On the Impact of the Pangenome and Annotation Discrepancies While Building Protein Sequence Databases for Bacteria Proteogenomics

iMetaLab 1.0: a web platform for metaproteomics data analysis

(2018) Bo Liao et al.   BIOINFORMATICS

Loose ends: almost one in five human genes still have unresolved coding status

(2018) Federico Abascal et al.   NUCLEIC ACIDS RESEARCH

Mining the cellular inventory of pyridoxal phosphate-dependent enzymes with functionalized cofactor mimics

(2018) Annabelle Hoegl et al.   Nature Chemistry

An integrative strategy to identify the entire protein coding potential of prokaryotic genomes by proteogenomics

(2017) Ulrich Omasits et al.   GENOME RESEARCH

Challenges and perspectives of metaproteomic data analysis

(2017) Robert Heyer et al.   JOURNAL OF BIOTECHNOLOGY

Methods, Tools and Current Perspectives in Proteogenomics

(2017) Kelly V. Ruggles et al.   MOLECULAR & CELLULAR PROTEOMICS

panX: pan-genome analysis and exploration

(2017) Wei Ding et al.   NUCLEIC ACIDS RESEARCH

Why prokaryotes have pangenomes

(2017) James O. McInerney et al.   Nature Microbiology

Genome-wide transcription start site mapping of Bradyrhizobium japonicum grown free-living or in symbiosis – a rich resource to identify new transcripts, proteins and to study gene regulation

(2016) Jelena Čuklina et al.   BMC GENOMICS

Metaproteomic data analysis at a glance: advances in computational microbial community proteomics

(2016) Thilo Muth et al.   Expert Review of Proteomics

MetaPro-IQ: a universal metaproteomic approach to studying human and mouse gut microbiota

(2016) Xu Zhang et al.   Microbiome

A peptide resource for the analysis ofStaphylococcus aureusin host-pathogen interaction studies

(2015) Maren Depke et al.   PROTEOMICS

Proteogenomics: concepts, applications and computational strategies

(2014) Alexey I Nesvizhskii   NATURE METHODS

High Performance Computational Analysis of Large-scale Proteome Data Sets to Assess Incremental Contribution to Coverage of the Human Genome

(2013) Nadin Neuhauser et al.   JOURNAL OF PROTEOME RESEARCH

Evaluating the Impact of Different Sequence Databases on Metaproteome Analysis: Insights from a Lab-Assembled Microbial Mixture

(2013) Alessandro Tanca et al.   PLoS One

A two-step database search method improves sensitivity in peptide sequence matches for metaproteomics and proteogenomics studies

(2013) Pratik Jagtap et al.   PROTEOMICS

Addressing Statistical Biases in Nucleotide-Derived Protein Databases for Proteogenomic Search Strategies

(2012) Paul Blakeley et al.   JOURNAL OF PROTEOME RESEARCH

GenBank

(2012) Dennis A. Benson et al.   NUCLEIC ACIDS RESEARCH

Comet: An open-source MS/MS sequence database search tool

(2012) Jimmy K. Eng et al.   PROTEOMICS

Andromeda: A Peptide Search Engine Integrated into the MaxQuant Environment

(2011) Jürgen Cox et al.   JOURNAL OF PROTEOME RESEARCH

Proteomic analysis of a multi-resistant clinical Escherichia coli isolate of unknown genomic background

(2011) Gisele G. Tomazella et al.   Journal of Proteomics

Software Lock Mass by Two-Dimensional Minimization of Peptide Mass Errors

(2011) Jürgen Cox et al.   JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY

SearchGUI: An open-source graphical user interface for simultaneous OMSSA and X!Tandem searches

(2011) Marc Vaudel et al.   PROTEOMICS

MSMSpdbb: providing protein databases of closely related organisms to improve proteomic characterization of prokaryotic microbes

(2010) Gustavo A. de Souza et al.   BIOINFORMATICS

Continuing Evolution of Burkholderia mallei Through Genome Reduction and Large-Scale Rearrangements

(2010) Liliana Losada et al.   Genome Biology and Evolution

A survey of computational methods and error rate estimation procedures for peptide and protein identification in shotgun proteomics

(2010) Alexey I. Nesvizhskii   Journal of Proteomics

Proteogenomic Analysis of Polymorphisms and Gene Annotation Divergences in Prokaryotes using a Clustered Mass Spectrometry-Friendly Database

(2010) Gustavo A. de Souza et al.   MOLECULAR & CELLULAR PROTEOMICS

Proteogenomics

(2010) Santosh Renuse et al.   PROTEOMICS

TubercuList – 10 years after

(2010) Jocelyne M. Lew et al.   TUBERCULOSIS

The Early Stage of Bacterial Genome-Reductive Evolution in the Host

(2010) Han Song et al.   PLoS Pathogens

The comprehensive microbial resource

(2009) Tanja Davidsen et al.   NUCLEIC ACIDS RESEARCH

Validating divergent ORF annotation of the Mycobacterium leprae genome through a full translation data set and peptide identification by tandem mass spectrometry

(2009) Gustavo A. de Souza et al.   PROTEOMICS

High accuracy mass spectrometry analysis as a tool to verify and improve gene annotation using Mycobacterium tuberculosis as an example

(2008) Gustavo A de Souza et al.   BMC GENOMICS

The Pangenome Structure of Escherichia coli: Comparative Genomic Analysis of E. coli Commensal and Pathogenic Isolates

(2008) D. A. Rasko et al.   JOURNAL OF BACTERIOLOGY

Discovery and revision of Arabidopsis genes by proteogenomics

(2008) N. E. Castellana et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Genome-Scale Proteomics Reveals Arabidopsis thaliana Gene Models and Proteome Dynamics

(2008) K. Baerenfaller et al.   SCIENCE