SalivaPRINT Toolkit - Protein profile evaluation and phenotype stratification

Abstract

The value of the molecular information obtained from saliva is dependent on the use of in vitro and in silico techniques. The main proteins of saliva when separated by capillary electrophoresis enable the establishment of individual profiles with characteristic patterns reflecting each individual phenotype. Different physiological or pathological conditions may be identified by specific protein profiles. The association of each profile to the particular protein composition provides clues as to which biological processes are compromised in each situation. Patient stratification according to different phenotypes often within a particular disease spectrum is especially important for the management of individuals carrying multiple diseases and requiring personalized interventions. In this work we present the SalivaPRINT Toolkit, which enables the analysis of protein profile patterns and patient phenotyping. Additionally, the SalivaPRINT Toolkit allows the identification of molecular weight ranges altered in a particular condition and therefore potentially involved in the underlying dysregulated mechanisms. This tutorial introduces the use of the SalivaPRINT Toolkit command line interface (https://github.com/salivatec/SalivaPRINT) as an independent tool for electrophoretic protein profile evaluation. It provides a detailed overview of its functionalities, illustrated by the application to the analysis of profiles obtained from a healthy population versus a population affected with inflammatory conditions.

Biological significance: We present SalivaPRINT, which serves as a patient characterization tool to identify molecular weights related with particular conditions and, from there, find proteins, which may be involved in the underlying dysregulated cellular mechanisms. The proposed analysis strategy has the potential to boost personalized diagnosis. To our knowledge this is the first independent tool for electrophoretic protein profile evaluation and is crucial when a large number of complex electrophoretic profiles needs to be compared and classified.

Keywords: Protein pattern recognition; Protein phenotypes; Protein profiling.