If we are to understand cellular function – and dysfunction – at a systems level, then we must understand how proteome state drives the diversity of form and function embodied by human cells. Thanks in large part to mass spectrometry-based proteomics technology, it has become possible to profile the proteome in its many dimensions, from protein abundance and post-translational modification status to protein stability, proximity, interactions, and subcellular localization. Nevertheless, this remains a daunting experimental challenge due to the complexity and malleability of the proteome.

By increasing throughput, consistency of detection, and precision of quantification, isobaric labeling can enable proteome profiling with exceptional breadth and accuracy. Yet considerable effort is required to attain optimal results. I will describe the rationale behind the methods the Gygi lab has developed to execute isobaric labeling experiments with optimal depth and quantitative accuracy. I will then describe how we have deployed these methods to identify short-lived proteins in multiple cell lines and to profile protein expression across hundreds of cancer cell lines. These prototypes will serve as useful examples of how isobaric labeling with TMT reagents and state-of-the-art mass spectrometry instrumentation can be deployed at small and large scale to address fundamental questions of proteome biology.