Reducing Peptide Sequence Bias in Quantitative Mass Spectrometry Data with Machine Learning

Quantitative mass spectrometry measurements of peptides necessarily incorporate sequence-specific biases that reflect the behavior of the peptide during enzymatic digestion and liquid chromatography and in a mass spectrometer. These sequence-specific effects impair quantification accuracy, yielding peptide quantities that are systematically under-or overestimated. We provide empirical evidence for the existence of such biases, and we use a deep neural network, called Pepper, to automatically identify and reduce these biases. The model generalizes to new proteins and new runs within a related set of tandem mass spectrometry experiments, and the learned coefficients themselves reflect expected physicochemical properties of the corresponding peptide sequences. The resulting adjusted abundance measurements are more correlated with mRNA-based gene expression measurements than the unadjusted measurements. Pepper is suitable for data generated on a variety of mass spectrometry instruments and can be used with labeled or label-free approaches and with data-independent or data-dependent acquisition.