Multiplexed mass spectrometry of individual ions improves measurement of proteoforms and their complexes.

An Orbitrap-based ion analysis procedure determines the direct charge for numerous individual protein ions to generate true mass spectra. This individual ion mass spectrometry (I2MS) method for charge detection enables the characterization of highly complicated mixtures of proteoforms and their complexes in both denatured and native modes of operation, revealing information not obtainable by typical measurements of ensembles of ions.

STORI Plots Enable Accurate Tracking of Individual Ion Signals.

Charge detection mass spectrometry (CDMS) of low-level signals is currently limited to the analysis of individual ions that generate a persistent signal during the entire observation period. Ions that disintegrate during the observation period produce reduced frequency domain signal amplitudes, which lead to an underestimation of the ion charge state, and thus the ion mass. The charge assignment can only be corrected through an accurate determination of the time of ion disintegration. The traditional mechanisms for temporal signal analysis have severe limitations for temporal resolution, spectral resolution, and signal-to-noise ratios. Selective Temporal Overview of Resonant Ions (STORI) plots provide a new framework to accurately analyze low-level time domain signals of individual ions. STORI plots allow for complete correction of intermittent signals, the differentiation of single and multiple ions at the same frequency, and the association of signals that spontaneously change frequency.

Charge Detection Mass Spectrometry with Almost Perfect Charge Accuracy.

Charge detection mass spectrometry (CDMS) is a single-particle technique where the masses of individual ions are determined from simultaneous measurement of each ion's mass-to-charge ratio (m/z) and charge. CDMS has many desirable features: it has no upper mass limit, no mass discrimination, and it can analyze complex mixtures. However, the charge is measured directly, and the poor accuracy of the charge measurement has severely limited the mass resolution achievable with CDMS. Since the charge is quantized, it needs to be measured with sufficient accuracy to assign each ion to its correct charge state. This goal has now been largely achieved. By reducing the pressure to extend the trapping time and by implementing a novel analysis method that improves the signal-to-noise ratio and compensates for imperfections in the charge measurement, the uncertainty has been reduced to less than 0.20 e rmsd (root-mean-square deviation). With this unprecedented precision peaks due to different charge states are resolved in the charge spectrum. Further improvement can be achieved by quantizing the charge (rounding the measured charge to the nearest integer) and culling ions with measured charges midway between the integral values. After ions with charges more than one standard deviation from the mean are culled, the fraction of ions assigned to the wrong charge state is estimated to be 6.4 × 10(-5) (i.e., less than 1 in 15 000). Since almost all remaining ions are assigned to their correct charge state, the uncertainty in the mass is now almost entirely limited by the uncertainty in the m/z measurement.

A frequency and amplitude scanned quadrupole mass filter for the analysis of high m/z ions.

Quadrupole mass filters (QMFs) are usually not used to analyze high m/z ions, due to the low frequency resonant circuit that is required to drive them. Here we describe a new approach to generating waveforms for QMFs. Instead of scanning the amplitude of a sine wave to measure the m/z spectrum, the frequency of a trapezoidal wave is digitally scanned. A synchronous, narrow-range (<0.2%) amplitude scan overlays the frequency scan to improve the sampling resolution. Because the frequency is the primary quantity that is scanned, there is, in principle, no upper m/z limit. The frequency signal is constructed from a stabilized base clock using a field programmable gate array. This signal drives integrating amplifiers which generate the trapezoidal waves. For a trapezoidal wave the harmonics can be minimized by selecting the appropriate rise and fall times. To achieve a high resolving power, the digital signal has low jitter, and the trapezoidal waveform is generated with high fidelity. The QMF was characterized with cesium iodide clusters. Singly and multiply charged clusters with z up to +5 were observed. A resolving power of ∼1200 (FWHM) was demonstrated over a broad m/z range. Resolution was lost above 20,000 Th, partly because of congestion due to overlapping multiply charged clusters. Ions were observed for m/z values well in excess of 150,000 Th.