PAnalyzer

PAnalyzer performs protein inference from peptide identifications in shotgun proteomics to resolve ambiguities arising from peptides shared among different proteins.

Key Features:

• Data Independent Acquisition (DIA) Support: Supports Data Independent Acquisition (DIA) workflows such as MSE for processing spectra and performing peptide and protein identifications.
• Transparent Grouping with Evidence Categories: Groups identified proteins based on shared peptide evidence and assigns confidence levels using distinct evidence categories.
• Compatibility with Standardized Formats: Reads ProteinLynx Global Server (PLGS) XML identification files from Waters MSE data and supports mzIdentML (HUPO-PSI) format.
• Handling of Technical Replicates: Processes multiple input files simultaneously by treating them as technical replicates for combined inference.
• Versatile Output Options: Exports results in CSV and HTML, and in mzIdentML when a single input file is used.

Scientific Applications:

• Enhancing Protein Identification Accuracy: Improves accuracy of protein identification in shotgun proteomics by resolving peptide-to-protein assignment ambiguities.
• Facilitating Comparative Studies: Enables more reliable comparative analyses across experimental conditions by supporting technical replicate processing.
• Streamlining Data Analysis Workflows: Reduces manual result inspection and reporting by producing grouped protein inferences with assigned evidence categories.

Methodology:

Processes identified proteins from MSE data, groups proteins by shared peptide evidence, assigns confidence levels through distinct evidence categories, reads PLGS XML and mzIdentML files, supports multiple-file (technical replicate) input, and exports results in CSV, HTML, or mzIdentML (single-file case).