Global Identification of Post-Translationally Spliced Peptides with Neo-Fusion

Post-translationally
spliced peptides have recently garnered significant
interest as potential targets for cancer immunotherapy and as contributors
to autoimmune diseases such as type 1 diabetes, yet feasible identification
methods for spliced peptides have yet to be developed. Here we
present Neo-Fusion, a search program for discovering spliced peptides
in tandem mass spectrometry data. Neo-Fusion utilizes two separated
ion database searches to identify the two halves of each spliced peptide,
and then it infers the full spliced sequence. This strategy allows
for the identification of spliced peptides without peptide length
constraints, providing a broadly applicable tool suitable for identification
of spliced peptides in a variety of systems, such as the HLA-I and
HLA-II immunopeptidomes and in vitro digested protein samples obtained
from organelles, cells, or tissues of interest. Using simulated spliced
peptides to benchmark Neo-Fusion, 25% of all simulated spliced peptides
were identified at a measured false-discovery rate of 5% for HLA-I.
Neo-Fusion provides the research community with a powerful new tool
to aid in the study of the prevalence and biological significance
of post-translationally spliced peptides.