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.

Ultrahigh Resolution Ion Isolation by Stored Waveform Inverse Fourier Transform 21 T Fourier Transform Ion Cyclotron Resonance Mass Spectrometry.

Stored waveform inverse Fourier transform (SWIFT) is a versatile method to generate complex isolation/ejection waveforms for precursor isolation prior to tandem mass spectrometry experiments. Here, we report ultrahigh resolving power ion isolation by SWIFT on a 21 T Fourier transform ion cyclotron resonance (FTICR) mass spectrometer. Individual histone proteoforms are isolated (0.6 m/z isolation window) with near 100% efficiency using a 52 ms SWIFT isolation, followed by in-cell fragmentation by ultraviolet photodissociation (UVPD). Ion isolation resolving power of 175 000 (m/Δm) is demonstrated by isolation of individual peaks at a spacing of 0.0034 Da at m/z 597 from a complex mixture of Canadian bitumen. An individual m/z ion, which corresponds to a single elemental composition, from a complex mixture is isolated and fragmented by infrared multiphoton dissociation (IRMPD). Theoretical and experimental considerations that limit achievable ion isolation resolving power are discussed.

Automated broadband phase correction of Fourier transform ion cyclotron resonance mass spectra.

It has been known for 35 years that phase correction of FTICR data can in principle produce an absorption-mode spectrum with mass resolving power as much as a factor of 2 higher than conventional magnitude-mode display, an improvement otherwise requiring a (much more expensive) increase in magnetic field strength. However, temporally dispersed excitation followed by time-delayed detection results in steep quadratic variation of signal phase with frequency. Here, we present a robust, rapid, automated method to enable accurate broadband phase correction for all peaks in the mass spectrum. Low-pass digital filtering effectively eliminates the accompanying baseline roll. Experimental FTICR absorption-mode mass spectra exhibit at least 40% higher resolving power (and thus an increased number of resolved peaks) as well as higher mass accuracy relative to magnitude mode spectra, for more complete and more reliable elemental composition assignments for mixtures as complex as petroleum.

Petroleomics: a test bed for ultra-high-resolution Fourier transform ion cyclotron resonance mass spectrometry.

Within a relative abundance dynamic range of approximately 10,000:1, the world's most compositionally complex organic mixture is petroleum crude oil. As such, it provides the most challenging target for mass spectral resolution and identification of molecules below m/z 2000. The mass "splits" in petroleum include most of those that also appear in proteomics, metabolomics and other complex organic mixture analysis. Therefore, petroleum provides an excellent test bed for optimizing mass spectrometer performance in general. The presence of multiple elemental compositions spanning less than 1 Da in mass facilitates mapping and correction of rf phase variation across a Fourier transform ion cyclotron resonance mass spectrum, as well as exposing otherwise inaccessible systematic mass deviations, for additional improvement in mass resolving power and mass accuracy by a factor of up to 5. Internal mass calibration, combined with systematic peak assignment for successive homologous series, enables automated elemental composition assignment of tens of thousands of peaks in a single mass spectrum.

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.

21 Tesla Fourier Transform Ion Cyclotron Resonance Mass Spectrometer: A National Resource for Ultrahigh Resolution Mass Analysis.

We describe the design and initial performance of the first 21 tesla Fourier transform ion cyclotron resonance (FT-ICR) mass spectrometer. The 21 tesla magnet is the highest field superconducting magnet ever used for FT-ICR and features high spatial homogeneity, high temporal stability, and negligible liquid helium consumption. The instrument includes a commercial dual linear quadrupole trap front end that features high sensitivity, precise control of trapped ion number, and collisional and electron transfer dissociation. A third linear quadrupole trap offers high ion capacity and ejection efficiency, and rf quadrupole ion injection optics deliver ions to a novel dynamically harmonized ICR cell. Mass resolving power of 150,000 (m/Δm(50%)) is achieved for bovine serum albumin (66 kDa) for a 0.38 s detection period, and greater than 2,000,000 resolving power is achieved for a 12 s detection period. Externally calibrated broadband mass measurement accuracy is typically less than 150 ppb rms, with resolving power greater than 300,000 at m/z 400 for a 0.76 s detection period. Combined analysis of electron transfer and collisional dissociation spectra results in 68% sequence coverage for carbonic anhydrase. The instrument is part of the NSF High-Field FT-ICR User Facility and is available free of charge to qualified users.

Excitation of radial ion motion in an rf-only multipole ion guide immersed in a strong magnetic field gradient.

Radiofrequency (rf) multipole ion guides are widely used to transfer ions through the strong magnetic field gradient between source and analyzer regions of external source Fourier transform ion cyclotron resonance mass spectrometers. Although ion transfer as determined solely by the electric field in a multipole ion guide has been thoroughly studied, transfer influenced by immersion in a strong magnetic field gradient has not been as well characterized. Recent work has indicated that the added magnetic field can have profound effects on ion transfer, ultimately resulting in loss of ions initially contained within the multipole. Those losses result from radial ejection of ions due to transient cyclotron resonance that occurs when ions traverse a region in which the magnetic field results in an effective cyclotron frequency equal to the multipole rf drive frequency divided by the multipole order (multipole order is equal to one-half the number of poles). In this work, we describe the analytical basis for ion resonance in a rf multipole ion guide with superposed static magnetic field and compare with results of numerical trajectory simulations.

Broadband phase correction of FT-ICR mass spectra via simultaneous excitation and detection.

In typical Fourier transform ion cyclotron resonance (FT-ICR) mass spectra, temporally dispersed excitation and the delay between excitation and detection result in continuous variation of signal phase with frequency in the detected time-domain ion signal. The complex frequency-domain spectrum of such a signal is a linear combination of absorption- and dispersion-mode spectral components with corresponding asymmetric peaks. For this reason, magnitude-mode spectral display is usually employed to yield a phase-independent uniform and symmetrical peak shape at the expense of spectral resolution. In this work, we implement simultaneous excitation and detection to enable Fourier deconvolution to recover absorption-mode spectra for both low- and high-field FT-ICR instruments. These spectra yield resolving power improvement factors approaching the maximum theoretical limit of 2.0, as well as reduction in frequency assignment errors relative to conventional magnitude-mode spectra. The Fourier deconvolution procedure has the additional benefit of correcting for spectral variation resulting from nonuniform power distribution over the excitation bandwidth and the potential benefit of providing useful diagnostic information for interpretation of experimental performance.