PeposX-Exhaust: A lightweight and efficient tool for identification of short peptides

•An open-source, lightweight and efficient tool, PeposX-Exhaust, was developed for short peptide identification.•The algorithm was proved of high accuracy with the adjusted accuracy rate reaching 98.55% for the known peptide mixtures.•Much higher accuracy and better performance was obtained by the tool rather than the other tools.•Hundreds of short peptides were efficiently identified from the food-derived protein hydrolysates. Short peptides have become the focus of recent research due to their variable bioactivities, good digestibility and wide existences in food-derived protein hydrolysates. However, due to the high complexity of the samples, identifying short peptides still remains a challenge. In this work, a tool, named PeposX-Exhaust, was developed for short peptide identification. Through validation with known peptides, PeposX-Exhaust identified all the submitted spectra and the accuracy rate reached 75.36%, and the adjusted accuracy rate further reached 98.55% when with top 5 candidates considered. Compared with other tools, the accuracy rate by PeposX-Exhaust was at least 70% higher than two database-search tools and 15% higher than the other two de novo-sequencing tools, respectively. For further application, the numbers of short peptides identified from soybean, walnut, collagen and bonito protein hydrolysates reached 1145, 628, 746 and 681, respectively. This fully demonstrated the superiority of the tool in short peptide identification.