An example of unique GENCODE V7 intergenic proteogenomic matches. Panel A shows that these unique proteogenomic matches overlap with a protein-coding exon predicted by NScan. Blue boxes represent proteogenomic matches, green boxes represent predicted protein-coding exons, and black lines represent introns. Panel B summarizes the total MS/MS spectral support for each of the two matches in this region, where each vertical dark blue bar represents a distinct spectral match for the same peptide, with the height of the bar showing the E-value for the identification (E-values ranging from 1.0×10-1 to 1.0×10-4). More and/or taller bars indicate stronger support. Panel C shows ENCODE/Caltech RNA-Seq evidence and other transcriptional data for the same region. Both matches are identified from multiple spectra, indicating relatively strong support.