SWATH represents an important development for establishing a comprehensive LC/MS based quantitative strategy for cancer based proteome projects.  The approach currently relies on the development of spectral libraries containing both product ion data and retention time information, and provides the basis for extensive data-independent quantitation.  Although significant progress has been made recently towards mapping the human proteome, spectral libraries remain an important target resource for proteomics.

Here we report on the assessment of new 6600 Triple TOF technology in providing extended proteome coverage and the establishment of a comprehensive spectral library for cancer research.  We have observed a two-fold increase in protein coverage using a 6600 Triple TOF compared with a 5600 Triple TOF, and now detect over 20,000 distinct peptides from 3000 proteins in a single two-hour 1-dimension chipLC/MS analysis.  Utilising this additional capacity in proteome coverage, we have developed a comprehensive spectral library for SWATH using a variety of human cancer cell lines, including melanoma, colorectal, thyroid, cervical and transformed embryonic kidney cells.  We  demonstrate the utility of this extended cancer database by characterising quantitative differences of each cancer cell line via SWATH.