Summary of Study ST001217

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 PR000816. The data can be accessed directly via it's Project DOI: 10.21228/M86Q4H 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 IDST001217
Study TitleLCMS untargeted Plasma analysis from COPD subjects
Study SummaryTo use LCMS untargeted metabolomics for the purpose of detecting metabolites in 115 matched BAL and plasma that are associated with COPD
Institute
University of Colorado Anschutz Medical Campus; National Jewish Health
Last NameReisdorph
First NameNichole
Address12850 E Montview Blvd
EmailNichole.Reisdorph@cuanschutz.edu
Phone303-720-9234
Submit Date2019-07-10
Raw Data AvailableYes
Raw Data File Type(s)d
Analysis Type DetailLC-MS
Release Date2020-07-15
Release Version1
Nichole Reisdorph Nichole Reisdorph
https://dx.doi.org/10.21228/M86Q4H
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

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Project:

Project ID:PR000816
Project DOI:doi: 10.21228/M86Q4H
Project Title:COPD Matched Lavage and Plasma
Project Summary:Matched BAL and plasma from 115 COPD subjects from the SPIROMICS cohort were analyzed using untargeted LCMS metabolomics
Institute:University of Colorado Anschutz Medical Campus; National Jewish Health
Last Name:Reisdorph
First Name:Nichole
Address:12850 E Montview Blvd
Email:Nichole.Reisdorph@cuanschutz.edu
Phone:303-724-9234
Publications:Eitan Halper-Stromberg. Bronchoalveolar Lavage Fluid from COPD Patients Reveals More Compounds Associated with Disease than Matched Plasma. Metabolites 2019, 9(8), 157; https://doi.org/10.3390/metabo9080157

Subject:

Subject ID:SU001284
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 GOLD_STAGE_COPD_SEVERITY
SA086028Plasma_931
SA086029Plasma_461
SA086030Plasma_941
SA086031Plasma_1151
SA086032Plasma_621
SA086033Plasma_171
SA086034Plasma_721
SA086035Plasma_011
SA086036Plasma_421
SA086037Plasma_831
SA086038Plasma_061
SA086039Plasma_051
SA086040Plasma_441
SA086041Plasma_1032
SA086042Plasma_552
SA086043Plasma_522
SA086044Plasma_1042
SA086045Plasma_472
SA086046Plasma_1062
SA086047Plasma_452
SA086048Plasma_1012
SA086049Plasma_482
SA086050Plasma_502
SA086051Plasma_972
SA086052Plasma_762
SA086053Plasma_872
SA086054Plasma_772
SA086055Plasma_792
SA086056Plasma_812
SA086057Plasma_912
SA086058Plasma_692
SA086059Plasma_992
SA086060Plasma_1002
SA086061Plasma_1072
SA086062Plasma_642
SA086063Plasma_652
SA086064Plasma_572
SA086065Plasma_412
SA086066Plasma_162
SA086067Plasma_152
SA086068Plasma_142
SA086069Plasma_1162
SA086070Plasma_392
SA086071Plasma_1132
SA086072Plasma_1142
SA086073Plasma_132
SA086074Plasma_122
SA086075Plasma_042
SA086076Plasma_032
SA086077Plasma_022
SA086078Plasma_072
SA086079Plasma_1172
SA086080Plasma_112
SA086081Plasma_102
SA086082Plasma_232
SA086083Plasma_192
SA086084Plasma_312
SA086085Plasma_1092
SA086086Plasma_362
SA086087Plasma_352
SA086088Plasma_342
SA086089Plasma_332
SA086090Plasma_372
SA086091Plasma_292
SA086092Plasma_1102
SA086093Plasma_382
SA086094Plasma_252
SA086095Plasma_282
SA086096Plasma_843
SA086097Plasma_853
SA086098Plasma_863
SA086099Plasma_893
SA086100Plasma_923
SA086101Plasma_963
SA086102Plasma_1023
SA086103Plasma_1113
SA086104Plasma_953
SA086105Plasma_1053
SA086106Plasma_1083
SA086107Plasma_1123
SA086108Plasma_903
SA086109Plasma_583
SA086110Plasma_403
SA086111Plasma_323
SA086112Plasma_303
SA086113Plasma_433
SA086114Plasma_493
SA086115Plasma_533
SA086116Plasma_513
SA086117Plasma_273
SA086118Plasma_263
SA086119Plasma_183
SA086120Plasma_093
SA086121Plasma_203
SA086122Plasma_213
SA086123Plasma_243
SA086124Plasma_223
SA086125Plasma_823
SA086126Plasma_543
SA086127Plasma_713
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Collection:

