As Director of the Quantitative Proteomics Center at Columbia University my work focuses on the identification of proteins with differential quantitative expression in cells, tissues or in affinity purifications. We have applied this technique employing mass spectrometry to many different research problems. A wide variety of proteomes can be processed including cells, tissues, organelles, biofluids, and affinity preparations. We routinely study clinical (schizophrenia, traumatic brain injury), bacterial, yeast, insect, viral and mammalian proteomes. Several innovative new hardware and software capabilities in mass spectrometry provide state-of-the-art support to our research projects. These include our capability to perform data-independent scanning which provides rich datasets from which we identify and quantify proteins.A recent position paper by the American Society for Biochemistry and Molecular Biology (ASBMB) has described the challenges in data handling in proteomics as “…destined to create an almost unimaginable amount of information.” Data-independent scanning produces an exceedingly comprehensive description of protein structure, but at the same time produces the largest data files. We have recently added ion-mobility spectrometry to our toolbox. This technique provides even more structural information, but at the cost of doubling the amount of data produced for each experiment, further increasing our big data challenges.