Pulsed fluorescence measurements of trapped molecular ions with zero background detection

Probing the Stability of a β-Hairpin Scaffold after Desolvation

Probing the structural characteristics of biomolecular ions in the gas phase following native mass spectrometry (nMS) is of great interest, because noncovalent interactions, and thus native fold features, are believed to be largely retained upon desolvation. However, the conformation usually depends heavily on the charge state of the species investigated. In this study, we combine transition metal ion Förster resonance energy transfer (tmFRET) and ion mobility-mass spectrometry (IM-MS) with molecular dynamics (MD) simulations to interrogate the β-hairpin structure of GB1p in vacuo. Fluorescence lifetime values and collisional cross sections suggest an unfolding of the β-hairpin motif for higher charge states. MD simulations are consistent with experimental constraints, yet intriguingly provide an alternative structural interpretation: preservation of the β-hairpin is not only predicted for 2+ but also for 4+ charged species, which is unexpected given the substantial Coulomb repulsion for small secondary structure scaffolds.

Gas-phase Förster resonance energy transfer in mass-selected and trapped ions

Förster Resonance Energy transfer (FRET) is a nonradiative process that may occur from an electronically excited donor to an acceptor when the emission spectrum of the donor overlaps with the absorption spectrum of the acceptor. FRET experiments have been done in the gas phase based on specially designed mass-spectroscopy setups with the goal to obtain structural information on biomolecular ions labeled with a FRET pair (i.e., donor and acceptor dyes) and to shed light on the energy-transfer process itself. Ions are accumulated in a radio-frequency ion trap or a Penning trap where mass selection of those of interest takes place, followed by photoexcitation. Gas-phase FRET is identified from detection of emitted light either from the donor, the acceptor, or both, or from a fragmentation channel that is specific to the acceptor when electronically excited. The challenge associated with the first approach is the collection and detection of photons emitted from a thin ion cloud that is not easily accessible while the second approach relies both on the photophysical and chemical behavior of the acceptor. In this review, we present the different instrumentation used for gas-phase FRET, including a discussion of advantages and disadvantages, and examples on how the technique has provided important structural information that is not easily obtainable otherwise. Furthermore, we describe how the spectroscopic properties of the dyes are affected by nearby electric fields, which is readily discernable from experiments on simple model systems with alkyl or π-conjugated bridges. Such spectral changes can have a significant effect on the FRET efficiency. Ideas for new directions are presented at the end with special focus on cold-ion spectroscopy.

Empirical Calibration of a Cylindrical Ion Trap for Mass-Selected Gas-Phase Fluorescence Spectroscopy

The ion motion in a quadrupole ion trap of hyperbolic geometry is well described by the Mathieu equations. A simpler cylindrical ion trap has also gained significance and has been used by us for fluorescence-spectroscopy experiments. This design allows for the easy replacement of the end-cap with a mesh, enhancing the photon collection. It is crucial to obtain a firm understanding of the ion motion in cylindrical ion traps and their capability as mass spectrometers. We present here an empirical method of calibrating a cylindrical ion trap based on fluorescence detection. This can be done nearly background-free in a pulsed experiment. The ions are located at the center of the trap, where the field is primarily quadrupolar, and here an effective Mathieu description is found through an effective geometry parameter. In spectroscopy experiments, high buffer-gas pressures are needed to efficiently cool the ions, which complicates the ions' motion and hence their stability. Still, simulations show that the stability diagram closely aligns with the Mathieu diagram, albeit shifted due to collisions. We map the stability diagram for six molecular ions by fluorescence collection from four cations and two anions spanning m/z from 212 to 647. The stability diagram is parametrized through the Mathieu functions with an m/z-dependent effective geometry parameter and a q-dependent shrinkage of the diagram. Based on the calibration, we estimate the mass resolution to be +7/-3 Da for ions with masses in the hundreds of Da.