Collection ID:CO001278
Collection Summary:Blood is drawn into a 10 ml heparin plasma tube, and immediately sent to the medical center clinical laboratory for further processing.
Sample Type:Blood (plasma)
Storage Conditions:-80℃

Treatment:

Treatment ID:TR001299
Treatment Summary:N/A

Sample Preparation:

Sampleprep ID:SP001292
Sampleprep Summary:Plasma samples were thawed and 100 uL was prepared using methanol precipitation and liquid-liquid extraction as previously described (PMCID PMC4214365, PMCID PMC3734953) . In short, following the addition of standards, 400uL of ice cold MeOH was added to 100uL of plasma to precipitate proteins, then vortexed for 10 seconds, and centrifgued at 0oC for 15 min at 18,000 rpm to pellet precipitated protein. The supernatant was transferred to a glass culture tube and dried under N2. 3.1mL MTBE was added to the dried methanol residue, vortexed for 30 seconds, 750uL of water added to the tube, and vortex 10 seconds. The sample was then spun at 1000 rpm for 10 min at RT to form bilayer. 2.5 mL of MTBE layer was aliquoted and transferred to a new, clean glass culture tube. Then 3.0 mL MTBE was added to remaining water layer of sample, vortexed for 10 seconds, and centrifuged at 200 x g for 10 min at RT to form bilayer. 3mL of MTBE was aliquoted and combined with previous MTBE tube. This MTBE layer was dried under nitrogen at 35oC, and quickly re-suspend in 200uL Methanol, vortexed for 5 seconds and transfered to glass autosampler vial. The aqueous layer was dried under N2, 100uL of water quickly added to minimize oxidation. Then 400uL of ice cold MeOH was added, vortexed for 10 seconds, transfered to a 1.5 ml low retention Fisher microtube and frozen at -80oC for 25 min to crash out any remaining residual proteins. Then centrifuged at 0oC for 15 min at 18,000 xg. The supernatant was transferred to a clean microtube, dried in speed vac at 45oC. The dried supernatant was quickly resuspended in 100uL of 5% ACN in water, vortexed for 30 sec, then transferred to autosampler vials, and stored at -80C prior to MS analysis.
Processing Storage Conditions:Described in summary
Extract Storage:Described in summary

Combined analysis:

Analysis ID AN002029 AN002030
Analysis type MS MS
Chromatography type Reversed phase HILIC
Chromatography system Agilent 6545 Agilent 6520
Column Agilent Zorbax RRHD SB-C18 (100 x 2.1mm,1.8um) Phenomenex Kinetex HILIC 100A (50 x 2.1 mm,2.6um)
MS Type ESI ESI
MS instrument type QTOF QTOF
MS instrument name Agilent 6545 QTOF Agilent 6520 QTOF
Ion Mode POSITIVE POSITIVE
Units Abundance (Log2) Abundance (Log2)

Chromatography:

