Table 6.

List of all peptides that matched to an NTR entry, which were retained after inspection of MS/MS data

Accession	Peptide	Enzyme	Inspection of sequencing data
ENST00000439303_10_10174230_ntr_100db1 Elongin C pseudogene 3, processed pseudogene	MDGEEKTCGGCEGPDAMYV KLISSDGHEFIVKR	Trypsin	Supported by one nonsynonymous and one synonymous variant. AA difference with UniProt protein is covered
ENST00000486575_22_20127011_ntr_100db1 RAN binding protein 1, Retained intron	MKEETKEDAEEKQ	Trypsin, chymotrypsin	Derived from a retained intron transcript carries no single-nucleotide variants compared with protein-coding transcripts of that gene but is supported by NTR transcript–specific intron-retaining reads
ENST00000458332_17_19446852_ntr_111db1 Ribosomal protein S2 pseudogene 46, processed pseudogene	ADDAGAAGGPGGPGGPEMG NRGGFRGGF	GluC	Supported by NTR-specific reads with a synonymous variant but lacks evidence for the nonsynonymous variant
ENST00000582213_17_7572835_ntr_100db1 Eukaryotic translation initiation factor 4A1, retained intron	FPSNWNEIVDSFDDMNLSESLLR	Trypsin	The translation of the retained intron is supported by both Ribo-Seq studies
ENST00000403258_6_88276364_ ntr_101db1 ACTB pseudogene 8, processed pseudogene	MASAASSSSLE	GluC	Supported by a synonymous variant but lacks evidence for the nonsynonymous variant
ENST00000530835_11_90283408_ntr_011db2 Tubulin alpha pseudogene 2, processed pseudogene	GDVVPKDANAAIATIKTKR	Trypsin	Lacks evidence for the NTR-specific variants
ENST00000530835_11_90283408_ntr_011db2 Tubulin alpha pseudogene 2, processed pseudogene	PKDANAAIATIKTKR	Trypsin	Lack evidence for the NTR-specific variants

For each peptide, the accessions (containing both the Ensembl accession and transcript information) are provided along with the identified peptide sequence and the enzyme (protease) the peptide was identified with.