Summary of Study ST003564
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 PR002198. The data can be accessed directly via it's Project DOI: 10.21228/M8HC23 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.
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| Study ID | ST003564 |
| Study Title | Metabolomics of Papanicolaou Tests for the Discovery of Ovarian Cancer Biomarkers |
| Study Type | Metabolomics Studies on Papanicolaou Tests |
| Study Summary | Ovarian cancer (OC) remains one of the most lethal cancers among female populations due to the vast majority of cases going undiagnosed until later stages (stage III, IV). Early detection and treatment of this malignancy provides the best prognosis, but the lack of accurate and sensitive screening tools combined with the presence of ambiguous symptoms hinders these diagnoses. In contrast, screening for cervical cancer via Papanicolaou (Pap) tests is a widespread practice with use spanning the past several decades, reducing this cancer’s morbidity and mortality rates. Two types of Pap smear tests exist: a conventional method where cells from the ectocervix are stained on a glass slide and a liquid-based cytology method. Interestingly, previous studies show evidence of OC cells in Pap tests, suggesting that lipids shed from ovarian tumors may end up in the cervix. The goal of this study is to evaluate the practicality of using liquid-based Pap tests as biospecimens for OC screening-related metabolic studies. Cell pellets, extracted from residual Pap test fluid (RPF), from liquid-based Pap tests from 29 healthy women were analyzed via ultra-high performance liquid chromatography mass spectrometry (UHPLC-MS). This approach facilitated the detection and annotation of 453 unique lipids across 20 lipid subclasses, including ceramides, triacylglycerols, and hexosylceramides. These results demonstrated the feasibility of using an MS-based approach to analyze residual Pap test samples for the discovery of OC-related lipid biomarkers with the goal of detecting OC at early stages of the disease. |
| Institute | Georgia Institute of Technology |
| Department | Chemistry and Biochemistry |
| Laboratory | Fernandez Lab |
| Last Name | Schwiebert |
| First Name | Elisabeth |
| Address | 311 Ferst Dr NW, Atlanta, Georgia, 30318, USA |
| eschwiebert3@gatech.edu | |
| Phone | 4043854432 |
| Submit Date | 2024-10-07 |
| Num Groups | 1 |
| Total Subjects | 29 |
| Num Females | 29 |
| Raw Data Available | Yes |
| Raw Data File Type(s) | mzML |
| Analysis Type Detail | LC-MS |
| Release Date | 2024-11-27 |
| Release Version | 1 |
Select appropriate tab below to view additional metadata details:
Project:
| Project ID: | PR002198 |
| Project DOI: | doi: 10.21228/M8HC23 |
| Project Title: | Metabolomics of Papanicolaou Tests for the Discovery of Ovarian Cancer Biomarkers |
| Project Type: | Untargeted Metabolomics |
| Project Summary: | Ovarian cancer (OC) remains one of the most lethal cancers among female populations due to the vast majority of cases going undiagnosed until later stages (stage III, IV). Early detection and treatment of this malignancy provides the best prognosis, but the lack of accurate and sensitive screening tools combined with the presence of ambiguous symptoms hinders these diagnoses. In contrast, screening for cervical cancer via Papanicolaou (Pap) tests is a widespread practice with use spanning the past several decades, reducing this cancer’s morbidity and mortality rates. Two types of Pap smear tests exist: a conventional method where cells from the ectocervix are stained on a glass slide and a liquid-based cytology method. Interestingly, previous studies show evidence of OC cells in Pap tests, suggesting that lipids shed from ovarian tumors may end up in the cervix. The goal of this study is to evaluate the practicality of using liquid-based Pap tests as biospecimens for OC screening-related metabolic studies. Cell pellets from liquid-based Pap tests from 29 healthy women were analyzed via ultra-high performance liquid chromatography mass spectrometry (UHPLC-MS). This approach facilitated the detection and annotation of 453 unique lipids across 20 lipid subclasses, including ceramides, triacylglycerols, and hexosylceramides. These results demonstrated the feasibility of using an MS-based approach to analyze residual Pap test samples for the discovery of OC-related lipid biomarkers with the goal of detecting OC at early stages of the disease. |
