Summary of Study ST001171

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 PR000783. The data can be accessed directly via it's Project DOI: 10.21228/M8G970 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.

Show all samples  |  Perform analysis on untargeted data  
Download mwTab file (text)   |  Download mwTab file(JSON)   |  Download data files (Contains raw data)
Study IDST001171
Study TitleMetabolomics of World Trade Center Exposed New York City Firefighters
Study TypeC18 Reversed-Phase Broad Spectrum Metabolomics
Study SummaryParticulate matter (PM) exposure and metabolic syndrome (MetSyn) coexist in both industrialized and developing nations. PM and MetSyn are strong risk factors for chronic obstructive pulmonary disease (COPD) and asthma. After the World Trade Center collapse in 9/11/2001, PM-exposed individuals from the Fire Department of New York City (FDNY) developed a progressively lung disease. This nested case-cohort study is composed of never smoking, WTC exposed firefighters with normal pre-9/11 lung function presenting for subspecialty pulmonary evaluation (SPE) before March 2008. Representative cohort controls with serum drawn within six months of 9/11 (n=100). FEV1 at subspecialty exam defined cases: susceptible World Trade Center Lung Injury (WTC-LI) cases (n=50) had FEV1< lower limit of normal (LLN) and resistant WTC-LI cases with FEV1 ≥107% predicted (n=50). This study will determine the metabolomics profile that differentiates firefighters with WTC-LI, firefighters resistant to WTC-LI, and similarly exposed cohort controls.
Institute
New York University
DepartmentSchool of Medicine
LaboratoryLaboratory at NYU/Bellevue
Last NameNolan
First NameAnna
AddressAcademic office 462 1st Avenue, New Bellevue 16, S 16(Office)/ N 20 (Lab) New York, NY 10016
Emailanna.nolan@nyulangone.org
Phone212-263-7283
Submit Date2019-02-22
Num Groups3
Total Subjects224, 200 study samples, 24 pools
Num Males200
Raw Data AvailableYes
Raw Data File Type(s)raw(Thermo)
Analysis Type DetailLC-MS
Release Date2021-02-26
Release Version1
Anna Nolan Anna Nolan
https://dx.doi.org/10.21228/M8G970
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

Select appropriate tab below to view additional metadata details:

Project:

Project ID:PR000783
Project DOI:doi: 10.21228/M8G970
Project Title:Metabolomics of World Trade Center Exposed New York City Firefighters
Project Type:C18 Reversed-Phase Broad Spectrum Metabolomics
Project Summary:Particulate matter (PM) exposure and metabolic syndrome (MetSyn) coexist in both industrialized and developing nations. PM and MetSyn are strong risk factors for chronic obstructive pulmonary disease (COPD) and asthma. After the World Trade Center collapse in 9/11/2001, PM-exposed individuals from the Fire Department of New York City (FDNY) developed a progressively lung disease. This nested case-cohort study is composed of never smoking, WTC exposed firefighters with normal pre-9/11 lung function presenting for subspecialty pulmonary evaluation (SPE) before March 2008. Representative cohort controls with serum drawn within six months of 9/11 (n=100). FEV1 at subspecialty exam defined cases: susceptible World Trade Center Lung Injury (WTC-LI) cases (n=50) had FEV1< lower limit of normal (LLN) and resistant WTC-LI cases with FEV1 ≥107% predicted (n=50). This study will determine the metabolomics profile that differentiates firefighters with WTC-LI, firefighters resistant to WTC-LI, and similarly exposed cohort controls.
Institute:University of North Carolina
Department:Nutrition Research Institute
Last Name:Sumner
First Name:Susan
Address:Eastern Regional Comprehensive Metabolomics Resource Core, UNC Nutrition Research Institute, 500 Laureate Way, Kannapolis, NC, 28081
Email:susan_sumner @unc.edu
Phone:704-250-5066

Subject:

Subject ID:SU001236
Subject Type:Human
Subject Species:Homo sapiens
Taxonomy ID:9606
Age Or Age Range:30-60
Gender:Male
Species Group:Mammals

Factors:

