Note: Optimized circuit for excitation and detection with one pair of electrodes for improved Fourier transform ion cyclotron resonance mass spectrometry.

A conventional Fourier transform-Ion Cyclotron Resonance (ICR) detection cell is azimuthally divided into four equal sections. One pair of opposed electrodes is used for ion cyclotron excitation, and the other pair for ion image charge detection. In this work, we demonstrate that an appropriate electrical circuit facilitates excitation and detection on one pair of opposed electrodes. The new scheme can be used to minimize the number of electrically independent ICR cell electrodes and/or improve the electrode geometry for simultaneously increased ICR signal magnitude and optimal post-excitation radius, which results in higher signal-to-noise ratio and decreased space-charge effects.

Surface-induced dissociation of multiply-protonated proteins.

A novel surface design compatible with the open cell geometry allows nonglancing angle collisions of selected ions stored in a Fourier transform mass spectrometer. Dissociation efficiencies of 36%, 22%, and 14% are achieved for gramicidin S, melittin, and carbonic anhydrase (29 kDa), respectively. Ion neutralization by the surface, which is highly competitive for many singly-charged ions, is minimal, and dissociation products of hypervalent neutral species are not detected. Instead, the spectra are similar to those from collisionally activated and infrared multiphoton dissociation; the fragmentation pathways are relatively independent of the method of energy deposition. For carbonic anhydrase, however, the single event excitation inherent to surface-induced dissociation appears to minimize secondary fragmentation, a critical advantage for tandem mass spectrometry of such large ions. Electrically floating the open cell below ground greatly enhances the collection efficiency.

Determination of monoisotopic masses and ion populations for large biomolecules from resolved isotopic distributions.

The coupling of electrospray ionization with Fourier-transform mass spectrometry allows the analysis of large biomolecules with mass-measuring errors of less than 1 ppm. The large number of atoms incorporated in these molecules results in a low probability for the all-monoisotopic species. This produces the potential to misassign the number of heavy isotopes in a specific peak and make a mass error of ±1 Da, although the certainty of the measurement beyond the decimal place is greater than 0.1 Da. Statistical tests are used to compare the measured isotopic distribution with the distribution for a model molecule of the same average molecular mass, which allows the assignment of the monoisotopic mass, even in cases where the monoisotopic peak is absent from the spectrum. The statistical test produces error levels that are inversely proportional to the number of molecules in a distribution, which allows an estimation of the number of ions in the trapped ion cell. It has been determined, via this method that 128 charges are required to produce a signal-to-noise ratio of 3:1, which correlates well with previous experimental methods.

Automated assignment of charge states from resolved isotopic peaks for multiply charged ions.

The recent proliferation of electrospray as an ionization method has greatly increased the ability to perform analyses of large biomolecules by using mass spectrometry. The major advantage of electrospray is the ability to produce multiply charged ions, which brings large molecules down to a mass-to-charge ratio range amenable to most instruments. Multiple charging is also a disadvantage because mass (m) becomes ambiguous unless charge (z) can be assigned. This is typically performed with simple algorithms that use multiple peaks of the same m and different z, but these methods are difficult to apply to complex mixtures and not applicable when only one z appears for each m. The use of mass analyzers with higher resolving powers, like the Fourier transform mass spectrometer, allows resolution of isotopic peaks, providing an internal 1-Da mass scale that can be used for unambiguous charge assignment. Manual assignment of charge state from the isotopic peaks is time consuming and becomes inaccurate when either the signal level or resolving power are low. For these cases, computer algorithms based on pattern recognition techniques have been developed to assist in assignment of charge states to isotopic clusters. These routines provide for more rapid analysis with higher accuracy than available manually.

High-resolution tandem mass spectrometry of carbonic anhydrase.

Electrospray ionization of carbonic anhydrase with ion dissociation yields a mass spectrum from which the masses of > 100 isotopic clusters are determined accurately, with the number of charges assigned directly from resolved isotopic peaks. Of these clusters, 80% correspond to fragmentation at or near the amino acid proline. The masses of combinations of two, three, and four of these clusters sum to the molecular mass with 0.1-Da accuracy, while further fragment ion dissociation provides additional sequence information. The capability of this methodology to detect sequence variations is illustrated with an isozyme having a single amino acid replacement.

Coexisting stable conformations of gaseous protein ions.

