A nature-inspired ion trap for parallel manipulation of ions on a massive scale.

Parallelization has revolutionized computing and DNA sequencing but remains largely unexploited in mass spectrometry (MS), which typically analyzes ions sequentially. Inspired by nuclear cytoplasmic transport, where diffusion governs transport to multiple gated channels (nuclear pore complexes), we introduce an ion trap (MultiQ-IT) that enables massively parallel MS. The device comprises a cubic array of small quadrupoles forming multiple ion entry and exit ports, allowing >109 ions to be cooled, confined, and manipulated simultaneously. This architecture enables selective depletion of singly charged ions, thereby enhancing signal-to-noise ratios and expanding the effective dynamic range. The trap also functions as a parallel ion splitter, transmitting ions into multiple mass/charge ratio-specific beams. We demonstrate scalable ion throughput, real-time charge discrimination, and parallel beam separation, suggesting a path toward truly parallel MS. Our results establish a conceptual framework for next-generation, high-throughput proteomic and metabolomic analyses.