PGA

PGA generates customized protein databases from RNA-Seq and enhances peptide identification from tandem mass spectrometry to detect novel peptides absent from reference protein databases.

Key Features:

• Customized Protein Database Construction: Constructs protein databases from RNA-Seq using reference-guided or reference-independent modes and incorporates reference sequences from Refseq and ENSEMBL alongside novel peptide sequences.
• R package implementation: Implemented as an R package that automates processing of tandem mass spectrometry (MS/MS) data obtained from various MS platforms.
• Novel Peptide Identification: Enables detection of single amino acid polymorphism (SAP) peptides, INDEL peptides, splice-junction peptides, and novel transcript-derived peptides not present in standard reference databases.

Scientific Applications:

• Proteomics discovery: Expands peptide detection beyond reference databases to discover novel peptides in proteomics studies.
• Genetic variation and splicing analysis: Supports identification of peptides arising from SAPs, INDELs, and alternative splicing events.
• Disease mechanisms and biomarker/target discovery: Facilitates identification of novel peptide-derived biomarkers and candidate therapeutic targets related to protein function and disease mechanisms.

Methodology:

Implemented as an R package that constructs customized protein databases from RNA-Seq (reference-guided or independent), incorporates Refseq and ENSEMBL sequences, and processes tandem mass spectrometry (MS/MS) data from various MS platforms to identify SAP, INDEL, splice-junction and novel transcript-derived peptides.