Cryogenic Fluorescence Spectroscopy of Ionic Fluorones in Gaseous and Condensed Phases: New Light on Their Intrinsic Photophysics

Fluorescence spectroscopy of gas-phase ions generated through electrospray ionization is an emerging technique able to probe intrinsic molecular photophysics directly without perturbations from solvent interactions. While there is ample scope for the ongoing development of gas-phase fluorescence techniques, the recent expansion into low-temperature operating conditions accesses a wealth of data on intrinsic fluorophore photophysics, offering enhanced spectral resolution compared with room-temperature measurements, without matrix effects hindering the excited-state dynamics. This perspective reviews current progress on understanding the photophysics of anionic fluorone dyes, which exhibit an unusually large Stokes shift in the gas phase, and discusses how comparison of gas- and condensed-phase fluorescence spectra can fingerprint structural dynamics. The capacity for temperature-dependent measurements of both fluorescence emission and excitation spectra helps establish the foundation for the use of fluorone dyes as fluorescent tags in macromolecular structure determination. We suggest ideas for technique development.

Laser-Induced Fluorescence (LIF) Spectroscopy of Trapped Molecular Ions in the Gas Phase

This review focuses on the laser-induced fluorescence (LIF) spectroscopy of trapped gas-phase molecular ions, a developing field of research. Following a brief description of the theory and experimental approaches employed in general for fluorescence spectroscopy, the review summarizes the current state-of-the-art intrinsic fluorescence measurement techniques employed for gas-phase ions. Whereas the LIF spectroscopy of condensed matter systems is a well-developed area of research, the instrumentation used for such studies is not directly applicable to gas-phase ions. However, some measurement schemes employed in condensed-phase experiments could be highly beneficial for gas-phase investigations. We have included a brief discussion on some of these techniques as well. Quadrupole ion traps are commonly used for spatial confinement of ions in the ion-trap-based LIF. One of the main challenges involved in such experiments is the poor signal-to-noise ratio (SNR) arising due to weak gas-phase fluorescence emission, high background noise, and small solid angle for the fluorescence collection optics. The experimental approaches based on the integrated high-finesse optical cavities employed for the condensed-phase measurements provide a better (typically an order of magnitude more) SNR in the detected fluorescence than the single-pass detection schemes. Another key to improving the SNR is to exploit the maximum solid angle of light collection by choosing high numerical aperture (NA) collection optics. A combination of these two approaches integrated with ion traps could transmogrify this field, allowing one to study even weak fluorescence emission from gas-phase molecular ions. The review concludes by discussing the scope of the advances in the LIF instrumentation for detailed spectral characterization of fluorophores of weak gas-phase fluorescence emission, considering fluorescein as one example.

Adapting a Fourier Transform Ion Cyclotron Resonance Mass Spectrometer for Gas-Phase Fluorescence Spectroscopy Measurement of Trapped Biomolecular Ions

Gas-phase fluorescence spectroscopy is still in its infancy, which demands further instrumental developments. In this study, a Fourier transform ion cyclotron resonance mass spectrometer (FT-ICR MS), equipped with a lab-developed data acquisition system, was coupled to a tunable femtosecond laser and a state-of-the-art optical system for fluorescence studies of mass-selected ions. For excitation, a laser beam was focused (beam size < 1.0 mm) into the cylindrical ICR cell. A wire mesh replaced the back trapping plate, allowing ∼10% of the fluorescence emitted from trapped ions to be collected by a lens installed beside the wire mesh. The collected fluorescence light was then transmitted outside of the mass spectrometer via fiber optics. A novel accumulation during detection (ADD) scheme was developed to increase the duty cycle of gas-phase fluorescence spectroscopy experiments. With ADD, >90% duty cycle for mass spectrometry and fluorescence experiments could be achieved. This instrument was able to perform fluorescence experiments on various ions, from simple rhodamine dyes to large biomolecules (i.e., peptides and proteins) labeled with dyes of various optical properties. A fluorescence lifetime measurement of trapped rhodamine 6G cations was also performed, yielding a value of 5.97 ± 0.23 ns. This setup has a broad mass range and decent fluorescence spectroscopy performance (i.e., the emission spectrum of rhodamine 6G can be acquired with good S/N in a minute). Finally, this setup also allows more challenging gas-phase fluorescence spectroscopy experiments, for example, of low quantum yield fluorophores and large biomolecules in their native state that appear at high m/z, which may not be doable with quadrupole ion traps (QIT).

