High throughput genomic and proteomic technologies continue to evolve rapidly in terms of sensitivity, coverage, reproducibility, quantitative accuracy and cost-efficiency. Members of the Technology Core have considerable knowledge and experience in selecting, evaluating, and rapidly implementing appropriate novel technologies to achieve the goals of the research projects. Furthermore, members of the Technology Core have developed some of the technologies that are essential for the success of the project. Critical to this is the development of efficient and robust processing pipelines that leverage tools, developed both in the wider scientific community and in house, and that are optimized for the biological questions under study.
The Core has incorporated multiple technical advances in the fields of genomics and proteomics. For example, a number of analytical tools and processing pipelines have been established for the acquisition and analysis of genomic data (http://baliga.systemsbiology.net/drupal/content/software-algorithms). The Aebersold laboratory has pioneered a number of novel proteomic methods including SRM and SWATH-MS and the software tools required to analyze the respective data. Proteomic studies have traditionally been limited by the sensitivity and poor reproducibility achievable in shotgun mass spectrometry. Selected Reaction Monitoring (SRM) techniques solve this problem since they enable accurate quantification of a defined set of proteins with high sensitivity and reproducibility over many samples. However, two main issues have limited the practical application of SRM. The first is the lack of available assays, particularly for murine and M. tuberculosis proteins. Over the last several years we have built a human and mouse peptide atlas and more recently we completed an M. tuberculosis peptide atlas containing high quality SRM assays for 97% of all annotated M. tuberculosis proteins. The second limitation of SRM is the number of proteins that can be quantified in a single analysis, which is currently in the order of 100. We have recently developed a new mass spectrometric technique termed SWATH-MS that largely extends the numbers of proteins that can be quantified in a single analysis while maintaining the favorable performance characteristics of SRM. Although SRM remains the gold standard for quantification and sensitivity we will use SWATH-MS where necessary to limit costs and to increase throughput.