Ion torrent sequencing of cell line SW1353 derived from a primary grade II chondrosarcoma

Proteogenomics helps improving human genome annotation per se and shows interesting applications in cancer research. Because cell lines used in cell biology fundamental research or cancer cells are genetically quickly evolving, their study by proteomics should take into consideration not only the human reference annotated genome, but also possible variants arising from drift mutations along cell cultivation or tumorigenesis. RNAseq of the cell line may provide the perfect protein sequence database for proteomics insightful studies. Here, we compared several database and RNAseq assembly strategies, and proposed a cascaded search strategy for maximizing proteogenomic results. We have shown that proteomics results obtained from the cell line SW1353 derived from a primary grade II chondrosarcoma of the right humerus obtained from a 72 year old female Caucasian could be further increase with this cascaded search.