Pout2Prot

Pout2Prot converts Percolator .pout files into protein group and subgroup .tsv files to support protein inference, taxonomic and functional analysis in metaproteomics.

Key Features:

• .pout to .tsv conversion: Converts Percolator output (.pout) into protein group and subgroup tab-separated files (.tsv) for downstream analysis.
• Prophane compatibility: Produces .tsv outputs formatted for direct use with Prophane for taxonomic and functional annotation.
• Protein grouping algorithms: Implements multiple protein grouping strategies including Occam's razor and anti-Occam's razor approaches.
• Multi-experiment support: Processes data from multiple experiments simultaneously for combined protein grouping.
• Weighted spectral counts: Assigns abundance to protein groups and subgroups using a weighted spectral count approach.
• Evaluated strategies: Incorporates protein grouping strategies that were evaluated during tool development.

Scientific Applications:

• Metaproteomic protein inference: Resolves peptide-to-protein ambiguity arising from isoforms and homologous proteins across closely related species.
• Taxonomic annotation: Provides protein group outputs suitable for taxonomic profiling via Prophane.
• Functional analysis and quantification: Enables functional annotation and quantitative comparison of protein (sub)groups across microbial community datasets using weighted spectral counts.

Methodology:

Conversion of Percolator .pout files to protein group and subgroup .tsv; protein grouping using Occam's and anti-Occam's algorithms; processing of multiple experiments; assignment of abundances via weighted spectral counts.