Dereplication of peptidic natural products through database search of mass spectra

Dereplication, sequencing and identification of peptidic natural products: from genome mining to peptidogenomics to spectral networks

(2016) Hosein Mohimani et al.   NATURAL PRODUCT REPORTS

Sharing and community curation of mass spectrometry data with Global Natural Products Social Molecular Networking

(2016) Mingxun Wang et al.   NATURE BIOTECHNOLOGY

Molecular Networking and Pattern-Based Genome Mining Improves Discovery of Biosynthetic Gene Clusters and their Products from Salinispora Species

(2015) Katherine R. Duncan et al.   CHEMISTRY & BIOLOGY

A new antibiotic kills pathogens without detectable resistance

(2015) Losee L. Ling et al.   NATURE

Minimum Information about a Biosynthetic Gene cluster

(2015) Marnix H Medema et al.   Nature Chemical Biology

Computational approaches to natural product discovery

(2015) Marnix H Medema et al.   Nature Chemical Biology

A chemocentric view of the natural product inventory

(2015) Christopher T Walsh   Nature Chemical Biology

The re-emergence of natural products for drug discovery in the genomics era

(2015) Alan L. Harvey et al.   NATURE REVIEWS DRUG DISCOVERY

Illuminating the dark matter in metabolomics: Fig. 1.

(2015) Ricardo R. da Silva et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Molecular cartography of the human skin surface in 3D

(2015) Amina Bouslimani et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Small molecules from the human microbiota

(2015) M. S. Donia et al.   SCIENCE

Using fragmentation trees and mass spectral trees for identifying unknown compounds in metabolomics

(2015) Arpana Vaniya et al.   TRAC-TRENDS IN ANALYTICAL CHEMISTRY

Automated Genome Mining of Ribosomal Peptide Natural Products

(2014) Hosein Mohimani et al.   ACS Chemical Biology

Insights into naturally minimised Streptomyces albus J1074 genome

(2014) Nestor Zaburannyi et al.   BMC GENOMICS

Cyclic Lipodepsipeptides Produced by Pseudomonas spp. Naturally Present in Raw Milk Induce Inhibitory Effects on Microbiological Inhibitor Assays for Antibiotic Residue Screening

(2014) Wim Reybroeck et al.   PLoS One

MS-GF+ makes progress towards a universal database search tool for proteomics

(2014) Sangtae Kim et al.   Nature Communications

MS/MS-based networking and peptidogenomics guided genome mining revealed the stenothricin gene cluster in Streptomyces roseosporus

(2013) Wei-Ting Liu et al.   JOURNAL OF ANTIBIOTICS

Molecular Networking as a Dereplication Strategy

(2013) Jane Y. Yang et al.   JOURNAL OF NATURAL PRODUCTS

Surugamides A–E, Cyclic Octapeptides with Four d-Amino Acid Residues, from a Marine Streptomyces sp.: LC–MS-Aided Inspection of Partial Hydrolysates for the Distinction of d- and l-Amino Acid Residues in the Sequence

(2013) Kentaro Takada et al.   JOURNAL OF ORGANIC CHEMISTRY

A New Approach to Evaluating Statistical Significance of Spectral Identifications

(2013) Hosein Mohimani et al.   JOURNAL OF PROTEOME RESEARCH

Champacyclin, a New Cyclic Octapeptide from Streptomyces Strain C42 Isolated from the Baltic Sea

(2013) Alexander Pesic et al.   Marine Drugs

Discovery and development of first in class antifungal caspofungin (CANCIDAS®)—A case study

(2013) James M. Balkovec et al.   NATURAL PRODUCT REPORTS

Interspecies Interactions Stimulate Diversification of the Streptomyces coelicolor Secreted Metabolome

(2013) M. F. Traxler et al.   mBio

Comparative genomics reveals evidence of marine adaptation in Salinispora species

(2012) Kevin Penn et al.   BMC GENOMICS

Ribosomally synthesized and post-translationally modified peptide natural products: overview and recommendations for a universal nomenclature

(2012) Paul G. Arnison et al.   NATURAL PRODUCT REPORTS

Mass spectral molecular networking of living microbial colonies

(2012) J. Watrous et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Dereplicating nonribosomal peptides using an informatic search algorithm for natural products (iSNAP) discovery

(2012) A. Ibrahim et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Multiplex De Novo Sequencing of Peptide Antibiotics

(2011) Hosein Mohimani et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Target-Decoy Approach and False Discovery Rate: When Things May Go Wrong

(2011) Nitin Gupta et al.   JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY

Microbial competition between Bacillus subtilis and Staphylococcus aureus monitored by imaging mass spectrometry

(2011) D. J. Gonzalez et al.   MICROBIOLOGY-SGM

A mass spectrometry–guided genome mining approach for natural product peptidogenomics

(2011) Roland D Kersten et al.   Nature Chemical Biology

NRPSpredictor2—a web server for predicting NRPS adenylation domain specificity

(2011) Marc Röttig et al.   NUCLEIC ACIDS RESEARCH

Predicting Intensity Ranks of Peptide Fragment Ions

(2009) Ari M. Frank   JOURNAL OF PROTEOME RESEARCH

A Ranking-Based Scoring Function for Peptide−Spectrum Matches

(2009) Ari M. Frank   JOURNAL OF PROTEOME RESEARCH

A proteomics approach to discovering natural products and their biosynthetic pathways

(2009) Stefanie B Bumpus et al.   NATURE BIOTECHNOLOGY

Dereplication and de novo sequencing of nonribosomal peptides

(2009) Julio Ng et al.   NATURE METHODS

Drug Discovery and Natural Products: End of an Era or an Endless Frontier?

(2009) J. W.-H. Li et al.   SCIENCE

Antibiotics for Emerging Pathogens

(2009) M. A. Fischbach et al.   SCIENCE

Spectral Probabilities and Generating Functions of Tandem Mass Spectra: A Strike against Decoy Databases

(2008) Sangtae Kim et al.   JOURNAL OF PROTEOME RESEARCH