Spritz

Spritz constructs sample-specific proteogenomic databases from raw RNA sequencing data to enable identification of sequence variants and post-translationally modified proteoforms by mass spectrometry.

Key Features:

• Sample-Specific Database Generation: Builds protein databases from raw RNA sequencing data compared against reference genomes such as Ensembl, annotating sequence variations and encoded proteoforms.
• Integration with Existing Data Sources: Annotates proteins with sequence variations discovered in RNA-seq and transfers post-translational modification annotations from UniProt.
• Advanced PTM Discovery: Integrates MetaMorpheus Global PTM Discovery (G-PTM-D) with bottom-up mass spectrometry data to discover and add novel post-translational modifications.
• Seamless Workflow Automation: Automates setup and execution of approximately 20 command-line tools using Snakemake and Docker for NGS analysis and database construction.

Scientific Applications:

• Variant Peptide and Proteoform Identification: Improves identification of variant peptides, modified variant peptides, and variant proteoforms from mass spectrometry data.
• Phosphoproteomic Variant Site Discovery: Enables detection of phosphorylated variant sites using phosphoproteomic datasets.
• Bottom-up and Top-down Proteomics: Supports both bottom-up and top-down proteomic analyses and has been demonstrated on Jurkat and U2OS cell line datasets.

Methodology:

Computational steps include alignment of raw RNA sequencing data to reference genomes (e.g., Ensembl) to call sequence variations, transfer of UniProt PTM annotations to annotated proteins, calibration of mass spectrometry measurements, integration of MetaMorpheus Global PTM Discovery (G-PTM-D) on bottom-up MS data to identify novel PTMs, execution of search tasks against the generated database to detect variant peptides and proteoforms, and workflow automation via Snakemake and Docker orchestrating approximately 20 command-line tools.