Summary of Study ST002368
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 PR001499. The data can be accessed directly via it's Project DOI: 10.21228/M8ZM62 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.
| Study ID | ST002368 |
| Study Title | Sperm Environmental Epigenetics and Development Study (SEEDS) |
| Study Summary | Infertility is one of the most common reproductive health disorders affecting 16% of couples in the U.S. Most concerning are the new meta-analysis data showing that sperm counts among men in developed countries have declined over 50% in the past four decades. With no sign of reversing this downward trajectory, we may not only be facing a fertility crisis, but low sperm count also has wider public health implications, including increased risks in morbidity and mortality. Given this dramatic decrease in sperm quality over a short period, genetic influences are likely not attributable, but rather, environmental factors encountered over the life-course. The objective of this pilot project is to determine the feasibility of generating metabolomic data from human seminal plasma collected as part of the ongoing SEEDS cohort. |
| Institute | Wayne State University |
| Last Name | Pilsner |
| First Name | Rick |
| Address | 275 E. Hancock Street, Detroit, MI, USA |
| rpilsner@wayne.edu | |
| Phone | 917-557-2499 |
| Submit Date | 2022-11-17 |
| Total Subjects | 10 |
| Raw Data Available | Yes |
| Raw Data File Type(s) | raw(Thermo) |
| Analysis Type Detail | LC-MS |
| Release Date | 2023-05-12 |
| Release Version | 1 |
Select appropriate tab below to view additional metadata details:
Project:
| Project ID: | PR001499 |
| Project DOI: | doi: 10.21228/M8ZM62 |
| Project Title: | Sperm Environmental Epigenetics and Development Study (SEEDS) |
| Project Type: | C18 Reversed-Phase Broad Spectrum Metabolomics |
| Project Summary: | Infertility is one of the most common reproductive health disorders affecting 16% of couples in the U.S. Most concerning are the new meta-analysis data showing that sperm counts among men in developed countries have declined over 50% in the past four decades. With no sign of reversing this downward trajectory, we may not only be facing a fertility crisis, but low sperm count also has wider public health implications, including increased risks in morbidity and mortality. Given this dramatic decrease in sperm quality over a short period, genetic influences are likely not attributable, but rather, environmental factors encountered over the life-course. The objective of this pilot project is to determine the feasibility of generating metabolomic data from human seminal plasma collected as part of the ongoing SEEDS cohort. |
| Institute: | NC HHEAR Hub |
| Department: | Untargeted Analysis |
| Laboratory: | Sumner Lab |
| Last Name: | Li |
| First Name: | Yuanyuan |
| Address: | 500 Laureate Way, Kannapolis, NC 28081 |
| Email: | yuanyli4@unc.edu |
| Phone: | 9843770693 |
Subject:
| Subject ID: | SU002457 |
| Subject Type: | Human |
| Subject Species: | Homo sapiens |
| Taxonomy ID: | 9606 |
| Gender: | Male |
Factors:
Subject type: Human; Subject species: Homo sapiens (Factor headings shown in green)
| mb_sample_id | local_sample_id | Seminal quality | Live Birth |
|---|---|---|---|
| SA237254 | S_3 | LSQ | Live birth |
| SA237255 | S_4 | LSQ | Live birth |
| SA237256 | S_5 | LSQ | Not-live birth |
| SA237257 | S_1 | LSQ | Not-live birth |
| SA237258 | S_2 | LSQ | Not-live birth |
| SA237259 | SP_2_2 | N/A | N/A |
| SA237260 | NIST_2_1 | N/A | N/A |
| SA237261 | SP_1_2 | N/A | N/A |
| SA237262 | NIST_1_1 | N/A | N/A |
| SA237263 | SP_2_1 | N/A | N/A |
| SA237264 | SP_1_1 | N/A | N/A |
| SA237265 | NIST_2_2 | N/A | N/A |
| SA237266 | NIST_1_2 | N/A | N/A |
| SA237267 | S_9 | NSQ | Live birth |
| SA237268 | S_7 | NSQ | Live birth |
| SA237269 | S_6 | NSQ | Not-live birth |
| SA237270 | S_10 | NSQ | Not-live birth |
| SA237271 | S_8 | NSQ | Not-live birth |
