Summary of Study ST000362
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 PR000288. The data can be accessed directly via it's Project DOI: 10.21228/M8TC7S This work is supported by NIH grant, U2C- DK119886.
See: https://www.metabolomicsworkbench.org/about/howtocite.php
| Study ID | ST000362 |
| Study Title | Associations between 69 Sphingolipids and Emphysema, Chronic Bronchitis, Exacerbations, and FEV1/FVC |
| Study Type | Association Study |
| Study Summary | One hundred twenty-nine current and former smokers from the COPDGene cohort had 69 distinct sphingolipid species detected in plasma by targeted mass spectrometry. Of these, 23 were also measured in 131 plasma samples (117 independent subjects) using an untargeted platform in an independent laboratory. Regression analysis with adjustment for clinical covariates, correction for false discovery rate, and metaanalysis were used to test associations between COPD subphenotypes and sphingolipids. Peripheral blood mononuclear cells were used to test associations between sphingolipid gene expression and plasma sphingolipids. |
| Institute | National Jewish Health |
| Department | Medicine |
| Laboratory | Bowler |
| Last Name | Jacobson |
| First Name | Sean |
| Address | 1400 Jackson St, Denver, CO 80206 |
| jacobsons@njhealth.org | |
| Phone | (303) 398-1355 |
| Submit Date | 2016-03-10 |
| Analysis Type Detail | LC-MS |
| Release Date | 2016-09-23 |
| Release Version | 1 |
Select appropriate tab below to view additional metadata details:
Project:
| Project ID: | PR000288 |
| Project DOI: | doi: 10.21228/M8TC7S |
| Project Title: | Plasma Sphingolipids Associated with Chronic Obstructive Pulmonary Disease Phenotypes |
| Project Type: | Association Study |
| Project Summary: | Sphingolipids association meta-analysis study from human sources |
| Institute: | National Jewish Health |
| Department: | Medicine |
| Laboratory: | Bowler |
| Last Name: | Jacobson |
| First Name: | Sean |
| Address: | 1400 Jackson St, Denver, CO 80206 |
| Email: | jacobsons@njhealth.org |
| Phone: | (303) 398-1355 |
Subject:
| Subject ID: | SU000383 |
| Subject Type: | Animal |
| Subject Species: | Homo sapiens |
| Taxonomy ID: | 9606 |
| Species Group: | Human |
Factors:
Subject type: Animal; Subject species: Homo sapiens (Factor headings shown in green)
| mb_sample_id | local_sample_id | Severe_Exacerbations | Chronic_Bronchitis | GoldStage | Gender | SmokingStatus |
|---|---|---|---|---|---|---|
| SA016155 | 24757L | 1 | 1 | 3 | 1 | - |
| SA016156 | 10056H | 1 | 1 | 4 | 2 | - |
| SA016149 | 12900A | 1 | - | 2 | 2 | - |
| SA016150 | 18213L | 1 | - | 3 | 1 | - |
| SA016151 | 21272Y | 1 | - | 3 | 1 | 1 |
| SA016152 | 21829V | 1 | - | 4 | 1 | - |
| SA016153 | 24064G | 1 | - | 4 | 2 | - |
| SA016154 | 21999U | 1 | - | 4 | 2 | - |
| SA016158 | 18869K | 2 | 1 | 3 | 1 | - |
| SA016157 | 21254W | 2 | - | 3 | 1 | 1 |
| SA016159 | 19059G | 3 | - | 3 | 1 | - |
| SA016160 | 18233R | 3 | - | 3 | 2 | - |
| SA016161 | 19156E | 3 | - | 4 | 2 | - |
| SA016162 | 22182C | 5 | - | 4 | 1 | - |
| SA016130 | 18951V | - | 1 | 1 | 1 | 1 |
| SA016131 | 24293V | - | 1 | 2 | 1 | - |
| SA016132 | 25218M | - | 1 | 2 | 1 | - |
| SA016133 | 18425A | - | 1 | 2 | 1 | - |
| SA016134 | 20230D | - | 1 | 2 | 1 | 1 |
| SA016135 | 20533V | - | 1 | 2 | 1 | 1 |
| SA016136 | 21842N | - | 1 | 2 | 1 | 1 |
| SA016137 | 17719M | - | 1 | 2 | 1 | 1 |
| SA016138 | 22662Q | - | 1 | 2 | 2 | - |
| SA016139 | 18793D | - | 1 | 2 | 2 | 1 |
| SA016140 | 22460E | - | 1 | 2 | 2 | 1 |
| SA016141 | 14457T | - | 1 | 3 | 1 | - |
| SA016142 | 25239U | - | 1 | 3 | 1 | - |
| SA016143 | 24536V | - | 1 | 3 | 1 | - |
