Summary of Study ST003859
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
| Study ID | ST003859 |
| Study Title | Evaluation of FASP protocol for a mass spectrometry based multiomics analysis of urine sample |
| 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 | +351968720613 |
| Submit Date | 2024-08-05 |
| Raw Data Available | Yes |
| Raw Data File Type(s) | mzML, d |
| Analysis Type Detail | LC-MS |
| Release Date | 2025-04-24 |
| Release Version | 1 |
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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: | SU003993 |
| 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 | Factor |
|---|---|---|
| SA424421 | Filtrate 01 | Metabolite peak Area |
| SA424422 | Filtrate 02 | Metabolite peak Area |
| SA424423 | Filtrate 03 | Metabolite peak Area |
| SA424424 | Conc 01 | Metabolite peak Area |
| SA424425 | Conc 02 | Metabolite peak Area |
| SA424426 | Conc 03 | Metabolite peak Area |
| SA424427 | Raw01 | Metabolite peak Area |
| SA424428 | Raw02 | Metabolite peak Area |
| SA424429 | Raw03 | Metabolite peak Area |
| Showing results 1 to 9 of 9 |
Collection:
| Collection ID: | CO003986 |
| Collection Summary: | Urine sample was collected from a 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 |
| Collection Method: | Midstream Clean-Catch Urine |
| Volumeoramount Collected: | 50 mL |
| Storage Conditions: | -80℃ |
Treatment:
| Treatment ID: | TR004002 |
| Treatment Summary: | No treatment was applied to the urine samples, as this study aimed to assess metabolic variations within the same sample using two different processing methods during preparation |
Sample Preparation:
| Sampleprep ID: | SP003999 |
| Sampleprep Summary: | Urine samples were divided into three analytical streams: (1) passed through a 10 kDa membrane (collecting both filtrate and residue), (2) untreated original urine. All samples were water-diluted before LC-MS analysis |
| Processing Storage Conditions: | Room temperature |
Combined analysis:
| Analysis ID | AN006341 |
|---|---|
| Chromatography ID | CH004812 |
| MS ID | MS006042 |
| Analysis type | MS |
| Chromatography type | Reversed phase |
| Chromatography system | Bruker TIMS tof MS |
| Column | Bruker Intensity Solo 1.8 C18-2 (2.1 × 100 mm 1.8 μm 90 Å) |
| MS Type | ESI |
| MS instrument type | QTOF |
| MS instrument name | Bruker TIMS tof MS |
| Ion Mode | POSITIVE |
| Units | Area |
Chromatography:
| Chromatography ID: | CH004812 |
| Instrument Name: | Bruker TIMS tof MS |
| Column Name: | Bruker Intensity Solo 1.8 C18-2 (2.1 × 100 mm 1.8 μm 90 Å) |
| Column Temperature: | 30℃ |
| Flow Gradient: | a 1% B solution was used for the first 2 minutes, after which it was gradually increased to 99% B between 2 and 17 minutes. The system was then held at 99% B for 3 minutes |
| Flow Rate: | of 0.25 mL/min |
| Solvent A: | 100% Water; 0.1% Formic Acid |
| Solvent B: | 100% Acetonitrile; 0.1% Formic Acid |
| Chromatography Type: | Reversed phase |
MS:
| MS ID: | MS006042 |
| Analysis ID: | AN006341 |
| Instrument Name: | Bruker TIMS tof MS |
| Instrument Type: | QTOF |
| MS Type: | ESI |
| MS Comments: | positive polarity as the most common metabolites were detected in positive polarity. The capillary voltage was 4500 V, 500V end plate offset, 10 L/min drying gas flow while the drying temperature was 220℃ and the nebulizer pressure was 2.2 bar. The time-of-flight scan range was 20–1300 m/z. Auto-MS/MS mode were operated with a collision energy of 20 eV, the cycle time to 0.5 s with a relative minimum intensity threshold of 400 counts per thousand and a target intensity of 20,000. |
| Ion Mode: | POSITIVE |
