Summary of Study ST001268

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 PR000853. The data can be accessed directly via it's Project DOI: 10.21228/M8F108 This work is supported by NIH grant, U2C- DK119886.

See: https://www.metabolomicsworkbench.org/about/howtocite.php

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 IDST001268
Study TitleMetabolome data to annotate metabolite origins
Study SummaryPlasma metabolomics from HIV subjects and controls was incorporated with microbiome data to develop Annotation of Metabolite Origins via Networks (AMON).
Institute
University of Colorado Denver
DepartmentAnschutz Medical Campus
Last NameReisdorph
First NameNichole
Address12850 East Montview Blvd, Aurora, CO, 80045, USA
Emailnichole.reisdorph@ucdenver.edu
Phone3037249234
Submit Date2019-10-22
Total Subjects63
Raw Data AvailableYes
Raw Data File Type(s)d
Analysis Type DetailLC-MS
Release Date2019-10-11
Release Version1
Nichole Reisdorph Nichole Reisdorph
https://dx.doi.org/10.21228/M8F108
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

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Project:

Project ID:PR000853
Project DOI:doi: 10.21228/M8F108
Project Title:Integrating microbiome and metabolome data to annotate metabolite origins
Project Summary:Untargeted metabolomics of host-associated samples has yielded insights into mechanisms by which microbes modulate health. However, data interpretation is challenged by the complexity of origins of the small molecules measured, which can come from the host, microbes that live within the host, or from other exposures such as diet or the environment. We address this challenge through development of AMON: Annotation of Metabolite Origins via Networks. AMON is an open-source bioinformatics application that can be used to annotate which compounds in the metabolome could have been produced by bacteria present or the host, to evaluate pathway enrichment of host verses microbial metabolites, and to visualize which compounds may have been produced by host versus microbial enzymes in KEGG pathway maps.
Institute:University of Colorado Denver
Department:Anschutz Medical Campus
Last Name:Reisdorph
First Name:Nichole
Address:12850 East Montview Blvd, Aurora, CO, 80045, USA
Email:nichole.reisdorph@ucdenver.edu
Phone:3037249234
Funding Source:NIH

Subject:

Subject ID:SU001336
Subject Type:Human
Subject Species:Homo sapiens
Taxonomy ID:9606
Gender:Male and female

Factors:

Subject type: Human; Subject species: Homo sapiens (Factor headings shown in green)

mb_sample_id local_sample_id HIV
SA092075GLD066Negative
SA092076GLD065Negative
SA092077GLD045Negative
SA092078GLD018Negative
SA092079GLD017Negative
SA092080GLD063Negative
SA092081GLD062Negative
SA092082GLD051Negative
SA092083GLD056Negative
SA092084GLD060Negative
SA092085GLD061Negative
SA092086GLD070Negative
SA092087GLD071Negative
SA092088GLD048Negative
SA092089GLD074Negative
SA092090GLD046Negative
SA092091GLD002Negative
SA092092GLD032Negative
SA092093GLD008Negative
SA092094GLD012Negative
SA092095GLD049Negative
SA092096GLD011Negative
SA092097GLD013Negative
SA092098GLD010Negative
SA092099GLD053Positive
SA092100GLD047Positive
SA092101GLD050Positive
SA092102GLD069Positive
SA092103GLD079Positive
SA092104GLD080Positive
SA092105GLD073Positive
SA092106GLD072Positive
SA092107GLD055Positive
SA092108GLD057Positive
SA092109GLD054Positive
SA092110GLD039Positive
SA092111GLD019Positive
SA092112GLD016Positive
SA092113GLD020Positive
SA092114GLD021Positive
SA092115GLD022Positive
SA092116GLD014Positive
SA092117GLD009Positive
SA092118GLD004Positive
SA092119GLD003Positive
SA092120GLD005Positive
SA092121GLD006Positive
SA092122GLD007Positive
SA092123GLD023Positive
SA092124GLD026Positive
SA092125GLD040Positive
SA092126GLD001Positive
SA092127GLD041Positive
SA092128GLD042Positive
SA092129GLD043Positive
SA092130GLD037Positive
SA092131GLD036Positive
SA092132GLD028Positive
SA092133GLD027Positive
SA092134GLD029Positive
SA092135GLD030Positive
SA092136GLD031Positive
SA092137GLD044Positive
Showing results 1 to 63 of 63

Collection:

Collection ID:CO001330
Collection Summary:During a clinic visit, blood was drawn from HIV positive individuals and controls as previously described as part of a larger study of differences in the fecal microbiome in HIV positive and high risk populations [Caporaso JG, et al. QIIME allows analysis of high-throughput community sequencing data. Nat Methods. 2010;7:335–6. doi:10.1038/nmeth.f.303].
Sample Type:Blood (plasma)
Storage Conditions:-80℃

Treatment:

Treatment ID:TR001351
Treatment Summary:Three cohorts based on HIV status: (1) HIV-1 infection untreated; (2) chronic HIV-1 infection on long-term ART; (3) healthy controls (HIV-negative individuals both high and low risk for contracting HIV).