Chromatography ID:CH001470
Chromatography Summary:Reversed phase samples from the lipid fraction were randomized in the worklist and run randomly in triplicate using an Agilent 1290 series pump with an Agilent Zorbax Rapid Resolution HD (RRHD) SB-C18, 1.8 micron (2.1 × 100 mm) analytical column and an Agilent Zorbax SB-C18, 1.8 micron (2.1 × 5 mm) guard column. The autosampler tray temperature was set at 4 °C, column temperature was set at 60 °C, and the sample injection volume was 8 µL for BAL and 4 µL for plasma. The flow rate was 0.7 mL/min with the following mobile phases: mobile phase A was water with 0.1% formic acid, and mobile phase B was 60:36:4 isopropyl alcohol:acetonitrile:water with 0.1% formic acid. Gradient elution was as follows: 0–0.5 minutes 30–70% B, 0.5–7.42 minutes 70–100% B, 7.42–10.4 minutes 100% B, 10.4–10.5 minutes 100–30% B, 10.5–15.1 minutes 30% B.
Instrument Name:Agilent 6545
Column Name:Agilent Zorbax RRHD SB-C18 (100 x 2.1mm,1.8um)
Column Temperature:60
Flow Gradient:0-0.5 minutes 30-70% B, 0.5-7.42 minutes 70-100% B, 7.42-10.4 minutes 100% B, 10.4-10.5 minutes 100-30% B, 10.5-15.1 minutes 30% B
Flow Rate:0.7 mL/min
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:CH001471
Chromatography Summary:The samples from the aqueous small molecule fraction were analyzed randomly in triplicate using an Agilent 1290 series pump using a Phenomenex Kinetex HILIC, 2.6 µm, 100 Å (2.1 × 50 mm) analytical column and an Agilent Zorbax Eclipse Plus-C8 5 µm (2.1 × 12.5 mm) narrow bore guard column. The autosampler tray temperature was set at 4 °C, column temperature was set at 20 °C, and the sample injection volume was 1 µL for both BAL and plasma. The flow rate of 0.6 mL/min with the following mobile phases: mobile phase A was 50% ACN with pH 5.8 ammonium acetate, and mobile phase B was 90% ACN with pH 5.8 ammonium acetate. Gradient elution was as follows: 0.2 minutes 100% B, 0.2–2.1 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 6520
Column Name:Phenomenex Kinetex HILIC 100A (50 x 2.1 mm,2.6um)
Column Temperature:20
Flow Gradient:0.2 minutes 100% B, 0.2-2.1 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.
Flow Rate:0.6 mL/min
Solvent A:50% acetonitrile/50% water; ammonium acetate, pH 5.8
Solvent B:90% acetonitrile/5% water, pH 5.8
Chromatography Type:HILIC

MS:

MS ID:MS001882
Analysis ID:AN002029
Instrument Name:Agilent 6545 QTOF
Instrument Type:QTOF
MS Type:ESI
MS Comments:Agilent 6545 Quadrupole Time-of-Flight mass spectrometer (QTOF-MS) in positive ionization mode with dual AJS ESI source, mass range 50–1700 m/z, scan rate 2.00, gas temperature 300 °C, gas flow 12.0 L/min, nebulizer 35 psi, sheath gas temperature 275°C, skimmer 65 V, capillary voltage 3500 V, fragmentor 120 V, reference masses 121.050873 and 922.009798 (Agilent reference mix). The analysis was replicated for tandem MS of selected compounds using a scan range 50–1700m/z, and 10, 20, and 40 eV collision energies with a 500 ms/spectra acquisition time, 1.3 m/z (narrow) isolation width, and 0.25 minute delta retention time.
Ion Mode:POSITIVE
  
MS ID:MS001883
Analysis ID:AN002030
Instrument Name:Agilent 6520 QTOF
Instrument Type:QTOF
MS Type:ESI
MS Comments:Agilent 6520 QTOF-MS in positive ionization mode with dual ESI source, mass range 50–1700 m/z, scan rate 2.00, gas temperature 325 °C, gas flow 12.0 L/min, nebulizer 30 psi, skimmer 60 V, capillary voltage 4000 V, fragmentor 120 V, reference masses 121.050873 and 922.009798 (Agilent reference mix). The analysis was replicated for tandem MS of selected compounds using a scan range 50–1700m/z, and 10, 20, and 40 eV collision energies with a 500 ms/spectra acquisition time, 1.3 m/z (narrow) isolation width, and 0.25 minute delta retention time.
Ion Mode:POSITIVE
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