mPies

mPies generates standardized protein search databases and computes taxonomic and functional consensus annotations for metaproteomic analyses of environmental microbial communities.

Key Features:

• Database Creation: Constructs protein databases from assembled and unassembled metagenomes and from public repositories using taxon IDs, gene names, or protein names.
• Automated Annotation: Automates taxonomic and functional consensus annotations at the protein group level to address protein inference in metaproteomics.
• Customizable Workflow: Allows adjustment of input data, workflow steps, and parameters to tailor analyses to specific datasets.
• Technical Implementation: Implemented in Python 3 using the Snakemake framework.

Scientific Applications:

• Environmental metaproteomics: Supports analysis of microbial community structure and functionality in environmental samples by generating relevant protein databases and annotations.
• Protein inference mitigation: Produces consensus annotations at the protein group level to reduce ambiguity from protein inference.
• Ecological and biotechnological research: Enables more accurate metaproteomic studies that inform ecological investigations and biotechnological applications.

Methodology:

Constructs databases from assembled and unassembled metagenomes and public repositories using taxon IDs/gene names/protein names, performs automated taxonomic and functional consensus annotation at the protein group level, and is implemented in Python 3 with Snakemake.