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

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

Meta-omics uncover temporal regulation of pathways across oral microbiome genera during in vitro sugar metabolism

(2015) Anna Edlund et al.   ISME Journal

The Generating Function Approach for Peptide Identification in Spectral Networks

(2015) Adrian Guthals et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

CycloBranch: De Novo Sequencing of Nonribosomal Peptides from Accurate Product Ion Mass Spectra

(2015) Jiří Novák et al.   JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY

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

The colibactin warhead crosslinks DNA

(2015) Maria I. Vizcaino et al.   Nature Chemistry

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

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

antiSMASH 3.0—a comprehensive resource for the genome mining of biosynthetic gene clusters

(2015) Tilmann Weber et al.   NUCLEIC ACIDS RESEARCH

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

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

Aggressive dereplication using UHPLC–DAD–QTOF: screening extracts for up to 3000 fungal secondary metabolites

(2014) Andreas Klitgaard et al.   ANALYTICAL AND BIOANALYTICAL CHEMISTRY

MIDAS: A Database-Searching Algorithm for Metabolite Identification in Metabolomics

(2014) Yingfeng Wang et al.   ANALYTICAL CHEMISTRY

NRPquest: Coupling Mass Spectrometry and Genome Mining for Nonribosomal Peptide Discovery

(2014) Hosein Mohimani et al.   JOURNAL OF NATURAL PRODUCTS

Competitive fragmentation modeling of ESI-MS/MS spectra for putative metabolite identification

(2014) Felicity Allen et al.   Metabolomics

Mass spectrometry of natural products: current, emerging and future technologies

(2014) Amina Bouslimani et al.   NATURAL PRODUCT REPORTS

An environmental bacterial taxon with a large and distinct metabolic repertoire

(2014) Micheal C. Wilson et al.   NATURE

A roadmap for natural product discovery based on large-scale genomics and metabolomics

(2014) James R Doroghazi et al.   Nature Chemical Biology

CFM-ID: a web server for annotation, spectrum prediction and metabolite identification from tandem mass spectra

(2014) Felicity Allen et al.   NUCLEIC ACIDS RESEARCH

MIDDAS-M: Motif-Independent De Novo Detection of Secondary Metabolite Gene Clusters through the Integration of Genome Sequencing and Transcriptome Data

(2014) Myco Umemura et al.   PLoS One

Improved Lanthipeptide Detection and Prediction for antiSMASH

(2014) Kai Blin et al.   PLoS One

Structural investigation of ribosomally synthesized natural products by hypothetical structure enumeration and evaluation using tandem MS

(2014) Q. Zhang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Automatic Chemical Structure Annotation of an LC–MSn Based Metabolic Profile from Green Tea

(2013) Lars Ridder et al.   ANALYTICAL CHEMISTRY

Quantitative molecular networking to profile marine cyanobacterial metabolomes

(2013) Jacob R Winnikoff et al.   JOURNAL OF ANTIBIOTICS

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

MetFusion: integration of compound identification strategies

(2013) Michael Gerlich et al.   JOURNAL OF MASS SPECTROMETRY

Molecular Networking as a Dereplication Strategy

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

A New Approach to Evaluating Statistical Significance of Spectral Identifications

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

CYCLONE—A Utility for De Novo Sequencing of Microbial Cyclic Peptides

(2013) Daniel Kavan et al.   JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY

The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of Pathway/Genome Databases

(2013) Ron Caspi et al.   NUCLEIC ACIDS RESEARCH

antiSMASH 2.0—a versatile platform for genome mining of secondary metabolite producers

(2013) Kai Blin et al.   NUCLEIC ACIDS RESEARCH

BAGEL3: automated identification of genes encoding bacteriocins and (non-)bactericidal posttranslationally modified peptides

(2013) Auke J. van Heel et al.   NUCLEIC ACIDS RESEARCH

MS/MS networking guided analysis of molecule and gene cluster families

(2013) D. D. Nguyen et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Interspecies Interactions Stimulate Diversification of the Streptomyces coelicolor Secreted Metabolome

(2013) M. F. Traxler et al.   mBio

Computational mass spectrometry for small molecules

(2013) Kerstin Scheubert et al.   Journal of Cheminformatics

Bacterial Biosynthesis and Maturation of the Didemnin Anti-cancer Agents

(2012) Ying Xu et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

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

ThioFinder: A Web-Based Tool for the Identification of Thiopeptide Gene Clusters in DNA Sequences

