title: MetaProSIP: automated inference of stable isotope incorporation rates in proteins for functional metaproteomics.
abstract: We propose a joint experimental and theoretical approach to the automated reconstruction of elemental fluxes in microbial communities. While stable isotope probing of proteins (protein-SIP) has been successfully applied to study interactions and elemental carbon and nitrogen fluxes, the volume and complexity of mass spectrometric data in protein-SIP experiments pose new challenges for data analysis. Together with a flexible experimental setup, the novel bioinformatics tool MetaProSIP offers an automated high-throughput solution for a wide range of (13)C or (15)N protein-SIP experiments with special emphasis on the analysis of metaproteomic experiments where differential labeling of organisms can occur. The information calculated in MetaProSIP includes the determination of multiple relative isotopic abundances, the labeling ratio between old and new synthesized proteins, and the shape of the isotopic distribution. These parameters define the metabolic capacities and dynamics within the investigated microbial culture. MetaProSIP features a high degree of reproducibility, reliability, and quality control reporting. The ability to embed into the OpenMS framework allows for flexible construction of custom-tailored workflows. Software and documentation are available under an open-source license at www.openms.de/MetaProSIP.
authors.affiliation: Applied Bioinformatics, Center for Bioinformatics, Quantitative Biology Center, and Department of Computer Science, University of Tübingen , 72074 Tübingen, Germany.
authors.forename: Timo
authors.initials: T
authors.lastname: Sachsenberg
authors.forename: Florian-Alexander
authors.initials: FA
authors.lastname: Herbst
authors.forename: Martin
authors.initials: M
authors.lastname: Taubert
authors.forename: René
authors.initials: R
authors.lastname: Kermer
authors.forename: Nico
authors.initials: N
authors.lastname: Jehmlich
authors.forename: Martin
authors.initials: M
authors.lastname: von Bergen
authors.forename: Jana
authors.initials: J
authors.lastname: Seifert
authors.forename: Oliver
authors.initials: O
authors.lastname: Kohlbacher
mesh_terms: D001331:Automation; D007554:Isotopes / Q000378:metabolism*; D011506:Proteins / Q000378:metabolism*; D040901:Proteomics
chemical_list: D007554:Isotopes; D011506:Proteins
keywords: bioinformatics; elemental flux; functional metaproteomics; mass spectrometry; microbial ecology; protein-based stable isotope probing