Long-read Proteogenomics Internal Standard triggered PRM (LRP-IS-PRM)

Long-read proteogenomic data was used to create sample-matched protein database for WTC11 sample. This includes many potential alternative protein isoforms (major and minor isoforms) per gene. The IS-PRM method called Tomahto was tested versus DDA to demonstrate improved coverage of isoform-specific peptides. We called this overall method of long-read RNA informed Tomahto targeting LRP-IS-PRM and used it for protein-level evidence of multiple isoforms derived from alternative splicing.