Summary of Study ST000344
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 PR000276. The data can be accessed directly via it's Project DOI: 10.21228/M83W3X This work is supported by NIH grant, U2C- DK119886.
See: https://www.metabolomicsworkbench.org/about/howtocite.php
| Study ID | ST000344 |
| Study Title | Effects of dietary supplement on hamster metabolism |
| Study Summary | This experiment aims to analyze spent media from a protein over-expression system. The treatment was a lipid supplement given to hamsters. The spent media was then analyzed to see how the lipid supplement affected lipid metabolism. |
| Institute | University of California, Davis |
| Department | Genome and Biomedical Sciences Facility |
| Laboratory | WCMC Metabolomics Core |
| Last Name | Fiehn |
| First Name | Oliver |
| Address | 1315 Genome and Biomedical Sciences Facility, 451 Health Sciences Drive, Davis, CA 95616 |
| ofiehn@ucdavis.edu | |
| Phone | (530) 754-8258 |
| Submit Date | 2016-02-09 |
| Num Groups | 6 |
| Total Subjects | 28 |
| Raw Data Available | Yes |
| Raw Data File Type(s) | d |
| Analysis Type Detail | LC-MS |
| Release Date | 2016-03-03 |
| Release Version | 1 |
Select appropriate tab below to view additional metadata details:
Project:
| Project ID: | PR000276 |
| Project DOI: | doi: 10.21228/M83W3X |
| Project Title: | Effects of dietary supplement on hamster metabolism |
| Project Summary: | This experiment aims to analyze spent media from a protein over-expression system. The treatment was a lipid supplement given to hamsters. The spent media was then analyzed to see how the lipid supplement affected lipid metabolism. |
| Institute: | University of California, Davis |
| Department: | Genome and Biomedical Sciences Facility |
| Laboratory: | WCMC Metabolomics Core |
| Last Name: | Fiehn |
| First Name: | Oliver |
| Address: | 1315 Genome and Biomedical Sciences Facility, 451 Health Sciences Drive, Davis, CA 95616 |
| Email: | ofiehn@ucdavis.edu |
| Phone: | (530) 754-8258 |
| Funding Source: | NIH U24DK097154 |
Subject:
| Subject ID: | SU000364 |
| Subject Type: | Animal |
| Subject Species: | Mesocricetus auratus |
| Taxonomy ID: | 10036 |
| Species Group: | Mammal |
Factors:
Subject type: Animal; Subject species: Mesocricetus auratus (Factor headings shown in green)
| mb_sample_id | local_sample_id | Treatment |
|---|---|---|
| SA015262 | CHO cells_Elhofy_d14 C_005.d | Control |
| SA015263 | CHO cells_Elhofy_d17 C_006.d | Control |
| SA015264 | CHO cells_Elhofy_d2 C_001.d | Control |
| SA015265 | CHO cells_Elhofy_d11 C_004.d | Control |
| SA015266 | CHO cells_Elhofy_d5 C_002.d | Control |
| SA015267 | CHO cells_Elhofy_d8 C_003.d | Control |
| SA015268 | CHO cells_Elhofy_d17 E_012.d | Lipid Supplement |
| SA015269 | CHO cells_Elhofy_d2 E_007.d | Lipid Supplement |
| SA015270 | CHO cells_Elhofy_d5 E_008.d | Lipid Supplement |
| SA015271 | CHO cells_Elhofy_d11 E_010.d | Lipid Supplement |
| SA015272 | CHO cells_Elhofy_d8 E_009.d | Lipid Supplement |
| SA015273 | CHO cells_Elhofy_d14 E_011.d | Lipid Supplement |
| Showing results 1 to 12 of 12 |
Collection:
| Collection ID: | CO000358 |
| Collection Summary: | This is spent media from a protein over-expression system. The media is serum free from the DG44 CHO cell line |
| Collection Protocol Filename: | StudyDesignAdamElhofy10202015.pdf |
| Sample Type: | Cultured cells |
Treatment:
| Treatment ID: | TR000378 |
| Treatment Summary: | 2x6 each: The treatment is the addition of a lipid supplement. |
| Treatment Protocol Filename: | StudyDesignAdamElhofy10202015.pdf |
Sample Preparation:
| Sampleprep ID: | SP000371 |
| Sampleprep Summary: | None |
Combined analysis:
| Analysis ID | AN000557 | AN000558 |
|---|---|---|
| Analysis type | MS | MS |
| Chromatography type | Reversed phase | Reversed phase |
| Chromatography system | Agilent 6530 | Agilent 6550 |
