Summary of Study ST001216

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 IDST001216
Study TitleLCMS untargeted BAL Fluid analysis from COPD subjects
Study SummaryWe performed untargeted liquid chromatography mass spectrometry (LCMS) on BAL and matched plasma from 115 subjects from the SPIROMICS cohort.
Institute
University of Colorado Anschutz Medical Campus; National Jewish Health
Last NameReisdorph
First NameNichole
Address12850 E Montview Blvd, Aurora, CO 80045
EmailNichole.Reisdorph@cuanschutz.edu
Phone303-724-9234
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:SU001283
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
SA085913BALF_931
SA085914BALF_461
SA085915BALF_941
SA085916BALF_1151
SA085917BALF_621
SA085918BALF_171
SA085919BALF_721
SA085920BALF_011
SA085921BALF_421
SA085922BALF_831
SA085923BALF_061
SA085924BALF_051
SA085925BALF_441
SA085926BALF_1032
SA085927BALF_552
SA085928BALF_522
SA085929BALF_1042
SA085930BALF_472
SA085931BALF_1062
SA085932BALF_452
SA085933BALF_1012
SA085934BALF_482
SA085935BALF_502
SA085936BALF_972
SA085937BALF_762
SA085938BALF_872
SA085939BALF_772
SA085940BALF_792
SA085941BALF_812
SA085942BALF_912
SA085943BALF_692
SA085944BALF_992
SA085945BALF_1002
SA085946BALF_1072
SA085947BALF_642
SA085948BALF_652
SA085949BALF_572
SA085950BALF_412
SA085951BALF_162
SA085952BALF_152
SA085953BALF_142
SA085954BALF_1162
SA085955BALF_392
SA085956BALF_1132
SA085957BALF_1142
SA085958BALF_132
SA085959BALF_122
SA085960BALF_042
SA085961BALF_032
SA085962BALF_022
SA085963BALF_072
SA085964BALF_1172
SA085965BALF_112
SA085966BALF_102
SA085967BALF_232
SA085968BALF_192
SA085969BALF_312
SA085970BALF_1092
SA085971BALF_362
SA085972BALF_352
SA085973BALF_342
SA085974BALF_332
SA085975BALF_372
SA085976BALF_292
SA085977BALF_1102
SA085978BALF_382
SA085979BALF_252
SA085980BALF_282
SA085981BALF_843
SA085982BALF_853
SA085983BALF_863
SA085984BALF_893
SA085985BALF_923
SA085986BALF_963
SA085987BALF_1023
SA085988BALF_1113
SA085989BALF_953
SA085990BALF_1053
SA085991BALF_1083
SA085992BALF_1123
SA085993BALF_903
SA085994BALF_583
SA085995BALF_403
SA085996BALF_323
SA085997BALF_303
SA085998BALF_433
SA085999BALF_493
SA086000BALF_533
SA086001BALF_513
SA086002BALF_273
SA086003BALF_263
SA086004BALF_183
SA086005BALF_093
SA086006BALF_203
SA086007BALF_213
SA086008BALF_243
SA086009BALF_223
SA086010BALF_823
SA086011BALF_543
SA086012BALF_713
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Collection:

Collection ID:CO001277
Collection Summary:BAL collection is performed in the right middle lobe and lingula by instilling two aliquots of 40 mL and one aliquot of 50 mL of sterile saline per lobe (i.e., 130 mL per lobe, total volume = 260 mL per subject), which is withdrawn by gentle manual suction. The BAL return is collected into specifically designated specimen traps, kept on ice.
Sample Type:Bronchoalveolar lavage
Storage Conditions:-80℃

Treatment:

Treatment ID:TR001298
Treatment Summary:N/A

Sample Preparation:

Sampleprep ID:SP001291
Sampleprep Summary:140uL BAL was aliquoted into a microcentrifuge tube containing 20 uL of internal standards. Samples were vortexed followed by protein precipitation with 560 uL cold methanol, and centrifugation (0 C for 15 mins at 18,000 x g). The supernatant was removed and placed into two autosampler vials (165 uL for Hydrophilic Interaction Liquid Chromatography (HILIC) and 495 uL for C18 analysis). The samples were dried in a centrifugal evaporator at 45 C for 2 hours. The samples for Hydrophilic Interaction Liquid Chromatography HILIC analysis were reconstituted in 30 uL of 95:5 water:acetonitrile. The samples for Reversed phase C18 analysis were reconstituted in 90 uL methanol. Samples were stored at -80C prior to MS analysis.
Processing Storage Conditions:Described in summary
Extract Storage:Described in summary

Combined analysis:

Analysis ID AN002027 AN002028
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:CH001468
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:CH001469
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:MS001880
Analysis ID:AN002027
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:MS001881
Analysis ID:AN002028
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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