Unique Peptide Finder (UPF)

Unique Peptide Finder (UPF) identifies unique peptides by generating a SQL-based database of theoretically digested peptides from a FASTA protein database and comparing in silico-generated peptides to that database to enable unambiguous protein identification in proteomics.

Key Features:

• SQL-Based Database Creation: Generates a SQL-based database of theoretically digested peptides from a provided FASTA-formatted protein database using a selected protease for digestion simulation.
• In Silico Peptide Comparison: Compares in silico-generated peptides from a predefined protein sequence against the peptide database to identify peptides unique to specific proteins.

Scientific Applications:

• Multiple Reaction Monitoring (MRM): Identifies peptides unique to specific proteins to support targeted quantification workflows such as MRM.
• Protein identification with sparse peptide evidence: Detects unique peptides to disambiguate protein assignments when peptide coverage is limited.

Methodology:

The workflow performs theoretical protease digestion of sequences from a FASTA file to populate a SQL database of peptides, then compares in silico-generated peptides from target protein sequences against that database to identify unique peptides.