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.