Quantitative profiling of microbial communities by de novo metaproteomics

HBC Kleikamp, M Pronk, C Tugui, LG da Silva… - bioRxiv, 2020 - biorxiv.org
Metaproteomics has emerged as one of the most promising approaches for determining the
composition and metabolic functions of complete microbial communities. Conventional …

Database-independent de novo metaproteomics of complex microbial communities

HBC Kleikamp, M Pronk, C Tugui, LG da Silva… - Cell Systems, 2021 - cell.com
Metaproteomics has emerged as one of the most promising approaches for determining the
composition and metabolic functions of complete microbial communities. Conventional …

Function is what counts: how microbial community complexity affects species, proteome and pathway coverage in metaproteomics

P Lohmann, SS Schäpe, SB Haange… - Expert review of …, 2020 - Taylor & Francis
Introduction: Metaproteomics is an established method to obtain a comprehensive
taxonomic and functional view of microbial communities. After more than a decade, we are …

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

T Muth, D Benndorf, U Reichl, E Rapp… - Molecular …, 2013 - pubs.rsc.org
In the past years the integral study of microbial communities of varying complexity has
gained increasing research interest. Mass spectrometry-driven metaproteomics enables the …

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

T Muth, BY Renard, L Martens - Expert review of proteomics, 2016 - Taylor & Francis
Introduction: Within the last decade, the study of microbial communities has gained
increasing research interest also driven by the recognition of the important role of these …

A straightforward and efficient analytical pipeline for metaproteome characterization

A Tanca, A Palomba, S Pisanu, M Deligios… - Microbiome, 2014 - Springer
Background The massive characterization of host-associated and environmental microbial
communities has represented a real breakthrough in the life sciences in the last years. In this …

Evaluating the impact of different sequence databases on metaproteome analysis: insights from a lab-assembled microbial mixture

A Tanca, A Palomba, M Deligios, T Cubeddu… - PloS one, 2013 - journals.plos.org
Metaproteomics enables the investigation of the protein repertoire expressed by complex
microbial communities. However, to unleash its full potential, refinements in bioinformatic …

A complete and flexible workflow for metaproteomics data analysis based on MetaProteomeAnalyzer and Prophane

H Schiebenhoefer, K Schallert, BY Renard, K Trappe… - Nature protocols, 2020 - nature.com
Metaproteomics, the study of the collective protein composition of multi-organism systems,
provides deep insights into the biodiversity of microbial communities and the complex …

Metagenomic taxonomy-guided database-searching strategy for improving metaproteomic analysis

J Xiao, A Tanca, B Jia, R Yang, B Wang… - Journal of proteome …, 2018 - ACS Publications
Metaproteomics provides a direct measure of the functional information by investigating all
proteins expressed by a microbiota. However, due to the complexity and heterogeneity of …

A decade of metaproteomics: where we stand and what the future holds

P Wilmes, A Heintz‐Buschart, PL Bond - Proteomics, 2015 - Wiley Online Library
We are living through exciting times during which we are able to unravel the “microbial dark
matter” in and around us through the application of high‐resolution “meta‐omics” …