(2012) Jing Li et al.   PLoS One

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

Precursor-centric genome-mining approach for lasso peptide discovery

(2012) M. O. Maksimov et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Interkingdom metabolic transformations captured by microbial imaging mass spectrometry

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

Algorithms for thede novosequencing of peptides from tandem mass spectra

(2011) Jens Allmer   Expert Review of Proteomics

Multiplex De Novo Sequencing of Peptide Antibiotics

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

Cycloquest: Identification of Cyclopeptides via Database Search of Their Mass Spectra against Genome Databases

(2011) Hosein Mohimani et al.   JOURNAL OF PROTEOME RESEARCH

Fast Multi-blind Modification Search through Tandem Mass Spectrometry

(2011) Seungjin Na et al.   MOLECULAR & CELLULAR PROTEOMICS

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

antiSMASH: rapid identification, annotation and analysis of secondary metabolite biosynthesis gene clusters in bacterial and fungal genome sequences

(2011) Marnix H. Medema et al.   NUCLEIC ACIDS RESEARCH

KEGG for integration and interpretation of large-scale molecular data sets

(2011) M. Kanehisa et al.   NUCLEIC ACIDS RESEARCH

Sequencing cyclic peptides by multistage mass spectrometry

(2011) Hosein Mohimani et al.   PROTEOMICS

Metabolite identification and quantitation in LC-MS/MS-based metabolomics

(2011) Jun Feng Xiao et al.   TRAC-TRENDS IN ANALYTICAL CHEMISTRY

Computational mass spectrometry for metabolomics: Identification of metabolites and small molecules

(2010) Steffen Neumann et al.   ANALYTICAL AND BIOANALYTICAL CHEMISTRY

LC–high resolution MS in environmental analysis: from target screening to the identification of unknowns

(2010) Martin Krauss et al.   ANALYTICAL AND BIOANALYTICAL CHEMISTRY

In silico fragmentation for computer assisted identification of metabolite mass spectra

(2010) Sebastian Wolf et al.   BMC BIOINFORMATICS

Genome mining for ribosomally synthesized natural products

(2010) Juan E Velásquez et al.   CURRENT OPINION IN CHEMICAL BIOLOGY

SMURF: Genomic mapping of fungal secondary metabolite clusters

(2010) Nora Khaldi et al.   FUNGAL GENETICS AND BIOLOGY

ChemSpider: An Online Chemical Information Resource

(2010) Harry E. Pence et al.   JOURNAL OF CHEMICAL EDUCATION

MassBank: a public repository for sharing mass spectral data for life sciences

(2010) Hisayuki Horai et al.   JOURNAL OF MASS SPECTROMETRY

SBSPKS: structure based sequence analysis of polyketide synthases

(2010) Swadha Anand et al.   NUCLEIC ACIDS RESEARCH

BAGEL2: mining for bacteriocins in genomic data

(2010) Anne de Jong et al.   NUCLEIC ACIDS RESEARCH

Highly Diverse Cyanobactins in Strains of the Genus Anabaena

(2009) N. Leikoski et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

CLUSEAN: A computer-based framework for the automated analysis of bacterial secondary metabolite biosynthetic gene clusters

(2009) T. Weber et al.   JOURNAL OF BIOTECHNOLOGY

Artificial Decoy Spectral Libraries for False Discovery Rate Estimation in Spectral Library Searching in Proteomics

(2009) Henry Lam et al.   JOURNAL OF PROTEOME RESEARCH

Ribosomal peptide natural products: bridging the ribosomal and nonribosomal worlds

(2009) John A. McIntosh et al.   NATURAL PRODUCT REPORTS

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

Multi-spectra peptide sequencing and its applications to multistage mass spectrometry

(2008) N. Bandeira et al.   BIOINFORMATICS

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

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

Automated de novo protein sequencing of monoclonal antibodies

(2008) Nuno Bandeira et al.   NATURE BIOTECHNOLOGY

ClustScan : an integrated program package for the semi-automatic annotation of modular biosynthetic gene clusters and in silico prediction of novel chemical structures

(2008) Antonio Starcevic et al.   NUCLEIC ACIDS RESEARCH

HMDB: a knowledgebase for the human metabolome

(2008) D. S. Wishart et al.   NUCLEIC ACIDS RESEARCH