For further insight into the role of solvent in protein conformer stabilization, the structural and dynamic properties of protein ions in vacuo have been probed by hydrogen-deuterium exchange in a Fourier-transform mass spectrometer. Multiply charged ions generated by electrospray ionization of five proteins show exchange reactions with 2H2O at 10(-7) torr (1 torr = 133.3 Pa) exhibiting pseudo-first-order kinetics. Gas-phase compactness of the S-S cross-linked RNase A relative to denatured S-derivatized RNase A is indicated by exchange of 35 and 135 hydrogen atoms, respectively. For pure cytochrome c ions, the existence of at least three distinct gaseous conformers is indicated by the substantially different values--52, 113, and 74--of reactive H atoms; the observation of these same values for ions of a number--2, 7, and 5, respectively--of different charge states indicates conformational insensitivity to coulombic forces. For each of these conformers, the compactness in vacuo indicated by these values corresponds directly to that of a known conformer structure in the solution from which the conformer ions are produced by electrospray. S-derivatized RNase A ions also exist as at least two gaseous conformers exchanging 50-140 H atoms. Gaseous conformer ions are isometrically stable for hours; removal of solvent greatly increases conformational rigidity. More specific ion-molecule reactions could provide further details of conformer structures.

Mass and charge assignment for electrospray ions by cation adduction.

The assignment of the mass (m) value from the m/z value for ions with a multiple number of charges (z) in electrospray mass spectra usually utilizes multiple peaks of the same m but different z values, or unit-mass-separated isotopic peaks of the same z value from high resolution spectra. The latter approach is also feasible with much less resolving power using adduct ions of much higher mass separation. The application of this to mixture spectra containing many masses, such as spectra from tandem mass spectrometry (MS/MS) ion dissociation, does not appear to have been pointed out previously. Thus, replacing two protons by one Cu(2+) ion increases the mass by 61.5 Da, with this shift providing a mass scale for assignment of m and z from this pair of m/z values. The more common Na(+) adduct peaks provide a 22.0 Da separation, of utility for 1000 resolving power only below approximately 10 kDa. Further, collisional dissociation lowers the degree of Cu(2+) adduction in the resulting sequence-specific fragment ions much less than that of the corresponding Na(+) adducts, making the Cu(2+) adducts far more useful for m and z determination in MS/MS studies.

Two-dimensional coulomb-induced frequency modulation in Fourier transform ion cyclotron resonance: A mechanism for line broadening at high mass and for large ion populations.

Fourier transform ion cyclotron resonance (FTICR) spectra generated for large ion populations exhibit frequency shifts and line broadening, apparently due to Coulomb forces between ions. Although previous two-dimensional (2D) models of Coulomb effects in FTICR accounted for frequency shifts, they did not account for spectral line broadening. In this article, a 2D model is proposed that predicts line broadening due to Coulomb-induced frequency modulation. The model considers the case of two different-mass ions orbiting at their respective cyclotron frequencies around a common guiding center. A mutual modulation of the cyclotron frequency occurs at the difference frequency between ions. If the modulation period is much shorter than the FTICR observation time, then sidebands spaced at intervals approximately equal to the modulation frequency are predicted. However, if the modulation period is similar in duration to the FTICR observation period, the sidebands can no longer be resolved, which results in spectral line broadening. This latter case is a necessary consequence for isotopic peaks in the high mass region around m/z 2000, where deterioration in FTICR performance has been observed. Computer simulations are used to confirm the mass dependence and to demonstrate other features of the model, including a strong dependence of the modulation on ion number. In support of the model, experimental FTICR spectra for large populations of methylnaphthalene ions at m/z 141 and 142 exhibit constant frequency sidebands corresponding to multiples of the difference frequency for the two ions extending from nominal values of m/z 136 to 147.

Fourier-transform electrospray instrumentation for tandem high-resolution mass spectrometry of large molecules.

Department of Chemistry, Baker Laboratory, Cornell University, Ithaca, New York, USA Mass spectrometry instrumentation providing unit resolution and lo-ppm mass accuracy for molecules larger than 10 kDa was first reported in 1991. This instrumentation has now been improved with a 6.2-T magnet replacing that of 2.8 T, a more efficient vacuum system, ion injection with controlled ion kinetic energies, accumulated ion trapping with an open-cylindrical ion cell, acquisition of 2M data points, and updated electrospray apparatus. The resulting capabilities include resolving power of 5 × 10(5) for a 29-kDa protein, less than l-ppm mass measuring error, and dissociation of protein molecular ions to produce dozens of fragment ions whose exact masses can be identified from their mass-to-charge ratio values and isotopic peak spacing.

Improved fourier-transform ion-cyclotron-resonance mass spectrometry of large biomolecules.

Initial results from a Fourier-transform mass spectrometer with a 6.2 Tesla magnet using electrospray ionization show substantial improvements in resolution, mass accuracy, mass range, signal/noise, and tandem mass spectromehy capabilities compared to our earlier 2.8 T instrument that demonstrated the first unit resolution mass spectra of molecules as large as myoglobin (17 kDa). The new instrument exhibits greater than 10(6) and 10(5) resolving power for 8.6 and 29 kDa, respectively, proteins. Using an internal standard, the mass measuring error for myoglobin is less than 1 ppm. Nozzle-skimmer dissociation during electrospray of carbonic anhydrase (29 kDa) has yielded 38 fragment ions for which both mass and charge are identifiable; of these, 21 have been assigned to expected oligopeptide fragments.