| Showing results 1 to 18 of 18 |
Collection:
| Collection ID: | CO002450 |
| Collection Summary: | Semen samples were collected in a sterile plastic specimen cup after a 2–3-day abstinence period. To separate motile sperm from the seminal plasma, semen samples were processed using a two-step (80 and 40%) gradient fractionation. The seminal plasma was removed from the top of the gradient and placed in a sterile tube and frozen at -80oC until analyses. |
| Sample Type: | Seminal plasma |
| Storage Conditions: | -80℃ |
Treatment:
| Treatment ID: | TR002469 |
| Treatment Summary: | N/A |
Sample Preparation:
| Sampleprep ID: | SP002463 |
| Sampleprep Summary: | Seminal plasma samples (500 µL each) were shipped from Dr. Pilsner’s lab at the University of Massachusetts Amherst to the NC HHEAR Hub with dry ice and stored at -80 °C until analysis. NIST blood plasma aliquots (SRM 1950, 50 µL) were provided by the NC HHEAR hub and used external reference materials. All samples (including study samples and NIST reference materials) were thawed at 4 °C overnight. The seminal plasma sample (50 µL) was transferred from the shipped original tubes to a new set of pre-labeled Lo-Bind Eppendorf tubes for sample preparation. A quality control total pool was made by pooling an additional 7-µL seminal plasma from each of the original samples into a new Lo-Bind Eppendorf tube and then distributed into multiple aliquots within 50 µL each to use as quality control study pools (QCSPs) ran throughout the whole study. LC-MS grade water aliquots (50 µL) were used as blanks. All samples, including study samples, QCSPs, NIST reference material samples, and blanks, were mixed with 400 µL methanol containing 500 ng/mL tryptophan-d5 (internal standard) and vortexed by the multiple tube vortex mixer for 2 min at 5000 rpm at room temperature. The supernatants (350 µL) were transferred into pre-labeled 2.0 mL Lo-bind Eppendorf tubes and then dried by a SpeedVac overnight. For immediate analysis, 100 µL of water-methanol solution (95:5, v/v) was used to reconstitute the dried extracts, and the samples were thoroughly mixed on the multiple tube vortex mixer for 10 min at 5000 rpm at room temperature and then centrifuged at 4°C for 10 min at 16,000 rcf. The supernatant was transferred to pre-labeled autosampler vials for data acquisition by the instrument. |
| Processing Storage Conditions: | On ice |
| Extract Storage: | Described in summary |
Combined analysis:
| Analysis ID | AN003863 |
|---|---|
| Analysis type | MS |
| Chromatography type | Reversed phase |
| Chromatography system | Thermo Scientific™ Vanquish™ UPHPLC |
| Column | Acquity UPLC HSS T3 C18 (100 x 2.1mm, 1.8um) |
| MS Type | ESI |
| MS instrument type | Orbitrap |
| MS instrument name | Thermo Q Exactive HF-X Orbitrap |
| Ion Mode | POSITIVE |
| Units | Intensity |
Chromatography:
| Chromatography ID: | CH002861 |
| Chromatography Summary: | Reverse phase |
| Instrument Name: | Thermo Scientific™ Vanquish™ UPHPLC |
| Column Name: | Acquity UPLC HSS T3 C18 (100 x 2.1mm, 1.8um) |
| Column Pressure: | 6000-10000 |
| 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 6. 22.00 0.4 99.0 1.0 5 |
| Flow Rate: | 0.4 ml/min |
| Injection Temperature: | 8 |
| Solvent A: | 100% water; 0.1% formic acid |
| Solvent B: | 100% methanol; 0.1% formic acid |
| Randomization Order: | Randomized |
| Chromatography Type: | Reversed phase |
MS:
| MS ID: | MS003604 |
| Analysis ID: | AN003863 |
| Instrument Name: | Thermo Q Exactive HF-X Orbitrap |
| Instrument Type: | Orbitrap |
| MS Type: | ESI |
| MS Comments: | Instrument: Thermo Q Exactive HFx Software: Xcalibur 4.1.31.9 for data acquisition; Progenesis QI 2.4 for data preprocessing |
| Ion Mode: | POSITIVE |
| Capillary Temperature: | 320 °C |
| Capillary Voltage: | 3.5 KV |
| Collision Energy: | 20-45, ramp |
| Collision Gas: | N2 |
| Dry Gas Flow: | 55 |
| Dry Gas Temp: | 400°C |
| Fragmentation Method: | CID |
| Desolvation Gas Flow: | 55 |
