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

Abstract

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 the 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 it was observed only under the condition of selecting a few Da mass range for the mass analysis. The Orbitrap's ultrahigh mass resolution enabled the intricate internal structure of the chemical noise to be uncovered. In addition to singly charged ions representing a bulk of chemical noise, 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 the MS analysis of low-abundance peptides could be significantly lower for 2+ or 3+ peptide ions compared to singly charged ones.