Improvement of molecular networking using in silico fragmentation and subnetwork storage and search

• Grant number: 15/03348-3
• Support Opportunities: Scholarships abroad - Research Internship - Post-doctor
• Start date: July 01, 2015
• End date: March 31, 2016
• Field of knowledge: Interdisciplinary Subjects
• Principal Investigator: Norberto Peporine Lopes
• Grantee: Ricardo Roberto da Silva
• Supervisor: Peter Dorrestein
• Host Institution: Faculdade de Ciências Farmacêuticas de Ribeirão Preto (FCFRP). Universidade de São Paulo (USP). Ribeirão Preto , SP, Brazil
• Institution abroad: University of California, San Diego (UC San Diego), United States
• Associated to the scholarship: 14/01884-2 - Analysis of metabolite profiles obtained by mass spectrometry using graphs, BP.PD

Abstract

Molecular networking combined with a large fragmentation database has a broad range of applications to natural products community. However, the compound identification is hampered by limitations on the chemical space coverage of fragmentation databases. Recent advances on in silico fragmentation have shown the potential to predict fragmentation spectrum from compound structure libraries, that can be matched against experimental spectrum. The fusion of molecular networking, spectral database matching and in silico fragmentation matching can extend the applications of networking beyond the known chemical space. Once we achieve a comprehensively annotated molecular network, expert knowledge for network manual inspection is still require. This project aims to create a simple proof of concept application, that can add in silico fragmentation annotation to the molecular network generated by GnPS, and search subnetworks created and stored by users. The ability of store annotated network signatures on large network can further impact on several applications and accelerate the understanding of metabolism. (AU)

Scientific publications

(6)

(References retrieved automatically from Web of Science and SciELO through information on FAPESP grants and their corresponding numbers as mentioned in the publications by the authors)

BOUSLIMANI, AMINA; MELNIK, ALEXEY V.; XU, ZHENJIANG; AMIR, AMNON; DA SILVA, RICARDO R.; WANG, MINGXUN; BANDEIRA, NUNO; ALEXANDROV, THEODORE; KNIGHT, ROB; DORRESTEIN, PIETER C.. Lifestyle chemistries from phones for individual profiling. Proceedings of the National Academy of Sciences of the United States of America, v. 113, n. 48, p. E7645-E7654, NOV 29 2016. (15/03348-3)

CRUSEMANN, MAX; O'NEILL, ELLIS C.; LARSON, CHARLES B.; MELNIK, ALEXEY V.; FLOROS, DIMITRIOS J.; DA SILVA, RICARDO R.; JENSEN, PAUL R.; DORRESTEIN, PIETER C.; MOORE, BRADLEY S.. Prioritizing Natural Product Diversity in a Collection of 146 Bacterial Strains Based on Growth and Extraction Protocols. Journal of Natural Products, v. 80, n. 3, SI, p. 588-597, MAR 2017. (15/03348-3)

DA SILVA, RICARDO R.; WANG, MINGXUN; NOTHIAS, LOUIS-FELIX; VAN DER HOOFT, JUSTIN J. J.; CARABALLO-RODRIGUEZ, ANDRES MAURICIO; FOX, EVAN; BALUNAS, MARCY J.; KLASSEN, JONATHAN L.; LOPES, NORBERTO PEPORINE; DORRESTEIN, PIETER C.. Propagating annotations of molecular networks using in silico fragmentation. PLOS COMPUTATIONAL BIOLOGY, v. 14, n. 4, APR 2018. (14/01884-2, 14/50265-3, 15/03348-3)

QUINN, ROBERT A.; NAVAS-MOLINA, JOSE A.; HYDE, EMBRIETTE R.; SONG, SE JIN; VAZQUEZ-BAEZA, YOSHIKI; HUMPHREY, GREG; GAFFNEY, JAMES; MINICH, JEREMIAH J.; MELNIK, ALEXEY V.; HERSCHEND, JAKOB; et al. From Sample to Multi-Omics Conclusions in under 48 Hours. MSYSTEMS, v. 1, n. 2, MAR-APR 2016. (15/03348-3)

CRUSEMANN, MAX; O'NEILL, ELLIS C.; LARSON, CHARLES B.; MELNIK, ALEXEY V.; FLOROS, DIMITRIOS J.; DA SILVA, RICARDO R.; JENSEN, PAUL R.; DORRESTEIN, PIETER C.; MOORE, BRADLEY S.. Prioritizing Natural Product Diversity in a Collection of 146 Bacterial Strains Based on Growth and Extraction Protocols. Journal of Natural Products, v. 80, n. 3, p. 10-pg., 2017-03-01. (15/03348-3)

BOUSLIMANI, AMINA; MELNIK, ALEXEY V.; XU, ZHENJIANG; AMIR, AMNON; DA SILVA, RICARDO R.; WANG, MINGXUN; BANDEIRA, NUNO; ALEXANDROV, THEODORE; KNIGHT, ROB; DORRESTEIN, PIETER C.. Lifestyle chemistries from phones for individual profiling. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, v. 113, n. 48, p. 10-pg., 2016-11-29. (15/03348-3)