Limits and Prospects of Molecular Fingerprinting for Phenotyping Biological Systems Revealed through In Silico Modeling

[Image: see text] Molecular fingerprinting via vibrational spectroscopy characterizes the chemical composition of molecularly complex media which enables the classification of phenotypes associated with biological systems. However, the interplay between factors such as biological variability, measurement noise, chemical complexity, and cohort size makes it challenging to investigate their impact on how the classification performs. Considering these factors, we developed an in silico model which generates realistic, but configurable, molecular fingerprints. Using experimental blood-based infrared spectra from two cancer-detection applications, we validated the model and subsequently adjusted model parameters to simulate diverse experimental settings, thereby yielding insights into the framework of molecular fingerprinting. Intriguingly, the model revealed substantial improvements in classifying clinically relevant phenotypes when the biological variability was reduced from a between-person to a within-person level and when the chemical complexity of the spectra was reduced. These findings quantitively demonstrate the potential benefits of personalized molecular fingerprinting and biochemical fractionation for applications in health diagnostics.