Olga Schubert Olga Schubert studied Biology at ETH Zurich (Switzerland). During her Masters she focused on cell biology and cancer research. Afterwards, she spent six month in Italy as a trainee at EMBL Monterotondo to gain more insights into mouse biology and neuroscience. In April 2010 she joined the group of Prof. Ruedi Aebersold at the Institute of Molecular Systems Biology, ETH Zurich, where she has been applying mass spectrometry to study the proteome of Mycobacterium tuberculosis. Recently, she developed the Mtb Proteome Library, a database containing quantitative assays for targeted mass spectrometry for all proteins of Mycobacterium tuberculosis. Her current research focus is on proteome-wide absolute quantification of Mycobacterium tuberculosis using SRM and data-independent acquisition (SWATH-MS).

Development and application of assays for targeted mass spectrometric analysis of the complete proteome of Mycobacterium tuberculosis

Worldwide, two billion people are infected with Mycobacterium tuberculosis (Mtb), the causative agent of tuberculosis. To facilitate basic and translational research into Mtb we developed a library of quantitative assays for the targeted mass spectrometric analysis of the Mtb proteome by selected reaction monitoring (SRM). The software tools Skyline and mProphet were used extensively in creating a resource that contains high quality SRM assays for 97% of the 4,012 proteins annotated in Mtb, of which 72% could be validated in whole cell lysates. From this proteome-wide SRM data, the absolute abundances of 55% of all Mtb proteins were estimated, revealing a dynamic range of the Mtb proteome of over four orders of magnitude. We used the thus generated assay library to gain protein-level insights into the dynamic regulation of almost the entire dormancy survival regulon in response to hypoxia by SRM. Currently, we are extending and optimising the library for targeted data extraction of MS/MS spectra generated by data-independent acquisition (SWATH-MS), which allows us to quantify hundreds of proteins in a single run. In conclusion, we present the development and application of a library of publicly available, quantitative assays for targeted proteomics by SRM and SWATH-MS to accurately monitor abundance changes of virtually all Mtb proteins with high sensitivity and reproducibility.

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