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Published on: July 19, 2019
Hierarchy of MS-Based Evidence
Charlotte Adams1, Michael G Leeming2, David Teschner3
1Adrem Data Lab, Department of Computer Science, University of Antwerp, 2020Antwerpen, Belgium.
Journal of Proteome Research
|June 30, 2026
Summary
Scientific confidence in proteomics requires verifiable raw mass spectrometry (MS) data. A proposed evidence hierarchy will enhance trust by assessing data provenance and traceability, safeguarding against simulated datasets.
Area of Science:
- Proteomics
- Computational Biology
- Data Science
Background:
- Scientific reproducibility hinges on verifiable primary observations.
- Proteomics relies on public deposition of raw mass spectrometry (MS) data for reanalysis.
- Advances in MS data simulation software pose risks to data integrity.
Purpose of the Study:
- To address the vulnerability of MS data to alteration or in silico generation.
- To propose a hierarchy of evidence for MS-based reporting.
- To enhance trust and robustness in published proteomics findings.
Main Methods:
- Developing a hierarchy of evidence for MS data reporting.
- Analogous to established hierarchies in medicine.
- Focusing on traceability and verifiable provenance of raw data files.
Main Results:
- Current standards do not adequately differentiate raw data formats regarding provenance.
- A proposed hierarchy offers a framework for assessing data integrity.
- The framework aims to increase confidence in reported proteomics findings.
Conclusions:
- A hierarchy of evidence is crucial for validating MS data.
- Enhanced data provenance safeguards against fraudulent or simulated results.
- Strengthening data integrity in proteomics is essential for scientific trust.
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