Deep proteogenomics; high throughput gene validation by multidimensional liquid chromatography and mass spectrometry of proteins from the fungal wheat pathogen Stagonospora nodorum

Table 5 Counts of S. nodorum version 1 and 2 gene annotations matching 6-frame translated genome-mapped peptide clusters.¹

Annotation version	Confirmed no conflict	UTR/intron conflict (EST support)	UTR/intron conflict (no EST support)	No-match	Total
1	11	0	30	5313	5354
2	300	355	209	9898	10762

¹Un-translated region (UTR)/intron conflicts were determined based on peptide matches outside of coding exon regions but within either 200 bp or within the boundaries of known UTRs. UTRs were known for genes for which EST alignments were available, where UTR regions were defined as EST-aligned regions not corresponding to coding exons or introns. 41% of peptide-supported version 2 (reliable) genes with UTR regions confirmed by EST support have suspected UTR/intron conflicts (355 out of 864).

ISSN: 1471-2105