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

mb_sample_id local_sample_id Age Group Group
SA080996S_11[20,30) yrs Control
SA080997S_60[20,30) yrs Resistant
SA080998S_91[20,30) yrs Resistant
SA080999S_94[20,30) yrs WTC-LI
SA081000S_195[30-40) yrs Control
SA081001S_183[30-40) yrs Control
SA081002S_182[30-40) yrs Control
SA081003S_178[30-40) yrs Control
SA081004S_103[30-40) yrs Control
SA081005S_19[30-40) yrs Control
SA081006S_106[30-40) yrs Control
SA081007S_20[30-40) yrs Control
SA081008S_52[30-40) yrs Control
SA081009S_33[30-40) yrs Control
SA081010S_32[30-40) yrs Control
SA081011S_51[30-40) yrs Control
SA081012S_38[30-40) yrs Control
SA081013S_40[30-40) yrs Control
SA081014S_10[30-40) yrs Control
SA081015S_48[30-40) yrs Control
SA081016S_101[30-40) yrs Control
SA081017S_29[30-40) yrs Control
SA081018S_21[30-40) yrs Control
SA081019S_199[30-40) yrs Control
SA081020S_58[30-40) yrs Control
SA081021S_22[30-40) yrs Control
SA081022S_24[30-40) yrs Control
SA081023S_53[30-40) yrs Control
SA081024S_54[30-40) yrs Control
SA081025S_197[30-40) yrs Control
SA081026S_70[30-40) yrs Control
SA081027S_87[30-40) yrs Control
SA081028S_88[30-40) yrs Control
SA081029S_139[30-40) yrs Control
SA081030S_86[30-40) yrs Control
SA081031S_114[30-40) yrs Control
SA081032S_108[30-40) yrs Control
SA081033S_113[30-40) yrs Control
SA081034S_90[30-40) yrs Control
SA081035S_134[30-40) yrs Control
SA081036S_124[30-40) yrs Control
SA081037S_96[30-40) yrs Control
SA081038S_93[30-40) yrs Control
SA081039S_128[30-40) yrs Control
SA081040S_132[30-40) yrs Control
SA081041S_130[30-40) yrs Control
SA081042S_8[30-40) yrs Control
SA081043S_83[30-40) yrs Control
SA081044S_167[30-40) yrs Control
SA081045S_165[30-40) yrs Control
SA081046S_73[30-40) yrs Control
SA081047S_97[30-40) yrs Resistant
SA081048S_56[30-40) yrs Resistant
SA081049S_78[30-40) yrs Resistant
SA081050S_9[30-40) yrs Resistant
SA081051S_57[30-40) yrs Resistant
SA081052S_3[30-40) yrs Resistant
SA081053S_166[30-40) yrs Resistant
SA081054S_13[30-40) yrs Resistant
SA081055S_17[30-40) yrs Resistant
SA081056S_191[30-40) yrs Resistant
SA081057S_174[30-40) yrs Resistant
SA081058S_28[30-40) yrs Resistant
SA081059S_105[30-40) yrs Resistant
SA081060S_89[30-40) yrs WTC-LI
SA081061S_136[30-40) yrs WTC-LI
SA081062S_69[30-40) yrs WTC-LI
SA081063S_67[30-40) yrs WTC-LI
SA081064S_65[30-40) yrs WTC-LI
SA081065S_179[30-40) yrs WTC-LI
SA081066S_116[30-40) yrs WTC-LI
SA081067S_194[30-40) yrs WTC-LI
SA081068S_107[30-40) yrs WTC-LI
SA081069S_102[30-40) yrs WTC-LI
SA081070S_77[30-40) yrs WTC-LI
SA081071S_159[30-40) yrs WTC-LI
SA081072S_55[30-40) yrs WTC-LI
SA081073S_154[30-40) yrs WTC-LI
SA081074S_164[30-40) yrs WTC-LI
SA081075S_184[30-40) yrs WTC-LI
SA081076S_2[30-40) yrs WTC-LI
SA081077S_171[30-40) yrs WTC-LI
SA081078S_44[40-50) yrs Control
SA081079S_45[40-50) yrs Control
SA081080S_79[40-50) yrs Control
SA081081S_95[40-50) yrs Control
SA081082S_61[40-50) yrs Control
SA081083S_92[40-50) yrs Control
SA081084S_74[40-50) yrs Control
SA081085S_80[40-50) yrs Control
SA081086S_192[40-50) yrs Control
SA081087S_121[40-50) yrs Control
SA081088S_122[40-50) yrs Control
SA081089S_172[40-50) yrs Control
SA081090S_119[40-50) yrs Control
SA081091S_175[40-50) yrs Control
SA081092S_18[40-50) yrs Control
SA081093S_177[40-50) yrs Control
SA081094S_140[40-50) yrs Control
SA081095S_137[40-50) yrs Control
Showing page 1 of 3     Results:    1  2  3  Next     Showing results 1 to 100 of 248

Collection:

Collection ID:CO001230
Collection Summary:Fasting blood drawn
Sample Type:Blood (serum)
Collection Location:Bureau of Health Services (BHS) and the FDNY Headquarters, (9 Metrotech Center, Brooklyn, NY)
Collection Duration:6 month after 9/11/2001 and once at 2008
Storage Conditions:-80℃

Treatment:

Treatment ID:TR001251
Treatment Summary:No available

Sample Preparation:

