NPS: scoring and evaluating the statistical significance of peptidic natural product-spectrum matches.

ABSTRACT: MOTIVATION:Peptidic natural products (PNPs) are considered a promising compound class that has many applications in medicine. Recently developed mass spectrometry-based pipelines are transforming PNP discovery into a high-throughput technology. However, the current computational methods for PNP identification via database search of mass spectra are still in their infancy and could be substantially improved. RESULTS:Here we present NPS, a statistical learning-based approach for scoring PNP-spectrum matches. We incorporated NPS into two leading PNP discovery tools and benchmarked them on millions of natural product mass spectra. The results demonstrate more than 45% increase in the number of identified spectra and 20% more found PNPs at a false discovery rate of 1%. AVAILABILITY AND IMPLEMENTATION:NPS is available as a command line tool and as a web application at http://cab.spbu.ru/software/NPS. SUPPLEMENTARY INFORMATION:Supplementary data are available at Bioinformatics online.

SUBMITTER: Tagirdzhanov AM 

PROVIDER: S-EPMC6612854 | biostudies-other | 2019 Jul

REPOSITORIES: biostudies-other