D283 Med, a Cell Line Derived from Peritoneal Metastatic Medulloblastoma: A Good Choice for Missing Protein Discovery

Since the Chromosome-Centric Human
Proteome Project (C-HPP) was
launched in 2010, many techniques have been adopted for the discovery
of missing proteins (MPs). Because of these efforts, only 1481 MPs
remained as of July 2020; however, by relying only on technique optimization,
researchers have reached a bottleneck in MP discovery. Protein expression
is tissue- or cell-type-dependent. The tissues of the human testis
and brain have been reported to harbor a large number of tissue-specific
genes and proteins; however, few studies have been performed on human
brain tissue or cells to identify MPs. Herein a metastatic cell line
derived from brain cancer, D283 Med, was used to search for MPs. With
a traditional and simple shotgun workflow to separate the peptides
into 20 fractions, 12 MPs containing at least two unique non-nested
peptides (amino acid length ≥9) were identified in this cell
line with a protein false discovery rate of <1%. Following the
same experimental protocol, only one MP was found in a nonmetastatic
brain cancer cell line, U-118 MG. Furthermore, 12 MPs were verified
as having two non-nested unique peptides by matching them with corresponding
chemically synthesized peptides through parallel reaction monitoring.
These results clearly demonstrate that the appropriate selection of
experimental materials, either tissues or cell lines, is imperative
for MP discovery. The data obtained in this study are available via
ProteomeXchange (PXD021482) and PeptideAtlas (PASS01627).