pepXMLTab

pepXMLTab parses pepXML files to extract peptide-spectrum-match (PSM) data, apply False Discovery Rate (FDR) filtering, and generate tabular outputs for downstream proteomics analyses.

Key Features:

• Parsing Capability: Parses pepXML files using an XML package framework to extract PSM-level information produced by mass spectrometry proteomics software.
• Output Generation: Produces a tabular file containing peptide-spectrum-match (PSM) information for downstream analysis and integration with other tools.
• False Discovery Rate (FDR) Filtering: Filters PSMs based on False Discovery Rate (FDR) criteria to reduce false positives in identifications.
• R/Bioconductor Integration: Implements parsing and filtering functionality within the R environment and integrates with the Bioconductor ecosystem.

Scientific Applications:

• Proteome Profiling: Supports comprehensive analysis of protein expression across biological conditions by providing curated PSM data.
• Post-translational Modifications (PTMs) Analysis: Enables identification and analysis of modified peptides by delivering annotated PSM entries for PTM investigation.
• Comparative Proteomics: Facilitates comparative studies of differential protein expression by supplying filtered, tabular PSM datasets for multiple samples.

Methodology:

Parses pepXML files using an XML package framework in R, applies FDR-based filtering to PSMs, and outputs the results as a tabular file within the R/Bioconductor environment.