protti

protti provides comprehensive quality control, analysis, and interpretation of quantitative bottom-up proteomics data, supporting both peptide-centric and protein-centric datasets.

Key Features:

• Data type support: Supports label-free, data-dependent (DDA), data-independent (DIA), and targeted proteomics datasets.
• Search engine/software compatibility: Processes outputs from Spectronaut, Skyline, MaxQuant, and Proteome Discoverer.
• Analytical scope: Performs quality control, quantitative analysis, and interpretation of bottom-up proteomics data.
• Dataset granularity: Handles both peptide-centric and protein-centric datasets for downstream analyses.

Scientific Applications:

• Protein expression analysis: Analysis of quantitative changes in protein abundance from bottom-up proteomics experiments.
• Limited proteolysis-coupled MS: Support for analyses related to limited proteolysis-coupled mass spectrometry workflows.

Methodology:

Implemented as an R package that processes outputs from Spectronaut, Skyline, MaxQuant, and Proteome Discoverer and supports label-free, DDA, DIA, and targeted datasets to perform quality control and peptide- and protein-centric quantitative analyses.