Summary of Study ST004249
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 PR002416. The data can be accessed directly via it's Project DOI: 10.21228/M8BN76 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 | ST004249 |
| Study Title | Evaluation of the FASP protocol for a mass spectrometry-based multiomics analysis of a urine sample by GC-MS |
| Study Summary | Integrative multi-omics analysis of biological specimens such as tissues and biofluids (e.g., plasma and urine) is a powerful approach for gaining comprehensive understanding of the complex biological systems as well as in the identification of disease biomarkers. The great majority of omics datasets collected thus far resulted from a single omic (e.g. proteomics, metabolomics, lipidomics and others) study, which represents a challenge for any subsequent multiomics integration analysis. Filter Aided Sample Preparation (FASP) is a rapid and well-established technique for facilitating bottom-up proteomics preparation. However, FASP has only been employed in proteomics analysis and its utility for simultaneously isolating other biomolecules remains largely unexplored. This study assesses the performance of FASP as a convenient protocol to isolate protein and metabolite fraction from the same urine sample. Here FASP based LC-MS/MS analysis resulted in the identification of 3163 non-redundant peptides, 957 of which were unique protein groups. In parallel, LC-Qtof-MS and GC-MS/MS analysis of metabolites fraction obtained from urine solvent based extraction, FASP filtrate, FASP residue (concentrated protein) detected 145 metabolites by LC-MS and 139 metabolites by GC-MS. Our study demonstrates that the outcomes from FASP filtrate are comparable to those from solid phase extraction or FASP residue, in terms of both qualitative and quantitative analysis. Arguing that the proposed multiomics- FASP protocol should be considered for a multiomics single-step sample preparation analysis. |
| Institute | Nova University of Lisbon |
| Department | Department of Chemistry |
| Laboratory | LAQV-REQUIMTE |
| Last Name | Mousa |
| First Name | Muath |
| Address | Largo da Torre, 2829-516 Caparica, Portugal |
| m.mousa@campus.fct.unl.pt | |
| Phone | +971528637857 |
| Submit Date | 2024-08-06 |
| Raw Data Available | Yes |
| Raw Data File Type(s) | qgd |
| Analysis Type Detail | GC-MS |
| Release Date | 2025-10-22 |
| Release Version | 1 |
Select appropriate tab below to view additional metadata details:
Project:
| Project ID: | PR002416 |
| Project DOI: | doi: 10.21228/M8BN76 |
| Project Title: | Evaluation of FASP protocol for a mass spectrometry based multiomics analysis of urine sample |
| Project Summary: | Integrative multi-omics analysis of biological specimens such as tissues and biofluids (e.g., plasma and urine) is a powerful approach for gaining comprehensive understanding of the complex biological systems as well as in the identification of disease biomarkers. The great majority of omics datasets collected thus far resulted from a single omic (e.g. proteomics, metabolomics, lipidomics and others) study, which represents a challenge for any subsequent multiomics integration analysis. Filter Aided Sample Preparation (FASP) is a rapid and well-established technique for facilitating bottom-up proteomics preparation. However, FASP has only been employed in proteomics analysis and its utility for simultaneously isolating other biomolecules remains largely unexplored. This study assesses the performance of FASP as a convenient protocol to isolate protein and metabolite fraction from the same urine sample. Here FASP based LC-MS/MS analysis resulted in the identification of 3163 non-redundant peptides, 957 of which were unique protein groups. In parallel, LC-Qtof-MS and GC-MS/MS analysis of metabolites fraction obtained from urine solvent based extraction, FASP filtrate, FASP residue (concentrated protein) detected 145 metabolites by LC-MS and 139 metabolites by GC-MS. Our study demonstrates that the outcomes from FASP filtrate are comparable to those from solid phase extraction or FASP residue, in terms of both qualitative and quantitative analysis. Arguing that the proposed multiomics- FASP protocol should be considered for a multiomics single-step sample preparation analysis. |
| Institute: | Nova University of Lisbon |