| Column | Waters Acquity CSH C18 (100 x 2.1mm,1.7um) | Waters Acquity CSH C18 (100 x 2.1mm,1.7um) |
| MS Type | ESI | ESI |
| MS instrument type | QTOF | QTOF |
| MS instrument name | Agilent 6530 QTOF | Agilent 6550 QTOF |
| Ion Mode | POSITIVE | NEGATIVE |
| Units | Peak height | Peak height |
Chromatography:
| Chromatography ID: | CH000394 |
| Chromatography Summary: | UPLC |
| Methods Filename: | Data_Dictionary_Fiehn_laboratory_CSH_QTOF_lipidomics_05-29-2014.pdf |
| Instrument Name: | Agilent 6530 |
| Column Name: | Waters Acquity CSH C18 (100 x 2.1mm,1.7um) |
| Column Pressure: | 450-850 bar |
| Column Temperature: | 65 C |
| Flow Gradient: | 15% B to 99% B |
| Flow Rate: | 0.6 mL/min |
| Sample Injection: | 1.67 uL |
| Solvent A: | 60% acetonitrile/40% water; 10mM formic acid; 10mM ammonium formate |
| Solvent B: | 90% isopropanol/10% acetonitrile; 10mM formic acid; 10mM ammonium formate |
| Analytical Time: | 13 min |
| Capillary Voltage: | 3500 |
| Time Program: | 15 min |
| Weak Wash Solvent Name: | Isopropanol |
| Weak Wash Volume: | 5 seconds |
| Strong Wash Solvent Name: | Same |
| Target Sample Temperature: | Autosampler temp 4 C |
| Randomization Order: | Excel |
| Chromatography Type: | Reversed phase |
| Chromatography ID: | CH000395 |
| Chromatography Summary: | UPLC |
| Methods Filename: | Data_Dictionary_Fiehn_laboratory_CSH_QTOF_lipidomics_05-29-2014.pdf |
| Instrument Name: | Agilent 6550 |
| Column Name: | Waters Acquity CSH C18 (100 x 2.1mm,1.7um) |
| Column Pressure: | 450-850 bar |
| Column Temperature: | 65 C |
| Flow Gradient: | 15% B to 99% B |
| Flow Rate: | 0.6 mL/min |
| Sample Injection: | 5.0 uL |
| Solvent A: | 40% water/60% acetonitrile; 0.1% formic acid; 10 mM ammonium formate |
| Solvent B: | 90% isopropanol/10% acetonitrile; 10mM acetic acid; 10mM ammonium acetate |
| Analytical Time: | 13 min |
| Capillary Voltage: | 3500 |
| Time Program: | 15 min |
| Weak Wash Solvent Name: | Isopropanol |
| Weak Wash Volume: | 5 seconds |
| Strong Wash Solvent Name: | Same |
| Target Sample Temperature: | Autosampler temp 4 C |
| Randomization Order: | Excel |
| Chromatography Type: | Reversed phase |
MS:
| MS ID: | MS000493 |
| Analysis ID: | AN000557 |
| Instrument Name: | Agilent 6530 QTOF |
| Instrument Type: | QTOF |
| MS Type: | ESI |
| MS Comments: | Lipidomics runs are MS1 data; Identifications made from pooled MS/MS runs |
| Ion Mode: | POSITIVE |
| Capillary Voltage: | 3500 |
| Collision Gas: | Nitrogen |
| Dry Gas Flow: | 8 l/min |
| Dry Gas Temp: | 325 |
| Fragment Voltage: | 120 |
| Fragmentation Method: | Auto MS/MS |
| Ion Source Temperature: | 325 |
| Ion Spray Voltage: | 1000 |
| Ionization: | Pos |
| Precursor Type: | Intact Molecule |
| Reagent Gas: | Nitrogen |
| Source Temperature: | 325 C |
| Dataformat: | .d |
| Desolvation Gas Flow: | 11 l/min |
| Desolvation Temperature: | 350 C |
| Nebulizer: | 35 psig |
| Octpole Voltage: | 750 |
| Scan Range Moverz: | 60-1700 Da |
| Scanning Cycle: | 2 Hz |
| Scanning Range: | 60-1700 Da |
| Skimmer Voltage: | 65 |
| MS ID: | MS000494 |
| Analysis ID: | AN000558 |
| Instrument Name: | Agilent 6550 QTOF |
| Instrument Type: | QTOF |
| MS Type: | ESI |
| MS Comments: | Lipidomics runs are performed in negative and positve mode (two filenames) |
| Ion Mode: | NEGATIVE |
| Capillary Voltage: | 3500 |
| Collision Gas: | Nitrogen |
| Dry Gas Flow: | 13 l/min |
| Dry Gas Temp: | 200 |
| Fragment Voltage: | 175 |
| Fragmentation Method: | Auto MS/MS |
| Ion Source Temperature: | 325 |
| Ion Spray Voltage: | 1000 |
| Ionization: | Neg |
| Precursor Type: | Intact Molecule |
| Reagent Gas: | Nitrogen |
| Source Temperature: | 325 C |
| Dataformat: | .d |
| Desolvation Gas Flow: | 11 l/min |
| Desolvation Temperature: | 350 C |
| Nebulizer: | 35 psig |
| Octpole Voltage: | 750 |
| Scan Range Moverz: | 60-1700 Da |
| Scanning Cycle: | 2 Hz |
| Scanning Range: | 60-1700 Da |
| Skimmer Voltage: | 65 |
