The impact of sequence database choice on metaproteomic results in gut microbiota studies

Error filtering, pair assembly and error correction for next-generation sequencing reads

(2015) Robert C. Edgar et al.   BIOINFORMATICS

The MetaProteomeAnalyzer: A Powerful Open-Source Software Suite for Metaproteomics Data Analysis and Interpretation

(2015) Thilo Muth et al.   JOURNAL OF PROTEOME RESEARCH

Effective Leveraging of Targeted Search Spaces for Improving Peptide Identification in Tandem Mass Spectrometry Based Proteomics

(2015) Avinash K. Shanmugam et al.   JOURNAL OF PROTEOME RESEARCH

ClustVis: a web tool for visualizing clustering of multivariate data using Principal Component Analysis and heatmap

(2015) Tauno Metsalu et al.   NUCLEIC ACIDS RESEARCH

2016 update of the PRIDE database and its related tools

(2015) Juan Antonio Vizcaíno et al.   NUCLEIC ACIDS RESEARCH

Navigating through metaproteomics data: A logbook of database searching

(2015) Thilo Muth et al.   PROTEOMICS

Estimating the computational limits of detection of microbial non-model organisms

(2015) Mathias Kuhring et al.   PROTEOMICS

Enrichment or depletion? The impact of stool pretreatment on metaproteomic characterization of the human gut microbiota

(2015) Alessandro Tanca et al.   PROTEOMICS

The Unipept metaproteomics analysis pipeline

(2015) Bart Mesuere et al.   PROTEOMICS

Microbial metaproteomics for characterizing the range of metabolic functions and activities of human gut microbiota

(2015) Weili Xiong et al.   PROTEOMICS

Colonic metaproteomic signatures of active bacteria and the host in obesity

(2015) Carolin A. Kolmeder et al.   PROTEOMICS

Strain-resolved microbial community proteomics reveals simultaneous aerobic and anaerobic function during gastrointestinal tract colonization of a preterm infant

(2015) Brandon Brooks et al.   Frontiers in Microbiology

Effects of Vendor and Genetic Background on the Composition of the Fecal Microbiota of Inbred Mice

(2015) Aaron C. Ericsson et al.   PLoS One

An integrated catalog of reference genes in the human gut microbiome

(2014) Junhua Li et al.   NATURE BIOTECHNOLOGY

UniProt: a hub for protein information

(2014)   NUCLEIC ACIDS RESEARCH

Symbiosis, dysbiosis, and rebiosis-The value of metaproteomics in human microbiome monitoring

(2014) Lei Mao et al.   PROTEOMICS

A straightforward and efficient analytical pipeline for metaproteome characterization

(2014) Alessandro Tanca et al.   Microbiome

Metaproteomics: Harnessing the Power of High Performance Mass Spectrometry to Identify the Suite of Proteins That Control Metabolic Activities in Microbial Communities

(2013) Robert L. Hettich et al.   ANALYTICAL CHEMISTRY

High-fat diet alters gut microbiota physiology in mice

(2013) Hannelore Daniel et al.   ISME Journal

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

The gut microbiota — masters of host development and physiology

(2013) Felix Sommer et al.   NATURE REVIEWS MICROBIOLOGY

Beyond phylotyping: understanding the impact of gut microbiota on host biology

(2013) Christopher S. Reigstad et al.   NEUROGASTROENTEROLOGY AND MOTILITY

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

(2013) Alessandro Tanca et al.   PLoS One

Comparison of detergent-based sample preparation workflows for LTQ-Orbitrap analysis of theEscherichia coliproteome

(2013) Alessandro Tanca et al.   PROTEOMICS

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

(2013) Pratik Jagtap et al.   PROTEOMICS

Inflammation-associated enterotypes, host genotype, cage and inter-individual effects drive gut microbiota variation in common laboratory mice

(2013) Falk Hildebrand et al.   GENOME BIOLOGY

‘Omics’ of the mammalian gut – new insights into function

(2012) Regina Lamendella et al.   CURRENT OPINION IN BIOTECHNOLOGY

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

(2012) Thilo Muth et al.   Molecular BioSystems

Survey of the camel urinary proteome by shotgun proteomics using a multiple database search strategy

(2012) Abdulqader A. Alhaider et al.   PROTEOMICS

An iterative workflow for mining the human intestinal metaproteome

(2011) Koos Rooijers et al.   BMC GENOMICS

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

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

Peptide identification quality control

(2011) Marc Vaudel et al.   PROTEOMICS

Metagenomic biomarker discovery and explanation

(2011) Nicola Segata et al.   GENOME BIOLOGY

Search and clustering orders of magnitude faster than BLAST

(2010) Robert C. Edgar   BIOINFORMATICS

Analysis of Biostimulated Microbial Communities from Two Field Experiments Reveals Temporal and Spatial Differences in Proteome Profiles

(2010) Stephen J. Callister et al.   ENVIRONMENTAL SCIENCE & TECHNOLOGY

QIIME allows analysis of high-throughput community sequencing data

(2010) J Gregory Caporaso et al.   NATURE METHODS

qvality: non-parametric estimation of q-values and posterior error probabilities

(2009) Lukas Käll et al.   BIOINFORMATICS

The Firmicutes/Bacteroidetes ratio of the human microbiota changes with age

(2009) D Mariat et al.   BMC MICROBIOLOGY

Universal sample preparation method for proteome analysis

(2009) Jacek R Wiśniewski et al.   NATURE METHODS

Velvet: Algorithms for de novo short read assembly using de Bruijn graphs

(2008) D. R. Zerbino et al.   GENOME RESEARCH

Shotgun metaproteomics of the human distal gut microbiota

(2008) Nathan C Verberkmoes et al.   ISME Journal

MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification

(2008) Jürgen Cox et al.   NATURE BIOTECHNOLOGY