PGx

PGx maps mass spectrometry (MS)-identified peptides to genomic coordinates to integrate MS-based proteomics with next-generation sequencing (NGS)-derived transcriptomic and genomic data for proteogenomic analyses.

Key Features:

• Seamless Data Integration: Integrates proteomics data from mass spectrometry (MS) with transcriptomic and genomic information from next-generation sequencing (NGS) to map peptides onto genomic coordinates.
• Minimal Preprocessing Requirement: Minimizes preprocessing by enabling linkage of existing MS proteomics datasets with NGS transcriptomic and genomic data without extensive data manipulation.

Scientific Applications:

• Gene Annotation: Refines gene annotations and identifies novel protein-coding regions and alternative splicing events by mapping peptides to genomic coordinates.
• Variant Analysis: Detects and contextualizes genetic variants at the protein level by linking peptide evidence to genomic variant sites.
• Pathway Analysis: Explores effects of genomic variation on proteomic profiles to investigate molecular pathways and disease mechanisms.

Methodology:

Identifies peptides by mass spectrometry and maps them to genomic coordinates by aligning peptide sequences to NGS-derived transcriptomic and genomic sequences to locate coding sequences and variant sites.