MetaProSIP: Automated Inference of Stable Isotope Incorporation Rates in Proteins for Functional Metaproteomics

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 13C or 15N 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.