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MB Sample ID: SA085930

Local Sample ID:BALF_47
Subject ID:SU001283
Subject Type:Human
Subject Species:Homo sapiens
Taxonomy ID:9606
Gender:Male and female

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Subject:

Subject ID:SU001283
Subject Type:Human
Subject Species:Homo sapiens
Taxonomy ID:9606
Gender:Male and female

Factors:

Local Sample IDMB Sample IDFactor Level IDLevel ValueFactor Name
BALF_47SA085930FL0128422GOLD_STAGE_COPD_SEVERITY

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one aliquot of 50 mL of sterile saline per lobe (i.e., 130 mL per lobe, total volume = 260 mL per subject), which is withdrawn by gentle manual suction.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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