Proteomics

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The Proteomics Facility provides a comprehensive suite of proteomics services to the Cancer Center membership. The primary emphasis is to provide expert consultation and state-of-the-art technologies operating at maximum performance at affordable costs to Cancer Center members. This is quite challenging because unlike genomics, proteomics technologies are highly varied; there are not consensus optimal approaches for most problems, and instruments, software and analytical strategies continue to evolve rapidly. Therefore, equipment and analytical methods must be continually updated. As a result, most of the instruments in the Facility were purchased within the past grant period, which includes $1.3 million invested in 2008 alone to replace obsolete mass spectrometers with 2 LTQ Orbitrap mass spectrometers and a high sensitivity triple quadropole mass spectrometer. Sensitivity of protein identifications has increased more than 100-fold over the past grant period through a combination of method optimization, acquisition of more sensitive instruments and development of an improved data analysis pipeline. Other methods have been similarly improved and new complementary methods have been implemented. The facility is also beginning to implement quantitative protein profile comparisons on LC-MS/MS based analyses using several complementary approaches, which will be expanded during the next grant period. During the past grant period (2003-present), 19 CC members used the Proteomics Facility and additional members benefited because many projects were collaborative between multiple CC investigators. CC members receive priority in sample analysis, substantial discounts on user fees (35-50% depending upon the service), more extensive consultation, training and assistance, and early access to methods/technologies not yet implemented as routine services. In the current year CCSG support covered 27% of non-equipment operating costs and will cover 23% of operating costs during the first year of the proposed grant. During 2007 44% of facility usage was by peer-reviewed CC members, and over the entire past grant period (2003-present) 61% of facility usage was by peer-reviewed CC members.