The Target of Ramapycin (TOR) pathway controls cell growth in response to environmental stresses and nutrient availability. Mammalian TOR (mTOR) is implicated in several disorders, including cancer, obesity and diabetes. A better understanding of TOR may allow novel strategies in the treatment for mTOR-related diseases. In the present work we aimed to find new players in the TOR signaling pathways in the model yeast Saccharomyces cerevisiae. We have produced a high quality, whole genome sequence of Saccharomyces cerevisiae TB50, a strain used in our lab with a specific rapamycin-sensitive phenotype that makes it a perfect tool to study TOR signaling in yeast. Variant analysis and pooled-linkage analysis allowed us to pinpoint the causative variant responsible for this phenotype, a single missense mutation in the gene MKT1. Additionally, state-of-the-art quantitative phosphoproteomics with an allosteric inhibitor of TOR, rapamycin, and an ATP-competitive inhibitor, CMB4563, identified several potential TOR targets containing rapamycin-insensitive phosphosites.