Effect of Freezing out Vibrational Modes on Gas-Phase Fluorescence Spectra of Small Ionic Dyes

While action spectroscopy of cold molecular ions is a well-established technique to provide vibrationally resolved absorption features, fluorescence experiments are still challenging. Here we report the fluorescence spectra of pyronin-Y and resorufin ions at 100 K using a newly constructed setup. Spectra narrow upon cooling, and the emission maxima blueshift. Temperature effects are attributed to the population of vibrational excited levels in S₁, and that frequencies are lower in S₁ than in S₀. This picture is supported by calculated spectra based on a Franck-Condon model that not only predicts the observed change in maximum, but also assigns Franck-Condon active vibrations. In-plane vibrational modes that preserve the mirror plane present in both S₀ and S₁ of resorufin and pyronin Y account for most of the observed vibrational bands. Finally, at low temperatures, it is important to pick an excitation wavelength as far to the red as possible to not reheat the ions.

A new setup for low-temperature gas-phase ion fluorescence spectroscopy

Here, we present a new instrument named LUNA2 (LUminescence iNstrument in Aarhus 2), which is purpose-built to measure dispersed fluorescence spectra of gaseous ions produced by electrospray ionization and cooled to low temperatures (<100 K). LUNA2 is, as an earlier room-temperature setup (LUNA), optimized for a high collection efficiency of photons and includes improvements based on our operational experience with LUNA. The fluorescence cell is a cylindrical Paul trap made of copper with a hole in the ring electrode to permit laser light to interact with the trapped ions, and one end-cap electrode is a mesh grid combined with an aspheric condenser lens. The entrance and exit electrodes are both in physical contact with the liquid-nitrogen cooling unit to reduce cooling times. Mass selection is done in a two-step scheme where, first, high-mass ions are ejected followed by low-mass ions according to the Mathieu stability region. This scheme may provide a higher mass resolution than when only one DC voltage is used. Ions are irradiated by visible light delivered from a nanosecond 20-Hz pulsed laser, and dispersed fluorescence is measured with a spectrometer combined with an iCCD camera that allows intensification of the signal for a short time interval. LUNA2 contains an additional Paul trap that can be used for mass selection before ions enter the fluorescence cell, which potentially is relevant to diminishing RF heating in the cold trap. Successful operation of the setup is demonstrated from experiments with rhodamine dyes and oxazine-4, and spectral changes with temperature are identified.

Breaking the Brightness Barrier: Design and Characterization of a Selected-Ion Fluorescence Measurement Setup with High Optical Detection Efficiency

A quadrupole ion trap (QIT) mass spectrometer has been modified and coupled with tunable laser excitation and highly sensitive fluorescence detection systems to perform fluorescence studies on mass-selected ions. Gaseous ions, generated using nanoelectrospray ionization (nano-ESI), are trapped in the QIT that allows optical access for laser irradiation. The emitted fluorescence is collected from a 5.0 mm diameter hole drilled into the ring electrode of the QIT and is directed toward the detection setup. Due to the small inner diameter (7.07 mm) of the ring electrode and a relatively large opening for fluorescence collection, a fluorescence collection efficiency of 2.3% is achieved. After some losses in transmission, around 1.8% of the emitted fluorescence reaches the detectors, more than any other similar instrument reported in the literature. This improved fluorescence collection translates to a much shorter measurement time for a fluorescence signal. Another key feature of this setup is the ability to perform a variety of fluorescence experiments on trapped ions including excitation and emission spectroscopy, lifetime measurement, and ion imaging. The capabilities of the instrument are demonstrated by measuring fluorescence spectra of dyes and biomolecules labeled with dyes in a range of different excitation and emission wavelengths, quantum yields, m/z, and different polarities. A fluorescence lifetime measurement and ion image of trapped rhodamine 6G cations are also shown. With a wide array of functionality and high fluorescence detection performance, this setup provides an opportunity to study biomolecular structures and photophysics of fluorophores in well-controlled environments.