| SA016144 | 16545A | - | 1 | 3 | 1 | - |
| SA016145 | 11699C | - | 1 | 3 | 1 | 1 |
| SA016146 | 24451N | - | 1 | 3 | 1 | 1 |
| SA016147 | 18048W | - | 1 | 4 | 1 | 1 |
| SA016148 | 23504D | - | 1 | 4 | 2 | 1 |
| SA016128 | 25229R | - | 1 | - | 1 | - |
| SA016129 | 17974C | - | 1 | - | 1 | 1 |
| SA016069 | 22035P | - | - | 1 | 1 | - |
| SA016070 | 18962A | - | - | 1 | 1 | - |
| SA016071 | 24438V | - | - | 1 | 1 | - |
| SA016072 | 20102U | - | - | 1 | 1 | - |
| SA016073 | 17855U | - | - | 1 | 1 | - |
| SA016074 | 15974S | - | - | 1 | 1 | 1 |
| SA016075 | 19648Z | - | - | 1 | 1 | 1 |
| SA016076 | 23351E | - | - | 1 | 1 | 1 |
| SA016077 | 16559L | - | - | 1 | 2 | - |
| SA016078 | 21957E | - | - | 1 | 2 | - |
| SA016079 | 17577S | - | - | 1 | 2 | - |
| SA016080 | 17066T | - | - | 1 | 2 | - |
| SA016081 | 21967H | - | - | 1 | 2 | 1 |
| SA016082 | 20778Z | - | - | 2 | 1 | - |
| SA016083 | 10544U | - | - | 2 | 1 | - |
| SA016084 | 20378J | - | - | 2 | 1 | - |
| SA016085 | 14724Q | - | - | 2 | 1 | - |
| SA016086 | 24714T | - | - | 2 | 1 | - |
| SA016087 | 16069U | - | - | 2 | 1 | - |
| SA016088 | 17144N | - | - | 2 | 1 | - |
| SA016089 | 18497Z | - | - | 2 | 1 | - |
| SA016090 | 23109X | - | - | 2 | 1 | - |
| SA016091 | 18990F | - | - | 2 | 1 | - |
| SA016092 | 22488A | - | - | 2 | 1 | - |
| SA016093 | 17932M | - | - | 2 | 1 | 1 |
| SA016094 | 15973Q | - | - | 2 | 1 | 1 |
| SA016095 | 21601R | - | - | 2 | 2 | - |
| SA016096 | 23622J | - | - | 2 | 2 | - |
| SA016097 | 11220Z | - | - | 2 | 2 | - |
| SA016098 | 21772S | - | - | 2 | 2 | - |
| SA016099 | 10072F | - | - | 2 | 2 | - |
| SA016100 | 16619D | - | - | 2 | 2 | - |
| SA016101 | 24437T | - | - | 2 | 2 | - |
| SA016102 | 15841Z | - | - | 2 | 2 | - |
| SA016103 | 22068E | - | - | 3 | 1 | - |
| SA016104 | 24447W | - | - | 3 | 1 | - |
| SA016105 | 24309K | - | - | 3 | 1 | - |
| SA016106 | 20534X | - | - | 3 | 1 | - |
| SA016107 | 15520F | - | - | 3 | 1 | - |
| SA016108 | 19785J | - | - | 3 | 1 | - |
| SA016109 | 18518H | - | - | 3 | 1 | - |
| SA016110 | 21044L | - | - | 3 | 1 | - |
| SA016111 | 10303Y | - | - | 3 | 1 | - |
| SA016112 | 12099J | - | - | 3 | 1 | - |
| SA016113 | 22592V | - | - | 3 | 1 | 1 |
| SA016114 | 22489C | - | - | 3 | 2 | - |
| SA016115 | 18352Z | - | - | 3 | 2 | - |
| SA016116 | 23746B | - | - | 3 | 2 | - |
| SA016117 | 20177Z | - | - | 3 | 2 | - |
| SA016118 | 10458B | - | - | 3 | 2 | - |
| SA016119 | 15665F | - | - | 3 | 2 | - |
| SA016120 | 17794A | - | - | 3 | 2 | - |
| SA016121 | 18605C | - | - | 4 | 1 | - |
| SA016122 | 16738L | - | - | 4 | 1 | - |
| SA016123 | 17573K | - | - | 4 | 1 | - |
| SA016124 | 23966P | - | - | 4 | 1 | - |
| SA016125 | 16463Y | - | - | 4 | 2 | - |
| SA016126 | 22728U | - | - | 4 | 2 | - |
| SA016127 | 19638W | - | - | 4 | 2 | - |
| SA016034 | 20586Q | - | - | - | 1 | - |
| SA016035 | 25041Z | - | - | - | 1 | - |
| SA016036 | 20583K | - | - | - | 1 | - |
| SA016037 | 24304A | - | - | - | 1 | - |
| SA016038 | 24716X | - | - | - | 1 | - |
| SA016039 | 21654M | - | - | - | 1 | - |
Collection:
| Collection ID: | CO000377 |
| Collection Summary: | Subjects had fresh frozen plasma collected using a p100 tube (BD) at two COPDGene sites (National Jewish Health and University of Iowa) |
| Sample Type: | Blood |
Treatment:
| Treatment ID: | TR000397 |
| Treatment Summary: | Association analysis was done between human subjects and statistical analysis performed using data collected from subjects using covariates and phenotypes as outcomes. |
Sample Preparation:
| Sampleprep ID: | SP000390 |
