Perseus

Perseus analyzes shotgun proteomics data and interprets quantitative protein abundance changes from MaxQuant output to enable functional interpretation and integration with other genome-wide datasets such as transcriptomics.

Key Features:

• MaxQuant compatibility: Processes MaxQuant output and uses abundance ratios for thousands of proteins across perturbations.
• 2D annotation enrichment: Implements 2D annotation enrichment to compare quantitative data across two omics types within a categorical framework.
• Categorical annotation support: Uses biochemical pathways, gene ontology terms, sub‑cellular localization, protein domains, and protein complex membership as annotation categories.
• Detection of correlated and uncorrelated changes: Identifies annotation terms whose members show consistent behavior across one or both data dimensions, including correlated or dimension‑specific regulation.
• Two-dimensional nonparametric testing: Applies a two-dimensional generalization of the nonparametric two-sample test for statistical assessment.
• Multiple testing correction: Corrects for multiple hypothesis testing to control the false discovery rate.
• One-dimensional annotation enrichment: Provides one-dimensional annotation enrichment for analysis of single-omics datasets.
• Functional interpretation and integration: Enables functional interpretation of protein abundance changes and correlation with other genome-wide datasets such as transcriptomic variations.

Scientific Applications:

• Proteome functional interpretation: Interpreting quantitative abundance changes to derive biological meaning across perturbations.
• Integrative omics analysis: Comparing and integrating proteomic data with transcriptomic and other genome-wide datasets.
• Annotation enrichment studies: Detecting enriched biochemical pathways, gene ontology terms, subcellular localization patterns, protein domain associations, and complex membership behaviors.
• Systems biology analyses: Supporting systems-level analysis of proteome responses across conditions.

Methodology:

Perseus applies 2D and 1D annotation enrichment on MaxQuant-derived abundance ratios, uses a two-dimensional generalization of the nonparametric two-sample test with multiple hypothesis testing correction to control the false discovery rate, and compares categories including biochemical pathways, gene ontology terms, sub‑cellular localization, protein domains, and protein complex membership across two omics dimensions.