Sampleprep ID:SP001244
Sampleprep Summary:The Fire Department of New York City (FDNY) serum sampling occurred at the Bureau of Health Services (BHS) and the FDNY Headquarters (9 Metrotech Center, Brooklyn, NY). Serum processing and analysis occurred in the PI’s Laboratory at New York University /Bellevue. The specimens were stored in the New York University-The Fire Department of New York City- World Trade Center Lung Injury Biorepository (NYU-FDNY WTC) in Dr. Nolan’s laboratory. Each stored specimen was labeled with a unique code. This unique code on the sample was linked to a specific subject. Samples were stored in -80 oC and shipped to the Eastern Regional Comprehensive Metabolomics Resource Core (ERCMRC) on dry ice. Table 1 lists the sample ID and associated metadata provided. Serum samples were thawed at 4 °C overnight. All samples were vortexed via multiple tube vortex mixer for 2 min at 3000 rpm. Serum samples were centrifuged at 1000 rpm for 30 sec. A volume of 8 µL aliquot of each studied samples was transferred into a 10.0 mL tube to make the Study Pool (SP). A volume of 1500 µL of CHEAR Reference Plasma was used for the CHEAR Pool (CP). An aliquot of 50 µL serum (including experimental samples, SP, and CP) was transferred to a new, pre-labeled Lo-Bind Eppendorf tube. There were total 200 experimental samples, 24 SP samples, and 24 CP samples in this study. The samples were extracted by 400 µL methanol with 500 ng/ml tryptophan-d5 as internal standard via a multiple tube vortex mixer for 2 min at 5000 rpm. Protein precipitate was pelleted using a centrifuge operating at room temperature for 4 min at 16,000 rcf. A volume of 350 µl of the supernatant was transferred into a pre-labeled 2.0 ml Low-bind Eppendorf tube, and then dried by a SpeedVac overnight. For immediate analysis, 100 µL of water-methanol solution (95:5, v/v) was added to reconstitute the dried extracts, and the samples were thoroughly mixed on multiple tube vortex mixer for 10 min at 5000 rpm. Samples were centrifuged at 4°C for 4 min at 16,000 rcf. The supernatant was transferred to pre-labeled autosampler vials for data acquisition by LC-MS. Broad-spectrum metabolomics was conducted using a Thermo Scientific™ Vanquish™ UPHPLC - Q Exactive™ HF-X Orbitrap System. Metabolites were separated on an Acquity UPLC HSS T3 C18 (2.1 X 100 mm, 1.8 µm) operating at 50 C using a reversed phase gradient separation with Water with 0.1% Formic Acid (v/v) as mobile phase A and Methanol with 0.1% Formic Acid (v/v) as mobile phase B. A 5 µL was injected into the instrument, and MS was collected between 50-750 m/z in positive mode with the MS/MS data triggered by the Data-Dependent Acquisition.
Extraction Method:Vortex with methanol containing 500ng/ml tryptophan-d5 as internal standard
Extract Storage:-80℃
Sample Resuspension:Water-Methanol (95:5, v/v)
Sample Spiking:Tryptophan-d5

Combined analysis:

Analysis ID AN001936
Analysis type MS
Chromatography type Reversed phase
Chromatography system Thermo Vanquish
Column Waters Acquity BEH HSS T3 (100 x 2.1mm,1.8um)
MS Type ESI
MS instrument type Orbitrap
MS instrument name Thermo Q Exactive HF hybrid Orbitrap
Ion Mode POSITIVE
Units peak area

Chromatography:

Chromatography ID:CH001405
Instrument Name:Thermo Vanquish
Column Name:Waters Acquity BEH HSS T3 (100 x 2.1mm,1.8um)
Column Temperature:50
Flow Gradient:Time(min) Flow Rate %A %B Curve 1. 0 0.4 99.0 1.0 5 2. 1.00 0.4 99.0 1.0 5 3. 16.00 0.4 1.0 99.0 5 4. 19.00 0.4 1.0 99.0 5 5. 19.50 0.4 99.0 1.0 5
Flow Rate:0.4 mL/min
Injection Temperature:8
Internal Standard:Tryptophan-d5
Solvent A:100% water; 0.1% formic acid
Solvent B:100% methanol; 0.1% formic acid
Chromatography Type:Reversed phase

MS:

MS ID:MS001792
Analysis ID:AN001936
Instrument Name:Thermo Q Exactive HF hybrid Orbitrap
Instrument Type:Orbitrap
MS Type:ESI
MS Comments:LC-MS/MS data was acquired by data dependent acquisition;Progenesis QI was used to process the raw data.
Ion Mode:POSITIVE
Capillary Temperature:275 C
Capillary Voltage:3.75 kV
Collision Energy:20, 30, 45
Collision Gas:N2
Dry Gas Flow:45 arbitary unit
Dry Gas Temp:325 oC
Fragmentation Method:CID
Gas Pressure:45 arbitary unit
Ion Source Temperature:325 oC
Ion Spray Voltage:3.75 kV
Ionization:ESI
Ionization Potential:positive
Mass Accuracy:5ppm
Source Temperature:325 oC
Spray Voltage:3.75 kV
Resolution Setting:120000
Scan Range Moverz:70-1050 m/z
Scanning Range:70-1050 m/z
  logo