| Institute: | Georgia Institute of Technology |
| Department: | Chemistry and Biochemistry |
| Laboratory: | Fernandez Lab |
| Last Name: | Schwiebert |
| First Name: | Elisabeth |
| Address: | 311 Ferst Dr NW, Atlanta, Georgia, 30318, USA |
| Email: | eschwiebert3@gatech.edu |
| Phone: | 4043854432 |
| Funding Source: | National Institutes of Health's National Center for Advancing Translational Sciences |
Subject:
| Subject ID: | SU003693 |
| Subject Type: | Human |
| Subject Species: | Homo sapiens |
| Taxonomy ID: | 9606 |
| Age Or Age Range: | 50+ |
| Gender: | Female |
| Species Group: | Mammals |
Factors:
Subject type: Human; Subject species: Homo sapiens (Factor headings shown in green)
| mb_sample_id | local_sample_id | Sample source | Sample Type |
|---|---|---|---|
| SA389409 | blank4 | Blank | Blank |
| SA389410 | blank3 | Blank | Blank |
| SA389411 | blank2 | Blank | Blank |
| SA389412 | blank1 | Blank | Blank |
| SA389413 | 111 | Cell Pellet (extracted from RPF) | Control |
| SA389414 | 84 | Cell Pellet (extracted from RPF) | Control |
| SA389415 | 96 | Cell Pellet (extracted from RPF) | Control |
| SA389416 | 99 | Cell Pellet (extracted from RPF) | Control |
| SA389417 | 101 | Cell Pellet (extracted from RPF) | Control |
| SA389418 | 105 | Cell Pellet (extracted from RPF) | Control |
| SA389419 | 132 | Cell Pellet (extracted from RPF) | Control |
| SA389420 | 113 | Cell Pellet (extracted from RPF) | Control |
| SA389421 | 119 | Cell Pellet (extracted from RPF) | Control |
| SA389422 | 76 | Cell Pellet (extracted from RPF) | Control |
| SA389423 | 151 | Cell Pellet (extracted from RPF) | Control |
| SA389424 | 154 | Cell Pellet (extracted from RPF) | Control |
| SA389425 | 160 | Cell Pellet (extracted from RPF) | Control |
| SA389426 | 77 | Cell Pellet (extracted from RPF) | Control |
| SA389427 | 93 | Cell Pellet (extracted from RPF) | Control |
| SA389428 | 74 | Cell Pellet (extracted from RPF) | Control |
| SA389429 | 26 | Cell Pellet (extracted from RPF) | Control |
| SA389430 | 6 | Cell Pellet (extracted from RPF) | Control |
| SA389431 | 73 | Cell Pellet (extracted from RPF) | Control |
| SA389432 | 14 | Cell Pellet (extracted from RPF) | Control |
| SA389433 | 18 | Cell Pellet (extracted from RPF) | Control |
| SA389434 | 20 | Cell Pellet (extracted from RPF) | Control |
| SA389435 | 10 | Cell Pellet (extracted from RPF) | Control |
| SA389436 | 34 | Cell Pellet (extracted from RPF) | Control |
| SA389437 | 43 | Cell Pellet (extracted from RPF) | Control |
| SA389438 | 49 | Cell Pellet (extracted from RPF) | Control |
| SA389439 | 61 | Cell Pellet (extracted from RPF) | Control |
| SA389440 | 69 | Cell Pellet (extracted from RPF) | Control |
| SA389441 | 35 | Cell Pellet (extracted from RPF) | Control |
| SA389442 | QC1 | QC | Pool |
| SA389443 | QC5 | QC | Pool |
| SA389444 | QC4 | QC | Pool |
| SA389445 | QC3 | QC | Pool |
| SA389446 | QC2 | QC | Pool |
| SA389447 | QC00 | QC | Pool |
| SA389448 | QC0 | QC | Pool |
| SA389449 | 45-01 | Supernatant (extracted from RPF) | Control |
| SA389450 | 27-03 | Supernatant (extracted from RPF) | Control |
| SA389451 | 45-02 | Supernatant (extracted from RPF) | Control |
| SA389452 | 45-03 | Supernatant (extracted from RPF) | Control |
| SA389453 | 27-02 | Supernatant (extracted from RPF) | Control |
| SA389454 | 27-01 | Supernatant (extracted from RPF) | Control |
| Showing results 1 to 46 of 46 |
Collection:
| Collection ID: | CO003686 |
| Collection Summary: | Samples were vortexed and centrifuged to separate samples' cell pellet and supernatant layers before undergoing separate extraction methods. The residual BD SurePathTM liquid-based Pap test samples (~2 mL each) were transferred to 2 mL microcentrifuge tubes. Samples were vortexed for 10s followed by centrifugation at approximately 7,130 x g (5000 rpm) for 5 minutes to pellet the cells. Supernatants were removed and saved for further analysis. |
| Sample Type: | Supernatants and cell pellets extracted from residual Pap test fluid |
Treatment:
| Treatment ID: | TR003702 |
| Treatment Summary: | Residual Papanicolaou tests were obtained from the University of Minnesota BioNext Tissue Procurement Facility and stored at 4-5C prior to analysis. |