Luminescence spectroscopy of oxazine dye cations isolated in vacuo

Gas-phase luminescence spectroscopy reveals transition energies of oxazine dye cations with no disturbance from counter ions or solvent molecules.

A Linear Ion Trap with an Expanded Inscribed Diameter to Improve Optical Access for Fluorescence Spectroscopy

We report a custom-geometry linear ion trap designed for fluorescence spectroscopy of gas-phase ions at ambient to cryogenic temperatures. Laser-induced fluorescence from trapped ions is collected from between the trapping rods, orthogonal to the excitation laser that runs along the axis of the linear ion trap. To increase optical access to the ion cloud, the diameter of the round trapping rods is 80% of the inscribed diameter, rather than the roughly 110% used to approximate purely quadrupolar electric fields. To encompass as much of the ion cloud as possible, the first collection optic has a 25.4 mm diameter and a numerical aperture of 0.6. The choice of geometry and collection optics yields 10⁷ detected photons/s from trapped rhodamine 6G ions. The trap is coupled to a closed-cycle helium refrigerator, which in combination with two 50 Ohm heaters enables temperature control to below 25 K on the rod electrodes. The purpose of the instrument is to broaden the applicability of fluorescence spectroscopy of gas-phase ions to cases where photon emission is a minority relaxation pathway. Such studies are important to understand how the microenvironment of a chromophore influences excited state charge transfer processes. Graphical Abstract ᅟ.

Laser-induced- and dispersed-fluorescence studies of rhodamine 590 and 640 ions formed by electrospray ionization: observation of fluorescence from highly-excited vibrational levels of S1 states

Fluorescence spectra of vibrationally very “hot” S₁ states were observed for the first time under gas phase conditions.

A cylindrical quadrupole ion trap in combination with an electrospray ion source for gas-phase luminescence and absorption spectroscopy

A relatively simple setup for collection and detection of light emitted from isolated photo-excited molecular ions has been constructed. It benefits from a high collection efficiency of photons, which is accomplished by using a cylindrical ion trap where one end-cap electrode is a mesh grid combined with an aspheric condenser lens. The geometry permits nearly 10% of the emitted light to be collected and, after transmission losses, approximately 5% to be delivered to the entrance of a grating spectrometer equipped with a detector array. The high collection efficiency enables the use of pulsed tunable lasers with low repetition rates (e.g., 20 Hz) instead of continuous wave (cw) lasers or very high repetition rate (e.g., MHz) lasers that are typically used as light sources for gas-phase fluorescence experiments on molecular ions. A hole has been drilled in the cylinder electrode so that a light pulse can interact with the ion cloud in the center of the trap. Simulations indicate that these modifications to the trap do not significantly affect the storage capability and the overall shape of the ion cloud. The overlap between the ion cloud and the laser light is basically 100%, and experimentally >50% of negatively charged chromophore ions are routinely photodepleted. The performance of the setup is illustrated based on fluorescence spectra of several laser dyes, and the quality of these spectra is comparable to those reported by other groups. Finally, by replacing the optical system with a channeltron detector, we demonstrate that the setup can also be used for gas-phase action spectroscopy where either depletion or fragmentation is monitored to provide an indirect measurement on the absorption spectrum of the ion.

