034, prefilter=c(3, 100), noise=100, gapInit=0.8448, gapExtend=2.0544, bw=5, mzwid=0.015, minfrac=0.5, max=50. All further analyses were performed in R programming language, Metaboanalyst 4.0 (https://www.nature.com/articles/nprot.2011.319), and GraphPad Prism version 5.0 (GraphPad Software). IDEOM software (http://mzmatch.sourceforge.net/ideom.php; https://academic.oup.com/bioinformatics/article/28/7/1048/210126) was used to eliminate noise and for putative peak annotation by exact mass within ±10 ppm against the Metabolomic Discoveries in house metabolite library (https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0125044) in negative and positive ESI mode, respectively. Retention time prediction was applied to aid metabolite annotation.
Ion Mode:UNSPECIFIED
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