ProteoClade

ProteoClade performs taxonomic annotation and quantification for multi-species and metaproteomic proteomics by assigning taxa-specific peptides, performing protein inference, and producing peptide- and protein-level quantitation.

Key Features:

• Implementation: Python-based implementation for computational processing of proteomic data.
• Taxa-specific peptide assignment: Assigns peptides to taxonomic identifiers for multi-species datasets.
• Protein inference: Infers protein-level identifications from peptide evidence.
• Quantitation: Produces peptide- and protein-level quantitation for downstream analysis.
• Scalability: Scales to accommodate hundreds of millions of protein sequences.
• Performance optimization: Optimized for speed and storage efficiency in large-scale analyses.
• Resource efficiency: Operates with minimal computational resource requirements.
• Application domain: Designed for multi-species and metaproteomic analyses.

Scientific Applications:

• Patient-derived xenograft proteomics: Processes quantitative proteomic data from patient-derived xenografts.
• Microbiota proteomics: Enables development of de novo proteomic workflows for analyzing complex microbiota samples.
• Multi-species proteomics research: Facilitates taxonomic analysis and quantification in studies involving multiple species.

Methodology:

Performs taxa-specific peptide assignment, protein inference, and quantitation in Python with optimizations for speed, storage efficiency, scalability to hundreds of millions of protein sequences, and minimal computational resource requirements.