sapFinder

sapFinder detects single amino acid polymorphisms (SAPs) arising from single nucleotide variations (SNVs) by integrating SNV data with tandem mass spectrometry (MS/MS)-based proteomics to identify variant peptides.

Key Features:

• Automated variation-associated database construction: Incorporates SNV information from public repositories or sample-specific next-generation sequencing (NGS) into protein sequence databases.
• Database searching: Searches constructed databases with MS/MS-based proteomics data to identify variant peptides corresponding to SAPs.
• Post-processing and analysis: Performs post-processing on search results to refine and validate identifications of SAP-containing peptides.
• HTML-based report generation: Produces HTML-formatted reports summarizing identified variant peptides and associated analyses.

Scientific Applications:

• Proteomic variation analysis: Identification and characterization of SAPs to study amino acid–level protein variation in proteomic datasets.
• Personalized medicine: Detection of individual-specific variant peptides that may inform patient-specific biomarker or therapeutic investigations.
• Evolutionary biology: Analysis of how genetic variation at the SNV level translates into protein sequence variation for evolutionary studies.
• Disease research: Mapping SNV-derived amino acid changes to proteins to investigate potential functional impacts in disease contexts.

Methodology:

Data integration of SNV information from public databases or NGS data into proteomic sequence databases. MS/MS-based proteomics data are searched against these constructed databases to identify peptides with sequence variants. Automated post-processing and reporting of search results are applied to refine SAP identifications.