Single cell profiling at a massive scale for applications such as target identification and biomarker discovery requires compatibility with diverse clinical sample types like blood, fresh or frozen tissues, and FFPE blocks along with higher-throughput capabilities. The demand is being further driven by landmark initiatives such as the Human Cell Atlas and the Billion Cells Project, and the increasing number of single cell foundation models. We introduce Flex Apex, with significantly expanded multiplexing capabilities for simultaneous processing of up to 384 samples and profiling of up to 100 million cells per kit.