Figure 1. The JUMPg proteogenomic pipeline.
(A) Schematic flowchart of JUMPg for peptide identification, with its simplified structure shown in a box. (B) An example of peptide identification table in the JUMPg output. The best scored PSMs are indicated by concatenated LC-MS/MS run name, scan number, the rank of precursor ion intensity in the isolation window, and charge state. (C) Data visualization to display related genes, transcripts and peptides/proteins. JUMPg generates peptide files containing the information of genomic locations (in BED format), which are uploaded into UCSC genome browser.