The advance of nanoparticle-based technologies (e.g. ProteographTM) in combination with high-end mass spectrometry (MS) has increased the depth of proteome coverage for biofluids like plasma, serum or cerebrospinal fluid (CSF), making it possible to routinely analyze 2.000-3,000 proteins per individual biofluid sample. Over the last two years we have extensively used this technology at Evotec to screen multiple different patient cohorts, each containing up to a few hundred serum or plasma samples from patients with very different disease backgrounds, including patients with multiple co-morbidities and a dedicated cohort of healthy subjects that were hospitalized over-night to ensure maximum control of biofluid and data collection.
While in the past, most activities in the field of Clinical Proteomics were limited to a specific patient cohort in a clearly defined disease context, the next challenge is to integrate proteomics signatures from multiple cohorts into a unified framework. Here, we show how this can be achieved by minimizing technical variability during sample collection, sample preparation and MS measurement using highly automated nanoparticle-based proteomics approaches. In addition, we present how PanHunter – a multi-omics tool optimized for collaborative data analysis – can support management of patient metadata as well as integration of multiple studies.