Time-Resolved Photodetachment Anisotropy: Gas-Phase Rotational and Vibrational Dynamics of the Fluorescein Anion

The photoelectron signal of the singly deprotonated fluorescein anion is found to be highly dependent on the relative polarization between pump and probe pulses, and time-resolved photodetachment anisotropy (TR-PA) is developed as a probe of the rotational dynamics of the chromophore. The total photoelectron signal shows both rotational and vibrational wavepacket dynamics, and we demonstrate how TR-PA can readily disentangle these dynamical processes. TR-PA in fluorescein presents specific opportunities for its development as a probe for rotational dynamics in large biomolecules as fluorescein derivatives are commonly incorporated in complex biomolecules and have been used extensively in time-resolved fluorescence anisotropy measurements, to which TR-PA is a gas-phase analogue.

Contribution of synchrotron radiation to photoactivation studies of biomolecular ions in the gas phase

Photon activation of ions in the visible and ultraviolet range attracts a growing interest, partly for its promising applications in tandem mass spectrometry. However, this task is not trivial, as it requires notably high brilliance photon sources. Hence, most of the work in that field has been performed using lasers. Synchrotron radiation is a source continuously tunable over a wide photon energy range and which possesses the necessary characteristics for ion activation. This review focuses on the array of applications of synchrotron radiation in photon activation of ions ranging from near UV to soft X-rays.

Substitutional photoluminescence modulation in adducts of a europium chelate with a range of alkali metal cations: a gas-phase study

We present gas-phase dispersed photoluminescence spectra of europium(III) 9-hydroxyphenalen-1-one (HPLN) complexes forming adducts with alkali metal ions ([Eu(PLN)3M](+) with M = Li, Na, K, Rb, and Cs) confined in a quadrupole ion trap for study. The mass selected alkali metal cation adducts display a split hypersensitive (5)D0 → (7)F2 Eu(3+) emission band. One of the two emission components shows a linear dependence on the radius of the alkali metal cation whereas the other component displays a quadratic dependence thereon. In addition, the relative intensities of both components invert in the same order. The experimental results are interpreted with the support of density functional calculations and Judd-Ofelt theory, yielding also structural information on the isolated [Eu(PLN)3M](+) chromophores.

Ions in size-selected aqueous nanodrops: sequential water molecule binding energies and effects of water on ion fluorescence

The effects of water on ion fluorescence were investigated, and average sequential water molecule binding energies to hydrated ions, M(z)(H(2)O)(n), at large cluster size were measured using ion nanocalorimetry. Upon 248-nm excitation, nanodrops with ~25 or more water molecules that contain either rhodamine 590(+), rhodamine 640(+), or Ce(3+) emit a photon with average energies of approximately 548, 590, and 348 nm, respectively. These values are very close to the emission maxima of the corresponding ions in solution, indicating that the photophysical properties of these ions in the nanodrops approach those of the fully hydrated ions at relatively small cluster size. As occurs in solution, these ions in nanodrops with 8 or more water molecules fluoresce with a quantum yield of ~1. Ce(3+) containing nanodrops that also contain OH(-) fluoresce, whereas those with NO(3)(-) do not. This indirect fluorescence detection method has the advantages of high sensitivity, and both the size of the nanodrops as well as their constituents can be carefully controlled. For ions that do not fluoresce in solution, such as protonated tryptophan, full internal conversion of the absorbed 248-nm photon occurs, and the average sequential water molecule binding energies to the hydrated ions can be accurately obtained at large cluster sizes. The average sequential water molecule binding energies for TrpH(+)(H(2)O)(n) and a doubly protonated tripeptide, [KYK + 2H](2+)(H(2)O)(n), approach asymptotic values of ~9.3 (n ≥ 11) and ~10.0 kcal/mol (n ≥ 25), respectively, consistent with a liquidlike structure of water in these nanodrops.