Sample Preparation:
| Sampleprep ID: | SP003700 |
| Sampleprep Summary: | Cell pellets, extracted from residual Pap test fluid, were dried in a SpeedVac and weighed. Six hundred µL of IPA and 0.2 grams of 500 µm glass beads were then added to each cell pellet, followed by homogenization in a Tissuelyser. Samples were then re-dried in a SpeedVac, and the metabolites were extracted with a biphasic solution comprised of 600 µL chloroform, 600 µL methanol, and 300 µL water. Extracts were sonicated for 5 minutes and then centrifuged at 21,100 x g (14,800 rpm) for 7 minutes. The chloroform extract from each sample was transferred to a 1.5 mL microcentrifuge tube and dried in the SpeedVac. An extraction mixture was prepared by mixing 50 µL of the isotopically labeled internal standards mixture with 3000 µL of IPA. Eighty microliters of this mixture were added to each of the dried chloroform extracts. After IPA extraction, samples underwent a second cycle of sonication for 5 minutes and centrifugation at 21,100 x g (14,800 rpm) for 7 minutes. Cell pellet extracts and supernatant extracts were then transferred to LC-vials for UHPLC-MS analysis. A blank sample was prepared with LC-MS grade IPA and underwent the same preparation process as the samples. A pooled quality control (QC) sample was prepared by mixing 3 µL aliquots of each of the sample extracts. Samples were stored at 4-5 ºC until analysis. |
Combined analysis:
| Analysis ID | AN005855 | AN005856 |
|---|---|---|
| Analysis type | MS | MS |
| Chromatography type | Reversed phase | Reversed phase |
| Chromatography system | Thermo Vanquish | Thermo Vanquish |
| Column | Thermo Accucore C30 (150 x 2.1mm,2.6um) | Thermo Accucore C30 (150 x 2.1mm,2.6um) |
| MS Type | ESI | ESI |
| MS instrument type | Orbitrap | Orbitrap |
| MS instrument name | Thermo Orbitrap ID-X Tribrid | Thermo Orbitrap ID-X Tribrid |
| Ion Mode | POSITIVE | NEGATIVE |
| Units | Peak area | Peak area |
Chromatography:
| Chromatography ID: | CH004447 |
| Chromatography Summary: | Positive Ion Mode; Solvent A: Ammonium Formate in Water/Acetonitrile (40:60 v/v) with 0.1% Formic Acid; Solvent B: 10 mM Ammonium Formate in 2-Isopropanol/Acetonitrile (90:10 v/v) with 0.1% Formic Acid |
| Methods Filename: | Pap_Positive_MS1.pdf |
| Instrument Name: | Thermo Vanquish |
| Column Name: | Thermo Accucore C30 (150 x 2.1mm,2.6um) |
| Column Temperature: | 50 |
| Flow Gradient: | 0 min: 20% B, 0-1 min: 20% B, 1-5 min: 60% B, 5-5.5 min: 70% B, 5.5-8 min: 85% B, 8-8.2: 90% B, 8.2-10.5: 100% B, 10.5-10.7: 100% B, 10.7-12: 20% B |
| Flow Rate: | 0.400 mL/min |
| Solvent A: | 40% water/60% acetonitrile; 10 mM Ammonium Formate; 0.1% Formic Acid |
| Solvent B: | 90% 2-Isopropanol/10% Acetonitrile; 10 mM Ammonium Formate; 0.1% Formic Acid |
| Chromatography Type: | Reversed phase |
| Chromatography ID: | CH004448 |
| Chromatography Summary: | Negative Ion Mode; Solvent A: 10 mM Ammonium Acetate in Water/Acetonitrile (40:60 v/v); Solvent B: 10 mM Ammonium Acetate in 2-Isopropanol/Acetonitrile (90:10 v/v) |
| Methods Filename: | Pap_Negative_MS1.pdf |
| Instrument Name: | Thermo Vanquish |
| Column Name: | Thermo Accucore C30 (150 x 2.1mm,2.6um) |
| Column Temperature: | 50 |
| Flow Gradient: | 0 min: 20% B, 0-1 min: 20% B, 1-5 min: 60% B, 5-5.5 min: 70% B, 5.5-8 min: 85% B, 8-8.2: 90% B, 8.2-10.5: 100% B, 10.5-10.7: 100% B, 10.7-12: 20% B |
| Flow Rate: | 0.400 mL/min |
| Solvent A: | 40% Water/60% Acetonitrile; 10 mM Ammonium Acetate in |
| Solvent B: | 90% 2-Isopropanol/10% Acetonitrile; 10 mM Ammonium Acetate |
| Chromatography Type: | Reversed phase |
MS:
| MS ID: | MS005575 |
| Analysis ID: | AN005855 |
| Instrument Name: | Thermo Orbitrap ID-X Tribrid |
| Instrument Type: | Orbitrap |
| MS Type: | ESI |
| MS Comments: | MS1 Analysis. Raw data files were processed using Compound Discoverer v3.3. |
| Ion Mode: | POSITIVE |
| Acquisition Parameters File: | Pap_Positive_MS1.pdf Pap_Positive_MS2.pdf |
| MS ID: | MS005576 |
| Analysis ID: | AN005856 |
| Instrument Name: | Thermo Orbitrap ID-X Tribrid |
| Instrument Type: | Orbitrap |
| MS Type: | ESI |
| MS Comments: | MS1 Analysis. Raw data files were processed using Compound Discoverer v3.3. |
| Ion Mode: | NEGATIVE |
| Acquisition Parameters File: | Pap_Negative_MS1.pdf Pap_Negative_MS2.pdf |
