title: Searching for a needle in a stack of needles: challenges in metaproteomics data analysis.
abstract: In the past years the integral study of microbial communities of varying complexity has gained increasing research interest. Mass spectrometry-driven metaproteomics enables the analysis of such communities on the functional level, but this fledgling field still faces various technical and semantic challenges regarding experimental data analysis and interpretation. In the present review, we outline the hurdles involved and attempt to cover the most valuable methods and software implementations available to researchers in the field today. Beyond merely focusing on protein identification, we provide an overview on different data pre- and post-processing steps, such as metabolic pathway analysis, that can be useful in a typical metaproteomics workflow. Finally, we briefly discuss directions for future work.
authors.affiliation: Max Planck Institute for Dynamics of Complex Technical Systems, Bioprocess Engineering, Magdeburg, Germany.
authors.forename: Thilo
authors.initials: T
authors.lastname: Muth
authors.forename: Dirk
authors.initials: D
authors.lastname: Benndorf
authors.forename: Udo
authors.initials: U
authors.lastname: Reichl
authors.forename: Erdmann
authors.initials: E
authors.lastname: Rapp
authors.forename: Lennart
authors.initials: L
authors.lastname: Martens
mesh_terms: D057225:Data Mining; D006801:Humans; D040901:Proteomics / Q000379:methods; D012984:Software; D057188:Workflow