Characterization of Rhodamine 6G Release in Electrospray Ionization by Means of Spatially Resolved Fluorescence Spectroscopy

In the present work, the density distribution of rhodamine 6G ions (R6G) in the gas phase and the droplets of an electrospray plume was studied by spatial and spectral imaging. The intention is to contribute to the fundamental understanding of the release mechanism of gaseous R6G in the electrospray ionization (ESI) process. Furthermore, the influence of ESI-parameters on the release efficiency of R6G, e.g. solvent flow, R6G and salt concentration were examined via direct fluorescence imaging of R6G. A solvent-shift of the fluorescence maximum, λ max = 555 nm in methanolic solution and λ max = 505 nm in gas phase, allows the discrimination between solvated and gaseous R6G. Two experimental setups were used for our measurements. In the first experiment, the R6G fluorescence and the light scattered from the spray plume were imaged in two spatial dimensions using a tunable wavelength fil ter. The second experiment was designed for obtaining 1-dimensional spatially resolved emission spectra of the spray. Here, the intensity distribution of solvated and gaseous R6G as well as scattered light (λ=355 nm) were measured simultaneously.

The results show the distribution of gaseous R6G in the plane, orthogonal to the ESI capillary, decreasing slightly towards the spray center and showing maxima at the cone margins. The distribution of gaseous R6G confirms the preferred release of gaseous ions from nano-droplets, indicating the ion evaporation model (IEM) to be the dominating release mechanism. Up to now, only a few fluorescence spectra of ionic compounds in the gas phase were published because the measurement of emission spectra of mass-selected ions in an ion trap is experimentally challenging. The fluorescence spectrum of gaseous lucigenin at atmospheric pressure is reported for the first time. This spectrum of lucigenin in the gas phase exhibits a blue shift of about Δλ=10 nm in comparison to the corresponding spectrum in methanol.

Gas-phase fluorescence excitation and emission spectroscopy of three xanthene dyes (rhodamine 575, rhodamine 590 and rhodamine 6G) in a quadrupole ion trap mass spectrometer

The gas-phase fluorescence excitation, emission and photodissociation characteristics of three xanthene dyes (rhodamine 575, rhodamine 590, and rhodamine 6G) have been investigated in a quadrupole ion trap mass spectrometer. Measured gas-phase excitation and dispersed emission spectra are compared with solution-phase spectra and computations. The excitation and emission maxima for all three protonated dyes lie at higher energy in the gas phase than in solution. The measured Stokes shifts are significantly smaller for the isolated gaseous ions than the solvated ions. Laser power-dependence measurements indicate that absorption of multiple photons is required for photodissociation. Redshifts and broadening of the dispersed fluorescence spectra at high excitation laser power provide evidence of gradual heating of the ion population, pointing to a mechanism of sequential multiple-photon activation through absorption/emission cycling. The relative brightness in the gas phase follows the order R575(1.00) < R590(1.15) < R6G(1.29). Fluorescence emission from several mass-selected product ions has been measured.

"Weighing" photon energies with mass spectrometry: effects of water on ion fluorescence

We report a new, highly sensitive method for indirectly measuring fluorescence from ions with a discrete number of water molecules attached. Absorption of a 248 nm photon by hydrated protonated proflavine, PH(+)(H(2)O)(n) (n = 13-50), results in two resolved product ion distributions that correspond to full internal conversion of the photon energy (loss of approximately 11 water molecules) and to partial internal conversion of the photon energy and emission of a lower energy photon (loss of approximately 6 water molecules). In addition to fluorescence, a long-lived triplet state with a half-life of approximately 0.5 s (for n = 50) is formed. The energy of the emitted photon can be obtained from the number of water molecules lost from the precursor to form each distribution. The photon energies generally red shift from approximately 450 to 580 nm with increasing cluster size (the onset of the PH(+)(aq) fluorescence spectrum is 600 nm and the maximum is 518 nm) consistent with preferential stabilization of the first excited singlet state versus the ground state. The fluorescence quantum yield of PH(+)(H(2)O)(n) for n > or = 30 is 0.36 +/- 0.02, the same as that in bulk solution, and increases dramatically with decreasing cluster sizes, due to less efficient conversion of electronic-to-vibrational energy. The high sensitivity of this method should make it possible to perform Forster resonance energy transfer experiments with gas-phase biomolecules in a microsolvated environment to investigate how a controlled number of water molecules facilitates dynamical motions in proteins or other molecules of interest.

