Single-cell proteomic technologies hold the potential to enable mechanistic investigations of key biological questions, such as signaling mechanisms based on protein binding, modifications, and degradation, that have long remained elusive. Realizing this potential requires scaling up their throughput and increasing the efficiency of ion sampling.
This might be achieved by accumulating ions in parallel as supported by data independent acquisition (DIA). Ideally such parallel accumulation should be synergistically combined with sample (i.e., single cell) multiplexing strategies to support the high throughput needed by most single-cell applications. The mass offsets introduced by multiplexing with non isobaric mass tags, such as precisely known offsets in mass/charge space, may provide additional constraints on peptide identification. Towards acheiving these aims, plexDIA introduced algorithms to acquire and analyze multiplexed DIA data:
Such simultaneous multiplexing allows for multiplicative increase in quantitative protein data points, both with bulk and with single-cell samples.
These results point to a framework for multiplicative scaling of single-cell proteomics.