Discovery of Missing Proteins from an Aneuploidy Cell Line Using a Proteogenomic Approach

With
the steadfast development of proteomic technology, the number
of missing proteins (MPs) has been continuously shrinking, with approximately
1470 MPs that have not been explored yet. Due to this phenomenon,
the discovery of MPs has been increasingly more difficult and elusive.
In order to face this challenge, we have hypothesized that a stable
aneuploid cell line with increased chromosomes serves as a useful
material for assisting MP exploration. Ker-CT cell line with trisomy
at chromosome 5 and 20 was selected for this purpose. With a combination
strategy of RNA-Seq and LC-MS/MS, a total of 22 178 transcripts
and 8846 proteins were identified in Ker-CT. Although the transcripts
corresponding to 15 and 15 MP genes located at chromosome 5 and 20
were detected, none of the MPs were found in Ker-CT. Surprisingly,
3 MPs containing at least two unique non-nest peptides of length ≥9
amino acids were identified in Ker-CT, whose genes are located on
chromosome 3 and 10, respectively. Furthermore, the 3 MPs were verified
using the method of parallel reaction monitoring (PRM). These results
suggest that the abnormal status of chromosomes may not only impact
the expression of the corresponding genes in trisomy chromosomes,
but also influence that of other chromosomes, which benefits MP discovery.
The data obtained in this study are available via ProteomeXchange
(PXD028647) and PeptideAtlas (PASS01700), respectively.