One of the major challenges of a chromosome-centric proteome project is to 
explore in a systematic manner the potential proteins identified from the 
chromosomal genome sequence, but not yet characterized on a protein level. Here, 
we describe the use of RNA deep sequencing to screen human cell lines for RNA 
profiles and to use this information to select cell lines suitable for 
characterization of the corresponding gene product. In this manner, the 
subcellular localization of proteins can be analyzed systematically using 
antibody-based confocal microscopy. We demonstrate the usefulness of selecting 
cell lines with high expression levels of RNA transcripts to increase the 
likelihood of high quality immunofluorescence staining and subsequent successful 
subcellular localization of the corresponding protein. The results show a path 
to combine transcriptomics with affinity proteomics to characterize the proteins 
in a gene- or chromosome-centric manner.