HPLC–MS-MS is the go-to technique for high throughput analysis of small molecule therapeutics, metabolites, and biomarkers. Through technological advancements in the last decade, developing quality methods for a novel analyte in the contract research environment has become easier and faster than ever. Increasingly shorter run times, higher sensitivity, and greater separation have all become possible in a standard method. This is, in part, due to column technologies that have enabled the standardization of the method development process. Method efficiency and productivity are also improving because of emerging column technologies such as sub-2 µm particle size coupled with UHPLC–MS-MS, superficially porous particle columns, and microflow HPLC–MS-MS. Increasing efficiency and productivity in high throughput bioanalysis is becoming more important as the applications for HPLC–MS-MS expand to large molecules such as peptides, proteins, and oligonucleotides.