Biomolecular ions

Mass spectrometry is widely used for the qualitative analysis of unknowns samples, and in particular, for the identification and characterization of biological macromolecules. Recent decades have seen the introduction and optimization of the so-called soft ionization methods that provide intact, vapor-phase biomolecular ions for separation and detection. This chapter considers MS fundamentals, ionization methods, and applications to biological macromolecules. Conventional mass spectrometers used for low volatile molecular weight samples that are introduced in the vapor phase are called single-focusing mass spectrometers, and use an electron-impact ion source.1 Figure 15.1 shows a diagram of this type of instrument. 

For reviews of ionization of neutral fragments as a structural probe see (a) MJ Polce, S Beranova, MJ Nold, C Wesdemiotis. Characterization of neutral fragments in tandem mass spectrometry a unique route to mechanistic and structural information. J Mass Spectrom 31 1073—1085,1996 (b) MM Cordero, C Wesdemiotis, Reionization and characterization of neutral losses from biomolecular ions. In Biological Mass Spectrometry Present and Future. New York Wiley, 1994, pp 119—126. 

Fig. 3.14. Electrospray ionization mass spectrum of bovine albumin protein (A4= 66,300), illustrating the ability of electrospray ionization to produce multiply charged, large biomolecular ions. Reprinted from Smith et al. (1990) with permission from the American Chemical Society.

G. Von Helden, T. Wyttenbach, and M. T. Bowers, Inclusion of a MALDI ion source in the ion chromatography technique Conformational information on polymer and biomolecular ions, Int. J. Mass Spectrom. Ion Process., 146/147 (1995) 349-364. 

Waters Corporation Synapt. The samples are solutions of biological material, and the ion sources are uniformly EIS, nanospray ionization, or matrix-assisted laser desorption and ionization as described in Chapters 4,9,15, and 18. Studies with the Synapt traveling wave instrument have revealed details of biomolecular ions in the gas phase that are not available by MS alone or by other methods. The full meaning of such studies and relevance for in vivo biomolecular activity is currently under discussion and debate " nonetheless, IM-MS for explorations of biomolecules certainly has affected the visibility of mobility as a measurement method and the level of technology that has been advanced through pharmaceutical and medical concerns. 

Our research group has developed a wide range of new experimental methods that are designed to be performed on ions stored within radio-frequency (RF) ion traps. In this chapter, we wiU phasize the integration of trap technology within different experimental arrangements in order to perform unique scientific measuranents. We will describe measurements of both trapped-ion electron diffraction (TIED) of metal cluster ions and radiative lifetimes of trapped biomolecular ions. Experiments will be discussed in sufficient detail to permit the advantages afforded by ion trap capabilities to be appreciated. This chapter is not intended as an extensive review of trap-related experimental measurements that are referred to and discussed elsewhere in the volumes of this series. 

FIGURE 7.17 Fluorescence lifetime temperature measurements for gas-phase biomolecular ions of (a) Trp-cage protein charge states (b) Dye-(Pro) -Arg-Trp peptide sequences, [M -H H] (c) Vancomycin-peptide non-covalent complexes, [M H- H] +. Best-fits for the quenching rate model are shown by lines through each set of data points. 

Freitas, M.A. Hendrickson, C.L. Marshall, A.G. Gas phase activation energy for unimo-lecular dissociation of biomolecular ions determined by Focused R Adiation for Gaseous Multiphoton ENergy Transfer (FRAGMENT). Rapid Commun. Mass Spectrom. 1999, 13, 1639-1642. 

The technical principle of MALDl imaging is summarized in Figure 4.1. A pulsed laser beam is focused to the size of the aspired lateral resolution. To date, mainly lasers with ultraviolet wavelengths (337, 355, and 266 nm) and pulse lengths of a few nanoseconds have been used. The focused laser beam is directed to the surface of the sample, which is then moved in steps in order to scan the sample according to the intended lateral resolution of the system. Before analysis, the sample must be prepared in such a way that the biomolecular ions can be desorbed and ionized by the laser beam, as in regular MALDl analyses. To achieve this, the sample (e.g., a biological tissue sample) must be covered with a suitable matrix, such as 2,5-dihydroxybenzoic acid (DHB), sinapinic acid (SA) or... 

Fig. 6.7. The Lausanne photofragment-spectrometer for measuring spectra of cold biomolecular ions as well as their clusters with solvent molecules. In the center of the tandem quadrupole mass spectrometer is a 22-pole ion trap which can be cooled to temperatures below 10 K. The ions of interest are produced by an electrospray source, mass-selected in a quadrupole, and then injected into the trap where they are cooled via collisions with cold helium. After irradiating the ions with IR and/or UV laser pulses, the contents of the trap are ejected and sent through an analyzing quadrupole before being detected. Spectra are generated by monitoring the appearance of a particular fragment ion mass as a function of the laser wave length.

The use of IR action spectroscopy in the stmctural characterization of gas-phase (bio-)molecular ions has become well established within the fields of ion chemistry and mass spectrometry. It has been the subject of various recent reviews [ 142,164, 172, 180-184] and has been applied to extract stmctural information from ions ranging in size from simple amino acids to entire proteins [185-187]. Applications to diverse classes of biomolecular ions are described in various chapters of this book. 

Cryogtmic Methods for the Spectroscopy of Large, Biomolecular Ions... 

To measure the spectra of cold, biomolecular ions, one must first produce them in the gas phase and cool them to low temperatures to eliminate thermal inhomogeneous broadening. Because of their net charge, one can use electric or magnetic fields to trap the ions in space before spectroscopic interrogation. To obtain a spectrum one has to detect the absorption of light, and because the density of ions is low, it is extremely difficult to do so directly. One typically uses some type of action spectroscopy in which the consequences of light absorption are detected... 

In the same year, our group in Lausanne published first results from a similar instrument which was equipped with an electrospray ion source for producing closed-shell biomolecular ions, the first demonstrations of which were the measurement of the UV spectra of cold, protmiated aromatic amino acids, tryptophan [46], tyrosine [46, 122], and phenylalanine [122]. Spectroscopic detection is achieved by measuring the small percentage of parent ions that fragment subsequent to UV absorption. The internal temperature of the ions was estimated to be 11-16 K from an analysis of the intensity of hot band transitions of low frequency vibrational modes. If the temperatures achieved in buffer-gas cooled ion traps are low enough and the spectra sufficiently simple, one can often resolve UV absorption spectra for different stable cOTiformers of the molecule [122]. In this case, one can use the IR-UV double resonance techniques so profitably employed in supersonic molecular beam studies [91,123-128] to measure conformer-specific infrared spectra, and this was applied by Steams et al. to both individual amino acids [129] as well as peptides with up to 12 amino acid residues [130]. Subsequent improvements to the Lausanne machine (Fig. 7) included the addition of an ion funnel to... 

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