| Department: | Department of Chemistry |
| Laboratory: | LAQV-REQUIMTE |
| Last Name: | Mousa |
| First Name: | Muath |
| Address: | Largo da Torre, 2829-516 Caparica, Portugal |
| Email: | m.mousa@campus.fct.unl.pt |
| Phone: | +351968720613 |
Subject:
| Subject ID: | SU004401 |
| Subject Type: | Human |
| Subject Species: | Homo sapiens |
| Taxonomy ID: | 9606 |
Factors:
Subject type: Human; Subject species: Homo sapiens (Factor headings shown in green)
| mb_sample_id | local_sample_id | Sample source | Factor |
|---|---|---|---|
| SA496416 | Filtrate 01 | Urine | Metabolite peak Area |
| SA496417 | Filtrate 02 | Urine | Metabolite peak Area |
| SA496418 | Filtrate 03 | Urine | Metabolite peak Area |
| SA496419 | Conc 01 | Urine | Metabolite peak Area |
| SA496420 | Conc 02 | Urine | Metabolite peak Area |
| SA496421 | Raw01 | Urine | Metabolite peak Area |
| SA496422 | Raw02 | Urine | Metabolite peak Area |
| SA496423 | Raw03 | Urine | Metabolite peak Area |
| Showing results 1 to 8 of 8 |
Collection:
| Collection ID: | CO004394 |
| Collection Summary: | Urine sample was collected from a volunteer member of disease biomarker group at the University of Sharjah. The participant gave informed consent for inclusion before enrollment in this study. The sample were centrifuged 5000 x g to remove the precipitated cells, the supernatant was transferred to new centrifuged tube and frozen at -80℃ until it is needed. |
| Sample Type: | Urine |
Treatment:
| Treatment ID: | TR004410 |
| Treatment Summary: | From each step, 100 µL of urine were diluted with 500 µL methanol, vortexed for 30 s and centrifuged at 10,000 x g. from the supernatant, 500 µL were transferred to 1.5 mL centrifuge tube and evaporated using centrifugal vacuum concentrator until drying. The samples were derivatized by adding 100 µL of N-Methyl-N-trimethylsilyltrifluoroacetamide (MSTFA) + 1% TMCS and 100 µL hexane then incubated at 60°C for 30 min. |
Sample Preparation:
| Sampleprep ID: | SP004407 |
| Sampleprep Summary: | From each step, 100 µL of urine were diluted with 500 µL methanol, vortexed for 30 s and centrifuged at 10,000 x g. from the supernatant, 500 µL were transferred to 1.5 mL centrifuge tube and evaporated using centrifugal vacuum concentrator until drying. The samples were derivatized by adding 100 µL of N-Methyl-N-trimethylsilyltrifluoroacetamide (MSTFA) + 1% TMCS and 100 µL hexane then incubated at 60°C for 30 min. The derivatized samples were filtered by 0.2 µm PTFE membrane syringe filter and transferred to HPLC vials for GC-MS/MS analysis. |
Combined analysis:
| Analysis ID | AN007072 |
|---|---|
| Chromatography ID | CH005369 |
| MS ID | MS006769 |
| Analysis type | MS |
| Chromatography type | GC |
| Chromatography system | Shimadzu GC-2010 |
| Column | Phenomenex Zebron ZB-5 (30 m x 0.25 mm, 1 µm) |
| MS Type | EI |
| MS instrument type | Triple quadrupole |
| MS instrument name | Shimazu TQ8040 |
| Ion Mode | POSITIVE |
| Units | Peak Area |
Chromatography:
| Chromatography ID: | CH005369 |
| Chromatography Summary: | The GC oven temperature maintained at 100°C for 4 min increased to 320°C at the rate of 4°C/min and kept for 8 min to have a total run of 67 min. The interface temperature was set at 280°C while the EI-MS ion source held at the temperature of 200°C. MRM mode for a total of 475 organic acid metabolites were operated by the triple quad mass detector |
| Instrument Name: | Shimadzu GC-2010 |
| Column Name: | Phenomenex Zebron ZB-5 (30 m x 0.25 mm, 1 µm) |
| Column Temperature: | 100°C |
| Flow Gradient: | The GC oven temperature maintained at 100°C for 4 min increased to 320°C at the rate of 4°C/min and kept for 8 min to have a total run of 67 min. The interface temperature was set at 280°C while the EI-MS ion source held at the temperature of 200°C. MRM mode for a total of 475 organic acid metabolites were operated by the triple quad mass detector |
| Flow Rate: | 1.1 mL/min |
| Solvent A: | He |
| Solvent B: | He |
| Chromatography Type: | GC |
MS:
| MS ID: | MS006769 |
| Analysis ID: | AN007072 |
| Instrument Name: | Shimazu TQ8040 |
| Instrument Type: | Triple quadrupole |
| MS Type: | EI |
| MS Comments: | EI-MS ion source held at the temperature of 200°C. MRM mode for a total of 475 organic acid metabolites were operated by the triple quad mass detector |
| Ion Mode: | POSITIVE |