Exploring fluorescence and fragmentation of ions produced by electrospray ionization in ultrahigh vacuum

Fluorescence spectroscopy and mass spectrometry have been extensively used for characterization of biomaterials, but usually separately. An instrument combining fluorescence spectroscopy and Fourier-transform ion cyclotron resonance mass spectrometry (FTICR-MS) has been developed to explore both fluorescence and mass spectrometric behavior of ions produced by electrospray ionization (ESI) in ultra high vacuum (<5 x 10(-9) mbar). Using rhodamine 6G (R6G) as a sample, the instrument was systematically characterized. Gas-phase fluorescence and mass spectral signal of the same ion population are detected immediately after each other. Effects of gas pressure, ion density, and excitation laser power on the fluorescence signal intensity and mass spectral fragmentation patterns are discussed. Characteristic times of ion photodissociation in ultra high vacuum were recorded for different irradiation powers. Photofragmentation patterns of rhodamine 6G ions in the Penning trap of an FTICR spectrometer obtained by photoinduced dissociation (PID) with visible light and sustained off-resonance irradiation collision-induced dissociation (SORI-CID) were compared. The lowest energy dissociation fragment of rhodamine 6G ions was identified by relating PID patterns of rhodamine 6G and rhodamine 575 dyes at various irradiation powers. The unique instrument provides a powerful platform for probing the intramolecular relaxation mechanisms of nonsolvated ions when interacting with light, which is of great fundamental interest for better understanding of their physical and chemical properties.

Rapid peptide fragmentation without electrons, collisions, infrared radiation, or native chromophores

Ultraviolet photodissociation of peptides followed by mass analysis has several desirable advantages relative to other methods, yet it has not found widespread use due to several limitations. One shortcoming is the inefficiency with which peptides absorb in the ultraviolet. This issue has a simple solution and can be circumvented by the attachment of noncovalent adducts that contain appropriate chromophores. Subsequent photoactivation of the chromophore leads to vibrational excitation of the complex and eventually to fragmentation of the peptide. Herein, the energetics that control the efficiency of this process are examined as a function of the characteristics of both the peptide and the noncovalently attached chromophore. Fragmentation efficiency decreases with increasing peptide size and is also constrained by the binding energy of the noncovalent adduct. The optimum chromophore should have excellent absorption at the excitation wavelength and a low luminescence quantum yield. It is demonstrated that a naphthyl based 18-crown-6 adduct is ideally suited for attaching to a variety peptides and fragmenting them following absorption of 266 nm light. Potential applications and limitations of this methodology are discussed.

Fluorescence and photodissociation of rhodamine 575 cations in a quadrupole ion trap

The fluorescence and photodissociation of rhodamine 575 cations confined to a quadrupole ion trap are observed during laser irradiation at 488 nm. The kinetics of photodissociation is measured by time-dependent mass spectra and time-dependent fluorescence. The rhodamine ion signal and fluorescence decay are studied as functions of buffer gas pressure, laser fluence, and irradiation time. The decay rates of the ions in the mass spectra agree with decay rates of the fluorescence. Some of the fragment ions also fluoresce and further dissociate. The photodissociation rate is found to depend on the incident laser fluence and buffer gas pressure. The implications of rapid absorption/fluorescence cycling for photodissociation of dye-labeled biomolecular ions under continuous irradiation are discussed.

Electron photodetachment dissociation of DNA anions with covalently or noncovalently bound chromophores