| Sampleprep Summary: | Sphingomyelins, dihydrosphingomyelins, ceramides and dihydroceramides: A modified Bligh-Dyer extraction method was used in the presence of internal standards (IS). Sample analysis was performed in four batches using a Shimadzu 10A HPLC system coupled to a TSQ Quantum Ultra triple quadrupole mass spectrometer operated in SRM mode under ESI(+). A Thermo Betasil C18 column was employed to achieve the optimal sensitivity and separation. Data processing was conducted with Xcalibur software (Thermo) to obtain the peak area ratios of analytes to the corresponding internal standards (Supplemental Table 2). A pooled lipid extract from study samples was used as a quality control (QC) sample, and was injected between every 6 study samples to verify the instrument consistency. The peak area ratios were then normalized to the average of QC peak area ratios in the same batch, so that the results for different batches were brought to the same baseline. Sphingoid bases, ceramide-1-phosphate, monohexosylsphingosine, monohexosylceramides, dihexosylceramides, trihexosylceramides, monohydroxylated monohexosylceramides, monohydroxylated dihexosylceramides, sulfatides, and gangliosides: Plasma protein was precipitated with methanol, followed by supernatant collection, drying, and reconstituting with 1:1 methanol/water in the presence of internal standards. Duplicate sample analysis (1 st analysis and 2 nd analysis) was performed in four batches with an online trapping API-4000 system, (consists of a API-4000 mass spectrometer, a Leap PAL autosampler, an Agilent 1100 HPLC, and a Shimadzu HPLC) operated in multiple reaction monitoring (MRM) mode under ESI(+) for all species except sulfatides and E2gangliosides ESI(-). An Agilent Eclipse XRB-C18 column was used for sphingoid bases and ceramide-1- phosphate and a Varian Metasil C18 column was used for analysis of monohexosylsphingosine, mono-, di-, tri- hexosylceramides as well as their monohydroxylated ceramides. An Agilent Zobax Eclipse Plus C18 column was used for analysis of sulfatides and gangliosides. A Thermo Betasil C18 trapping column was also used for all analytes. Data processing was conducted with Analyst software (Applied Sciences) to obtain the peak area ratios of analytes to the corresponding internal standards. A pooled lipid extract from study samples was used as a quality control (QC) sample, and was injected between every 10 study samples to verify the instrumental consistency. All duplicated sample runs were averaged. The values for each sphingolipid were peak area ratios that were normalized to internal standard and then normalized to QC standards. Values were relative peak area ratios and unitless. |
Combined analysis:
| Analysis ID | AN000594 |
|---|---|
| Analysis type | MS |
| Chromatography type | Reversed phase |
| Chromatography system | Shimadzu 10A |
| Column | Thermo Betasil C18 |
| MS Type | ESI |
| MS instrument type | Triple quadrupole |
| MS instrument name | Shimadzu 10A |
| Ion Mode | POSITIVE |
| Units | Peak Area Ratio |
Chromatography:
| Chromatography ID: | CH000425 |
| Chromatography Summary: | A modified Bligh-Dyer extraction method was used in the presence of internal standards (IS). Sample analysis was performed in four batches with a Shimadzu 10A HPLC system coupled to a TSQ Quantum Ultra triple quadrupole mass spectrometer operated in SRM mode under ESI(+). A Thermo Betasil C18 column was employed to achieve the optimal sensitivity and separation. |
| Instrument Name: | Shimadzu 10A |
| Column Name: | Thermo Betasil C18 |
| Chromatography Type: | Reversed phase |
MS:
| MS ID: | MS000530 |
| Analysis ID: | AN000594 |
| Instrument Name: | Shimadzu 10A |
| Instrument Type: | Triple quadrupole |
| MS Type: | ESI |
| Ion Mode: | POSITIVE |
