MetaRiPPquest: A Peptidogenomics Approach for the Discovery of Ribosomally Synthesized and Post-translationally Modified Peptides

Hosein Mohimani; Alexey A. Gurevich; Kelsey L. Alexander; C. Benjamin Naman; Tiago Leão; Evgenia Glukhov; Nathan A. Moss; Tal Luzzatto‐Knaan; Fernando Vargas; Louis-Félix Nothias-Scaglia; Nitin  Kumar Singh; Jon G. Sanders; Rodolfo Antonio Salido Benítez; Luke Thompson; Md-Nafiz Hamid; James T. Morton; Alla Mikheenko; Alexander Shlemov; Anton Korobeynikov; Iddo Friedberg; Rob D. Knight; Kasthuri Venkateswaran; William H. Gerwick; Lena G. Gerwick; Pieter C. Dorrestein; Pavel A. Pevzner

doi:10.1101/227504

BioinformaticsbioRxivDec 3, 2017

Preprint

MetaRiPPquest: A Peptidogenomics Approach for the Discovery of Ribosomally Synthesized and Post-translationally Modified Peptides

Hosein Mohimani iD, Alexey A. Gurevich iD, Kelsey L. Alexander iD, C. Benjamin Naman iD, Tiago Leão iD, Evgenia Glukhov iD, Nathan A. Moss, Tal Luzzatto‐Knaan iD, Fernando Vargas iD, Louis-Félix Nothias-Scaglia iD, Nitin Kumar Singh iD, Jon G. Sanders iD, Rodolfo Antonio Salido Benítez, Luke Thompson iD, Md-Nafiz Hamid iD, James T. Morton iD, Alla Mikheenko iD, Alexander Shlemov iD, Anton Korobeynikov iD, Iddo Friedberg iD, Rob D. Knight iD, Kasthuri Venkateswaran iD, William H. Gerwick iD, Lena G. Gerwick iD, Pieter C. Dorrestein iD, Pavel A. Pevzner iD

Abstract

Ribosomally synthesized and post-translationally modified peptides (RiPPs) are an important class of natural products that include many antibiotics and a variety of other bioactive compounds. While recent breakthroughs in RiPP discovery raised the challenge of developing new algorithms for their analysis, peptidogenomic-based identification of RiPPs by combining genome/metagenome mining with analysis of tandem mass spectra remains an open problem. We present here MetaRiPPquest, a software tool for addressing this challenge that is compatible with large-scale screening platforms for natural product discovery. After searching millions of spectra in the Global Natural Products Social (GNPS) molecular networking infrastructure against just six genomic and metagenomic datasets, MetaRiPPquest identified 27 known and discovered 5 novel RiPP natural products.

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