Our lab studies a variety of host-pathogen combinations. We mostly use quantitative proteomics, employing stable isotope labeling and liquid chromatography-tandem mass spectrometry (LC-MS/MS) but also use other high-throughput methods, such as high content screening and massively parallel sequencing. To fill in the gaps we then turn to more focused biochemical and cell biological methods. Recently we have described a novel method for mapping the protein interaction network within cells (the interactome) that drives the time and cost involved in such an analysis down by nearly two orders of magnitude; this technique will play an important role in many current and future projects.