De novo prediction of the elemental composition of peptides and proteins based on a single mass

Abstract

Identification of peptides and proteins is a common task in mass spectrometry-based proteomics but often fails to deliver a comprehensive list of identifications. Downstream analysis, quantitative or qualitative, depends on the outcome of this process. Despite continuous improvement of computational methods, a large fraction of the screened peptides and/or proteins remains unidentified. We introduce here pacMASS, a method that de novo predicts the elemental composition of peptides and small proteins based on a single accurate mass, ie, the observed monoisotopic or average mass. This novel approach returns in a fast and memory efficient manner a limited number of elemental compositions per queried peptide or protein.