Sample Preparation:

Sampleprep ID:SP001344
Sampleprep Summary:100 µL of plasma spiked with internal standards underwent a protein crash with 400 µL ice cold methanol. The supernatant was dried under nitrogen. Methyl tert-butyl ether (MTBE) and water were added to extract the hydrophobic and hydrophilic compounds, respectively. The upper hydrophobic layer was transferred to a new tube and the lower hydrophilic layer was re-extracted with MTBE. The upper hydrophobic layer was combined, dried under nitrogen and reconstituted in 200 µL of methanol. The hydrophilic layer was dried under nitrogen, underwent a second protein crash with water and ice-cold methanol (1:4 water-methanol). The supernatant was removed, dried by SpeedVac at 45 °C and reconstituted in 100 µL of 5% acetonitrile in water. Both fractions were stored at -80 °C until LCMS analysis.
Processing Storage Conditions:On ice

Combined analysis:

Analysis ID AN002105 AN002106 AN002107 AN002108
Analysis type MS MS MS MS
Chromatography type Reversed phase Reversed phase HILIC HILIC
Chromatography system Agilent 1290 Agilent 1290 Agilent 1290 Agilent 1290
Column Agilent Zorbax RRHD SB-C18 (100 x 2.1mm,1.8um) Agilent Zorbax RRHD SB-C18 (100 x 2.1mm,1.8um) Phenomenex Kinetex HILIC 100A (50 x 2.1 mm,2.6um) Phenomenex Kinetex HILIC 100A (50 x 2.1 mm,2.6um)
MS Type ESI ESI ESI ESI
MS instrument type QTOF QTOF QTOF QTOF
MS instrument name Agilent 6520 QTOF Agilent 6520 QTOF Agilent 6550 QTOF Agilent 6550 QTOF
Ion Mode POSITIVE NEGATIVE POSITIVE NEGATIVE
Units Abundance Abundance Abundance Abundance

Chromatography:

Chromatography ID:CH001537
Chromatography Summary:Gradient was as follows: 0–1 minutes 30–70% B, 1–7.92 minutes 70–100% B, 7.92–10.4 minutes 100% B, 10.4–10.5 minutes 100–30% B, 10.5–15.1 minutes 30% B.
Instrument Name:Agilent 1290
Column Name:Agilent Zorbax RRHD SB-C18 (100 x 2.1mm,1.8um)
Column Temperature:60 °C
Flow Rate:0.7 mL/min
Injection Temperature:4 °C
Solvent A:100% water; 0.1% formic acid
Solvent B:60% isopropanol/36% acetonitrile/4% water; 0.1% formic acid
Chromatography Type:Reversed phase
  
Chromatography ID:CH001538
Chromatography Summary:Gradient elution was as follows: 0–2 minutes 100% B, 2–2.1 minutes 100–90% B, 2.1–8.6 minutes 90–50% B, 8.6–8.7 minutes 50–0% B, 8.7–14.7 minutes 0% B, 14.7–14.8 minutes 0–100% B, 14.8–24.8 minutes 100% B.
Instrument Name:Agilent 1290
Column Name:Phenomenex Kinetex HILIC 100A (50 x 2.1 mm,2.6um)
Column Temperature:20 °C
Flow Rate:0.6 mL/min
Injection Temperature:4 °C
Solvent A:50% acetonitrile/50% water; ammonium acetate, pH 5.8
Solvent B:90% acetonitrile/10% water; pH 5.8 ammonium acetate
Chromatography Type:HILIC

MS:

MS ID:MS001956
Analysis ID:AN002105
Instrument Name:Agilent 6520 QTOF
Instrument Type:QTOF
MS Type:ESI
MS Comments:Scan range 50-1700 m/z, scan rate 2.2 spectra/sec, gas temp 300C, gas flow 12 L/min, nebulizer 30 psig, Vcap 4000 V, fragmentor 120 V. Data processed with Profinder B.08 using small molecule chromatographic extraction.
Ion Mode:POSITIVE
  
MS ID:MS001957
Analysis ID:AN002106
Instrument Name:Agilent 6520 QTOF
Instrument Type:QTOF
MS Type:ESI
MS Comments:Scan range 50-1700 m/z, scan rate 1.0 spectra/sec, gas temp 300C, gas flow 12 L/min, nebulizer 30 psig, Vcap 4000 V, fragmentor 120 V. Data processed with Profinder B.08 using small molecule chromatographic extraction.
Ion Mode:NEGATIVE
  
MS ID:MS001958
Analysis ID:AN002107
Instrument Name:Agilent 6550 QTOF
Instrument Type:QTOF
MS Type:ESI
MS Comments:Scan range 75-1700 m/z, scan rate 2.0 spectra/sec, gas temp 225C, gas flow 18 L/min, nebulizer 45 psig, Vcap 3500 V, fragmentor 360 V. Data processed with Profinder B.08 using small molecule chromatographic extraction.
Ion Mode:POSITIVE
  
MS ID:MS001959
Analysis ID:AN002108
Instrument Name:Agilent 6550 QTOF
Instrument Type:QTOF
MS Type:ESI
MS Comments:Scan range 75-1700 m/z, scan rate 2.0 spectra/sec, gas temp 225C, gas flow 18 L/min, nebulizer 45 psig, Vcap 3500 V, fragmentor 360 V. Data processed with Profinder B.08 using small molecule chromatographic extraction.
Ion Mode:NEGATIVE
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