In-depth Membrane Proteomic Study of Breast Cancer Tissues for the Generation of a Chromosome-based Protein List

The Chromosome-centric Human Proteome Project (C-HPP)
aims to define
all proteins encoded in each chromosome and especially to identify
proteins that currently lack evidence by mass spectrometry. The C-HPP
also prioritizes particular protein subsets such as membrane proteins,
post-translational modifications, and low-abundance proteins. In this
study, we aimed to generate deep profiling of the membrane proteins
of human breast cancer tissues on a chromosome-by-chromosome basis
using shotgun proteomics. We identified 7092 unique proteins using
membrane fractions isolated from pooled breast cancer tissues with
high confidence. A total of 3282 proteins were annotated as membrane
proteins by Gene Ontology analysis, which covered 45% of the membrane
proteins predicted in 20 859 protein-coding genes. Furthermore,
we were able to identify 851 membrane proteins that currently lack
evidence by mass spectrometry in neXtProt. Our results will contribute
to the accomplishment of the primary goal of the C-HPP in identifying
so-called “missing proteins” and generating a whole
protein catalog for each chromosome.