Spritz: A Proteogenomic Database Engine

Proteoforms are the workhorses of
the cell, and subtle differences
between their amino acid sequences or post-translational modifications
(PTMs) can change their biological function. To most effectively identify
and quantify proteoforms in genetically diverse samples by mass spectrometry
(MS), it is advantageous to search the MS data against a sample-specific
protein database that is tailored to the sample being analyzed, in
that it contains the correct amino acid sequences and relevant PTMs
for that sample. To this end, we have developed Spritz (https://smith-chem-wisc.github.io/Spritz/), an open-source software tool for generating protein databases
annotated with sequence variations and PTMs. We provide a simple graphical
user interface for Windows and scripts that can be run on any operating
system. Spritz automatically sets up and executes approximately 20
tools, which enable the construction of a proteogenomic database from
only raw RNA sequencing data. Sequence variations that are discovered
in RNA sequencing data upon comparison to the Ensembl reference genome
are annotated on proteins in these databases, and PTM annotations
are transferred from UniProt. Modifications can also be discovered
and added to the database using bottom-up mass spectrometry data and
global PTM discovery in MetaMorpheus. We demonstrate that such sample-specific
databases allow the identification of variant peptides, modified variant
peptides, and variant proteoforms by searching bottom-up and top-down
proteomic data from the Jurkat human T lymphocyte cell line and demonstrate
the identification of phosphorylated variant sites with phosphoproteomic
data from the U2OS human osteosarcoma cell line.