Recent advances in mass spectrometry-based proteomics allow the systematic measurement of proteome-wide posttranslational modifications, such as phosphorylation (termed 'phosphoproteomics'), in response to stimuli. Such phosphoproteomics experiments can track highly dynamic changes in over 10,000 different phosophosites in >5,000 proteins. However analysing and gaining insight from these complex datasets can be challenging. The first part of this talk will describe ongoing work aimed at addressing this challenge by developing 'Minardo', an integrated system that combines data analysis and visualization to reveal the key events, such as kinase or phosphatase switching, that underlie most observed events. I will illustrate this approach by showcasing how Minardo has recently been used to summarize phosporegulation of mitosis (http://www.cell.com/cell/enhanced/odonoghue2).
The second part of this talk focuses on the 'dark' proteome of structural biology - i.e., regions of proteins for which no structural information can be inferred, even using the best available homology modeling methods (http://www.pnas.org/content/112/52/15898.full). About half of the eukaryotic proteome is 'dark' - and this includes many regions involved in posttranslational modifications. I will describe unpublished work - using statistical and visualization methods - that has reveal new, unexpected features of the dark proteome.