The good, the bad, and the ugly: opportunities, challenges, and pitfalls in spatial proteomics modeling

Spatial proteomics has become one of the mainstays of spatial biology at an impressive speed. It enables the in-depth study of protein abundance, localization, and microenvironmental context at the levels of tissues, cells, and subcellular structures. Preserving the native tissue architecture and capturing the functional molecular states that cannot be deduced from transcriptomics, spatial proteomics is breaking new grounds in cellular heterogeneity, small-unit physiological niches, and disease-related tissue organization. This review covers the major strengths ("Good") of the field, including mass spectrometry imaging, single-cell, and subcellular proteomics, by which these technological advancements in protein biology mapping at different scales have been merged. This review also discussed the limitations and trade-offs ("Bad") that consist of issues that cause throughput bottlenecks, sensitivity constraints, antibody specificity problems, and multi-omics integration challenges. Afterwards, this review also points out the pitfalls ("Ugly") that can result in misguided research judgments associated with false spatial gradients, protein delocalization, segmentation artifacts, batch effects, and improperly validated spatial maps. Finally, the review discusses the future research directions that can lead spatial proteomics towards greater advancement, which will lead to revolutionary improvements in biological mechanisms, translational research, and precision medicine.