MaxQuant Summer School 2013: 

Fragmentation and computational analysis of PTMs

Lecture by Kirti Sharma


MaxQuant Summer School 2013: Modifications

Tutorial by Kirti Sharma



Global mapping and localization of post-translational modifications (PTMs) is crucial for understanding the signaling networks that regulate essentially all of the biology of cells and organisms in normal and disease states. Large-scale 'precision proteomics' based on mass spectrometry (MS) has emerged as an increasingly powerful and indispensable technology for studying PTMs because of its unbiased approach and the ability to locate the PTM with single amino acid resolution. Our main focus areas in PTM analysis include phosphorylation, glycosylation, and acetylation.



Signal processing and amplification by plasma membrane proximal events are followed by communication of the signal to different cellular compartments. This process involves the activation of multiple signal cascades by receptors, different protein post-translational modifications (PTMs), crosstalk between signaling pathways and feedback loops to ensure optimal signaling output.



Recent Update:

We developed a stringent experimental and computational workflow, capable of mapping more than 50,000 distinct phosphorylated peptides in a single human cancer cell line. We describe our computational pipeline for reliable identification, site localization, and absolute stoichiometry. Using this method, we detected more than three-quarters of cellular proteins as phosphoproteins and determined very high stoichiometries in mitosis or growth factor signaling. (Sharma et al, Cell Reports, 2014).

We developed a generic spike-in SILAC approach to study phosphorylation responses in vivo. Using this method, we identified 15,000 phosphosites and quantitatively compared 10,000 sites in response to insulin treatment in the mouse liver (Monetti M et al, Nature methods, 2011).

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