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RNF168 promotes noncanonical K27 ubiquitination to signal DNA damage
(2015)Cell ReportsUbiquitination regulates numerous cellular processes by generating a versatile communication system based on eight structurally and functionally different chains linked through distinct residues. Except for K48 and K63, the biological relevance of different linkages is largely unclear. Here, we show that RNF168 ubiquitin ligase promotes noncanonical K27-linked ubiquitination both in vivo and in vitro. We demonstrate that residue K27 of ...Journal Article -
Using synthetic peptides to benchmark peptide identification software and search parameters for MS/MS data analysis
(2014)EuPA open proteomicsTandem mass spectrometry and sequence database searching are widely used in proteomics to identify peptides in complex mixtures. Here we present a benchmark study in which a pool of 20,103 synthetic peptides was measured and the resulting data set was analyzed using around 1800 different software and parameter set combinations. The results indicate a strong relationship between the performance of an analysis workflow and the applied ...Journal Article -
The Protein Interaction Landscape of the Human CMGC Kinase Group
(2013)Cell ReportsCellular information processing via reversible protein phosphorylation requires tight control of the localization, activity, and substrate specificity of protein kinases, which to a large extent is accomplished by complex formation with other proteins. Despite their critical role in cellular regulation and pathogenesis, protein interaction information is available for only a subset of the 518 human protein kinases. Here we present a global ...Journal Article -
Yeast Endosulfines Control Entry into Quiescence and Chronological Life Span by Inhibiting Protein Phosphatase 2A
(2013)Cell ReportsThe TORC1 and PKA protein kinases are central elements of signaling networks that regulate eukaryotic cell proliferation in response to growth factors and/or nutrients. In yeast, attenuation of signaling by these kinases following nitrogen and/or carbon limitation activates the protein kinase Rim15, which orchestrates the initiation of a reversible cellular quiescence program to ensure normal chronological life span. The molecular elements ...Journal Article -
Proteome-wide selected reaction monitoring assays for the human pathogen Streptococcus pyogenes
(2012)Nature CommunicationsSelected reaction monitoring mass spectrometry (SRM-MS) is a targeted proteomics technology used to identify and quantify proteins with high sensitivity, specificity and high reproducibility. Execution of SRM-MS relies on protein-specific SRM assays, a set of experimental parameters that requires considerable effort to develop. Here we present a proteome-wide SRM assay repository for the gram-positive human pathogen group A Streptococcus. ...Journal Article -
Mapping the interaction of Snf1 with TORC1 in Saccharomyces cerevisiae
(2011)Molecular Systems BiologyNutrient sensing and coordination of metabolic pathways are crucial functions for all living cells, but details of the coordination under different environmental conditions remain elusive. We therefore undertook a systems biology approach to investigate the interactions between the Snf1 and the target of rapamycin complex 1 (TORC1) in Saccharomyces cerevisiae. We show that Snf1 regulates a much broader range of biological processes compared ...Journal Article -
PhosphoPep—a phosphoproteome resource for systems biology research in Drosophila Kc167 cells
(2007)Molecular Systems BiologyThe ability to analyze and understand the mechanisms by which cells process information is a key question of systems biology research. Such mechanisms critically depend on reversible phosphorylation of cellular proteins, a process that is catalyzed by protein kinases and phosphatases. Here, we present PhosphoPep, a database containing more than 10 000 unique high‐confidence phosphorylation sites mapping to nearly 3500 gene models and 4600 ...Journal Article