Navigating through metaproteomics data: A logbook of database searching

Flexible and Accessible Workflows for Improved Proteogenomic Analysis Using the Galaxy Framework

(2014) Pratik D. Jagtap et al.   JOURNAL OF PROTEOME RESEARCH

Metaproteomics of soils from semiarid environment: Functional and phylogenetic information obtained with different protein extraction methods

(2014) F. Bastida et al.   Journal of Proteomics

PepExplorer: A Similarity-driven Tool for Analyzingde NovoSequencing Results

(2014) Felipe V. Leprevost et al.   MOLECULAR & CELLULAR PROTEOMICS

Metaproteomics: Evaluation of protein extraction from activated sludge

(2014) Susan Hove Hansen et al.   PROTEOMICS

High-throughput parallel proteogenomics: A bacterial case study

(2014) Brett Chapman et al.   PROTEOMICS

High-fat diet alters gut microbiota physiology in mice

(2013) Hannelore Daniel et al.   ISME Journal

When Target–Decoy False Discovery Rate Estimations Are Inaccurate and How to Spot Instances

(2013) Robert J. Chalkley   JOURNAL OF PROTEOME RESEARCH

DeNovoGUI: An Open Source Graphical User Interface for de Novo Sequencing of Tandem Mass Spectra

(2013) Thilo Muth et al.   JOURNAL OF PROTEOME RESEARCH

A metaproteomic pipeline to identify newborn mouse gut phylotypes

(2013) Federica Del Chierico et al.   Journal of Proteomics

Beyond gene expression: The impact of protein post-translational modifications in bacteria

(2013) Joel A. Cain et al.   Journal of Proteomics

Metaproteomics of our microbiome — Developing insight in function and activity in man and model systems

(2013) Carolin A. Kolmeder et al.   Journal of Proteomics

Combining Results of Multiple Search Engines in Proteomics

(2013) David Shteynberg et al.   MOLECULAR & CELLULAR PROTEOMICS

Host-centric Proteomics of Stool: A Novel Strategy Focused on intestinal Responses to the Gut Microbiota

(2013) Joshua S. Lichtman et al.   MOLECULAR & CELLULAR PROTEOMICS

Human intestinal microbiota composition is associated with local and systemic inflammation in obesity

(2013) Froukje J. Verdam et al.   Obesity

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

The Problem with Peptide Presumption and the Downfall of Target–Decoy False Discovery Rates

(2012) Bret Cooper   ANALYTICAL CHEMISTRY

Current methods for global proteome identification

(2012) Marc Vaudel et al.   Expert Review of Proteomics

Gut microbiota disturbance during antibiotic therapy: a multi-omic approach

(2012) Ana Elena Pérez-Cobas et al.   GUT

Metaproteogenomic analysis of a community of sponge symbionts

(2012) Michael Liu et al.   ISME Journal

A Complex Standard for Protein Identification, Designed by Evolution

(2012) Marc Vaudel et al.   JOURNAL OF PROTEOME RESEARCH

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

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

Searching for a needle in a stack of needles: challenges in metaproteomics data analysis

(2012) Thilo Muth et al.   Molecular BioSystems

Comparative Metaproteomics and Diversity Analysis of Human Intestinal Microbiota Testifies for Its Temporal Stability and Expression of Core Functions

(2012) Carolin A. Kolmeder et al.   PLoS One

Learning from Decoys to Improve the Sensitivity and Specificity of Proteomics Database Search Results

(2012) Amit Kumar Yadav et al.   PLoS One

An iterative workflow for mining the human intestinal metaproteome

(2011) Koos Rooijers et al.   BMC GENOMICS

Algorithms for thede novosequencing of peptides from tandem mass spectra

(2011) Jens Allmer   Expert Review of Proteomics

Analysis of the Resolution Limitations of Peptide Identification Algorithms

(2011) Niklaas Colaert et al.   JOURNAL OF PROTEOME RESEARCH

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

Strategies for Metagenomic-Guided Whole-Community Proteomics of Complex Microbial Environments

(2011) Brandi L. Cantarel et al.   PLoS One

Quality assessments of peptide-spectrum matches in shotgun proteomics

(2011) Viktor Granholm et al.   PROTEOMICS

Peptide identification quality control

(2011) Marc Vaudel et al.   PROTEOMICS

Metaproteogenomic analysis of a dominant green sulfur bacterium from Ace Lake, Antarctica

(2010) Charmaine Ng et al.   ISME Journal

Environmental proteomics of microbial plankton in a highly productive coastal upwelling system

(2010) Sarah M Sowell et al.   ISME Journal

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

A human gut microbial gene catalogue established by metagenomic sequencing

(2010) Junjie Qin et al.   NATURE

Data maximization by multipass analysis of protein mass spectra

(2010) Ravi Tharakan et al.   PROTEOMICS

Improved results in proteomics by use of local and peptide-class specific false discovery rates

(2009) Lau Sennels et al.   BMC BIOINFORMATICS

Improving sensitivity in proteome studies by analysis of false discovery rates for multiple search engines

(2009) Andrew R. Jones et al.   PROTEOMICS

Decoy Methods for Assessing False Positives and False Discovery Rates in Shotgun Proteomics

(2008) Guanghui Wang et al.   ANALYTICAL CHEMISTRY

Non-parametric estimation of posterior error probabilities associated with peptides identified by tandem mass spectrometry

(2008) L. Kall et al.   BIOINFORMATICS

Improving Sensitivity by Probabilistically Combining Results from Multiple MS/MS Search Methodologies

(2008) Brian C. Searle et al.   JOURNAL OF PROTEOME RESEARCH

Building consensus spectral libraries for peptide identification in proteomics

(2008) Henry Lam et al.   NATURE METHODS