Christina Ludwig   Christina Ludwig, Ph.D., has studied Chemistry at the Philipps-University in Marburg (Germany) and performed her PhD in the biochemical research group of Professor Henning Mootz at the Technische Universität Dortmund. There she developed a general technique for the N-terminal modification of proteins based on protein splicing, a posttranslational reaction catalyzed by a class of proteins called inteins. In March 2009 Christina joined the laboratory of Prof. Ruedi Aebersold at the ETH Zürich as a postdoctoral fellow. Her current research interests are focused on technical development projects related to targeted mass spectrometry, including Selected Reaction Monitoring (SRM-MS) and SWATH-MS. She is involved in projects aiming for the specific identification and quantification of post-translational modifications, in particular protein phosphorylation, and her second field of interest focuses on the estimation of absolute protein abundances from label-free, targeted mass spectrometric data.

Pinpointing phosphorylation sites using Selected Reaction Monitoring and Skyline

The precise and confident assignment of protein phosphorylation sites within a given peptide sequence still remains one of the major challenges in the field of phosphoproteomics. Typically, this issue becomes especially apparent when several possibly phosphorylated amino acids are located in close proximity. To test the utility of Selected Reaction Monitoring (SRM) as a method for specific phosphosite assignments we extensively investigated two metabolic proteins from Saccharomyces cerevisiae, which both show multiple possibly phosphorylated serine residues in very close proximity. All data analysis was performed manually using the software Skyline and exploiting its inherent capability to generate and optimize SRM assays for any type of phosphorylated (or generally modified) peptide and by predicting highly accurate, calibrated retention time information based on the iRT approach (independent retention time, Finally we applied our assays onto phospho-enriched yeast samples for the unambiguous assignment and accurate quantification of endogenously occurring phosphopeptides.

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