customProDB

customProDB generates customized protein sequence databases for proteomics searches by processing RNA-Seq data to incorporate sample-specific genetic variations such as single nucleotide polymorphisms, short insertions and deletions, and novel exon-exon junctions to improve peptide and protein identification by mass spectrometry.

Key Features:

• Sample-Specific Databases: Creates protein sequence databases from RNA-Seq data that include sample-specific single nucleotide polymorphisms, short insertions and deletions, and novel exon-exon junctions.
• Improved Protein Identification: Enhances sensitivity and specificity of peptide and protein identification in mass spectrometry-based proteomics by representing sample-derived sequence variants.
• Cross-Omics Data Integration: Integrates RNA-Seq-derived genomic variant and junction information with proteomic database generation to support cross-omics analyses.

Scientific Applications:

• Cancer research: Supports identification of tumor-specific protein variants and novel peptides in cancer proteogenomics studies.
• Biomarker discovery: Facilitates detection of variant-derived or novel peptides as candidate biomarkers from mass spectrometry data.
• Personalized medicine: Enables generation of individualized proteome databases for patient-specific proteomic profiling.

Methodology:

Processes RNA-Seq data to identify genetic variations and novel exon-exon junctions, translates those sequences into protein sequences, and assembles them into customized databases for subsequent proteomics searches using mass spectrometry.