A commercial quadrupole/time-of-flight (QqTOF) tandem mass spectrometer has been adapted for ion/ion reaction studies. To enable mutual storage of oppositely charged ions in a linear ion trap, the oscillating quadrupole field of the second quadrupole of the system (Q2) serves to store ions in the radial dimension while auxiliary RF is superposed on the end lenses of Q2 during the reaction period to create barriers in the axial dimension. A pulsed dual electrospray (ESI) source is directly coupled to the instrument interface for the purpose of proton transfer reactions. Singly and doubly charged protein ions as high in mass as 66 kDa are readily formed and observed after proton transfer reactions. For the modified instrument, the mass resolving power is about 8000 for a wide m/z range and the mass accuracy is ~20 ppm for external calibration and ~5 ppm for internal calibration after ion/ion reactions. Parallel ion parking is demonstrated with a six-component protein mixture, which shows the potential application of reducing spectral complexity and concentrating certain charge states. The current system has high flexibility with respect to defining MS n experiments involving collisioninduced dissociation (CID) and ion/ion reactions. Protein precursor and CID product masses can be determined with good accuracy, providing an attractive platform for top-down proteomics. Electron transfer dissociation (ETD) ion/ion reactions are implemented by using a pulsed nano-ESI/ atmospheric pressure chemical ionization (APCI) dual source for ionization. The reaction between protonated peptide ions and radical anions of 1,3-dinitrobenzene formed exclusively c-and z-type fragment ions.

No abstract

Cation radicals formed via gas-phase electron transfer to multiply protonated polypeptides have been found to react with molecular oxygen. Such cation radicals are of interest within the context of electron transfer dissociation, a phenomenon with high utility for the characterization of peptide and protein primary structures. Most of the cation radicals show the attachment of O(2) under room temperature storage conditions in an electrodynamic ion trap. At higher temperatures and under conditions of collisional activation, the oxygen adduct species lose O(2), HO(*), or HO(2)(*), depending upon the identity of the side chain at the radical site. The fragments containing the C-terminus, the so-called z-ions, which are predominantly radical species, engage in reactions with molecular oxygen. This allows for the facile distinction between z-ions and their complementary even-electron c-ion counterparts. Such a capability has utility in protein identification and characterization via mass spectrometry. Intact electron transfer products also show oxygen attachment. Subsequent activation of such adducts show dissociation behavior very similar to that noted for z-ion adducts. These observations indicate that ion/radical reactions can be used to probe the locations of radical sites in the undissociated electron transfer products as well as distinguish between c- and z-type ions.

Currently, proton-transfer reaction mass spectrometry (PTR-MS) allows for quantitative determination of volatile organic compounds in real time at concentrations in the low ppt range, but cannot differentiate isomers or isobaric molecules, using the conventional quadrupole mass filter. Here we pursue the application of linear quadrupole ion trap (LIT) mass spectrometry in combination with proton-transfer reaction chemical ionization to provide the advantages of specificity from MS/MS. A commercial PTR-MS platform composed of a quadrupole mass filter with the addition of end cap electrodes enabled the mass filter to operate as a linear ion trap. The rf drive electronics were adapted to enable the application of dipolar excitation to opposing rods, for collision-induced dissociation (CID) of trapped ions. This adaptation enabled ion isolation, ion activation, and mass analysis. The utility of the PTR-LIT was demonstrated by distinguishing between the isomeric isoprene oxidation pair, methyl vinyl ketone (MVK) and methacrolein (MACR). The CID voltage was adjusted to maximize the m/ z 41 to 43 fragment ratio of MACR while still maintaining adequate sensitivity. Linear calibration curves for MVK and MACR fragments at m/ z 41 and 43 were obtained with limits of detection of approximately 100 ppt, which should enable ambient measurements. Finally, the PTR-LIT method was compared to an established GC/MS method by quantifying MVK and MACR production during a smog chamber isoprene-NO x irradiation experiment.

Computer simulations of electrospray ionization (ESI) and collision-induced dissociation (CID) experiments were employed to examine the informing power associated with "top-down" proteomics implemented with some commonly used mass analyzers, i.e. the quadrupole ion trap (QIT), the Fourier transform-ion cyclotron resonance mass spectrometer (FT-ICRMS) and the time-of-flight (TOF) mass spectrometer. Using a ratio of the separated (or resolved) peaks to the total number of predicted peaks as a measure of informing power, the ESI/MS simulation of a mixture of proteins showed that the FT-ICRMS exhibited the highest informing power among the three instruments being studied, with the QIT giving the lowest informing power, which was expected from the analysis of the "component capacity" of the three approaches. Also as expected on the basis of resolving elements per component, a dramatic increase in the informing power of the approach was obtained when ion/ ion proton-transfer reactions were used to reduce the number of peaks and to minimize overlap between ions of different mass and charge but similar mass-to-charge ratio. With the assumptions made in this study, the informing power of the TOF+ion/ion approach rivaled or even exceeded that of the FT-ICRMS approach, despite significantly lower mass resolution. This result stemmed both from a reduction in the number of peaks and their dispersion over a much wider range of mass-tocharge ratios. Similar results were obtained from the CID simulation, where the informing power of different approaches was evaluated on the basis of the ratio of the number of ions for which a mass could be determined unambiguously to the total number of ions in the spectra.