Mass Spectrometry-Based Omics: An Integrated Framework for Analytical Quality, Data Integrity, and Biological Interpretation
- 1University of Warsaw, Faculty of Chemistry, Biological and Chemical Research Centre, Żwirki i Wigury 101, 02-089 Warsaw, Poland
Abstract
Results obtained with mass spectrometry-based omics depend on every stage of the work, from sample collection to data processing. Quality guidance exists for individual omics fields and for individual stages, but it rarely states when a dataset is ready for statistical analysis or how far its interpretation may go. We present a step-by-step protocol for proteomics, metabolomics, lipidomics, glycomics/glycoproteomics, and metallomics that brings existing recommendations and international standards together in six steps: (1) defining the intended use and the target claim, (2) checking that each specimen is fit for analysis, (3) preparing samples and acquiring data under control, (4) checking the dataset before release, (5) analysing and interpreting the data, including the use of tools based on artificial intelligence, and (6) verifying the findings and reporting. For each step, the protocol lists the required input, the actions to be taken, a checkpoint with acceptance criteria set in advance, the corrective action to be taken when the criteria are not met, and the record to be kept. Five claim levels show which conclusions the collected evidence supports. Separate criteria are given for qualitative, semi-quantitative, and quantitative studies, and numerical values from the literature are offered as starting points that each laboratory should replace with its own limits. The protocol can be used as a practical guide for planning, carrying out, and reporting omics studies and for deciding when a finding needs further verification.
Related
- Integrated High-Throughput Mass Spectrometry Framework for Multiplexed Substrate Screening in Enzyme Discovery and Development
- Mass Spectrometry-Based Structural Proteomics and Analytical Ultracentrifugation Characterize the Structures of Oligomeric Apolipoprotein E4 and its Variants
- Automated Virtual Pathology Panels for ML-Assisted Interpretation of Mass Spectrometry Imaging
- Chemical Constructions, Mechanism and Biological Interpretation of Nitroreductase-Responsive Systems: From Hypoxia-Associated Imaging to Activatable Therapy
- Molecular Determinants of IgE-Mediated Food Allergenicity: Structural Dynamics, Processing-Induced Remodeling, and Analytical Interpretation
BibTeX
@article{gawor2026mass,
title = {{Mass Spectrometry-Based Omics: An Integrated Framework for Analytical Quality, Data Integrity, and Biological Interpretation}},
author = {Andrzej Gawor and Ewa Bulska},
journal = {Molecules},
year = {2026},
month = oct,
doi = {10.3390/molecules31203604},
url = {https://www.mdpi.com/1420-3049/31/20/3604},
note = {CC BY 4.0},
}
RIS
TY - JOUR
TI - Mass Spectrometry-Based Omics: An Integrated Framework for Analytical Quality, Data Integrity, and Biological Interpretation
AU - Andrzej Gawor
AU - Ewa Bulska
PY - 2026
DA - 2026/10/10
JO - Molecules
DO - 10.3390/molecules31203604
UR - https://www.mdpi.com/1420-3049/31/20/3604
AB - Results obtained with mass spectrometry-based omics depend on every stage of the work, from sample collection to data processing. Quality guidance exists for individual omics fields and for individual stages, but it rarely states when a dataset is ready for statistical analysis or how far its interpretation may go. We present a step-by-step protocol for proteomics, metabolomics, lipidomics, glycomics/glycoproteomics, and metallomics that brings existing recommendations and international standards together in six steps: (1) defining the intended use and the target claim, (2) checking that each specimen is fit for analysis, (3) preparing samples and acquiring data under control, (4) checking the dataset before release, (5) analysing and interpreting the data, including the use of tools based on artificial intelligence, and (6) verifying the findings and reporting. For each step, the protocol lists the required input, the actions to be taken, a checkpoint with acceptance criteria set in advance, the corrective action to be taken when the criteria are not met, and the record to be kept. Five claim levels show which conclusions the collected evidence supports. Separate criteria are given for qualitative, semi-quantitative, and quantitative studies, and numerical values from the literature are offered as starting points that each laboratory should replace with its own limits. The protocol can be used as a practical guide for planning, carrying out, and reporting omics studies and for deciding when a finding needs further verification.
SN - 1420-3049
ER -