Improving throughput in Orbitrap using the ion funnel with orthogonal injection and observation of chemical noise in high-resolution MS instruments

Overall, the nanoflow chromatographic separation, nano-electrospray source, and Orbitrap Elite mass spectrometer with the dual-stage ion funnel that replaced the standard heated-cone inlet were used in the MS analysis of low-abundance peptide samples. The analytical advantage of the ion funnel was demonstrated in the LC-MS analysis of HeLa protein digest mixture. Chemical noise patterns in Orbitrap, linear ion traps, and quadrupole time-of-flight mass spectrometers were compared. The chemical noise patterns in Orbitrap were found to be generally similar to those observed in linear ion traps and time-of-flight instruments, yet under conditions of selecting a limited mass range for the mass analysis. Ultrahigh mass resolution attained in Orbitrap allowed revealing internal structure in the chemical noise patterns. In addition to singly charged ions representing a bulk of chemical noise, the doubly charged ions were also observed, though the intensity of the latter was found to be significantly lower, suggesting that chemical noise-limited detection levels in low-abundance peptide MS analysis could be significantly lower for 2+ or 3+ peptide ions compared to singly charged ones.