Double stranded DNA multiply charged anions coupled to chromophores were subjected to UV-Vis photoactivation in a quadrupole ion trap mass spectrometer. The chromophores included noncovalently bound minor groove binders (activated in the near UV), noncovalently bound intercalators (activated with visible light), and covalently linked fluorophores and quenchers (activated at their maximum absorption wavelength). We found that the activation of only chromophores having long fluorescence lifetimes did result in efficient electron photodetachment from the DNA complexes. In the case of ethidium-dsDNA complex excited at 500 nm, photodetachment is a multiphoton process. The MS(3) fragmentation of radicals produced by photodetachment at lambda = 260 nm (DNA excitation) and by photodetachment at lambda > 300 nm (chromophore excitation) were compared. The radicals keep no memory of the way they were produced. A weakly bound noncovalent ligand (m-amsacrine) allowed probing experimentally that a fraction of the electronic internal energy was converted into vibrational internal energy. This fragmentation channel was used to demonstrate that excitation of the quencher DABSYL resulted in internal conversion, unlike the fluorophore 6-FAM. Altogether, photodetachment of the DNA complexes upon chromophore excitation can be interpreted by the following mechanism: (1) ligands with sufficiently long excited-state lifetime undergo resonant two-photon excitation to reach the level of the DNA excited states, then (2) the excited-state must be coupled to the DNA excited states for photodetachment to occur. Our experiments also pave the way towards photodissociation probes of biomolecule conformation in the gas-phase by Förster resonance energy transfer (FRET).

MS/MS simplification by 355 nm ultraviolet photodissociation of chromophore-derivatized peptides in a quadrupole ion trap

Ultraviolet photodissociation (UVPD) of chromophore-modified peptides enhances the capabilities for de novo sequencing in a quadrupole ion trap mass spectrometer. Attachment of UV chromophores allows efficient photoactivation of not only the precursor ions but also any fragments that retain the chromophore functionality. For doubly protonated peptides, UVPD leads to a vast reduction in MS/MS complexity. The array of b and y ions typically seen upon collisionally activated dissociation is reduced to a single series of either y or b ions by UVPD depending on the location of the chromophore (i.e., N- or C-terminus). The sulfonation reagent Alexa Fluor 350 (AF350) provided the best overall results for the singly and doubly charged peptides by UVPD. The nonsulfonated analogue of AF350, 7-amino-4-methylcoumarin-3-acetic acid, also led to simplified spectra for doubly charged, but not singly charged, peptides by UVPD. Dinitrophenyl-peptides also yielded simplified spectra by UVPD albeit with a small amount of internal fragments accompanying the series of diagnostic y ions. The success of this MS/MS simplification process stems from extensive secondary fragmentation of any chromophore-containing fragments upon exposure to subsequent laser pulses. Energy-variable UVPD reveals that the abundances of non-chromophore-containing y fragment ions increase linearly with laser pulse energy, suggesting secondary dissociation of these species is insignificant. The abundances of chromophore-containing a/b fragment ions follow a quadratic trend due to the extensive secondary fragmentation at higher laser energies or multiple pulses.

Fluorescence probe of Trp-cage protein conformation in solution and in gas phase

Measurements of protein unfolding in the absence of solvent, when combined with unfolding studies in solution, offer a unique opportunity to measure the effects of solvent on protein structure and dynamics. The experiments presented here rely on the fluorescence of an attached dye to probe the local conformational dynamics through interactions with a Trp residue and fields originating on charge sites. We present fluorescence measurements of thermal fluctuations accompanying conformational change of a miniprotein, Trp-cage, in solution and in gas phase. Molecular dynamics (MD) simulations are performed as a function of temperature, charge state, and charge location to elucidate the dye-protein conformational dynamics leading to the changes in measured fluorescence. The results indicate that the stability of the unsolvated protein is dominated by hydrogen bonds. Substituting asparagine for aspartic acid at position 9 results in a dramatic alteration of the solution unfolding curve, indicating that the salt bridge involving Lys8, Asp9, and Arg16 (+ - +) is essential for Trp-cage stability in solution. In contrast, this substitution results in minor changes in the unfolding curve of the unsolvated protein, showing that hydrogen bonds are the major contributor to the stability of Trp-cage in gas phase. Consistent with this hypothesis, the decrease in the number of hydrogen bonds with increasing temperature indicated by MD simulations agrees reasonably well with the experimentally derived enthalpies of conformational change. The simulation results display relatively compact conformations compared with NMR structures that are generally consistent with experimental results. The measured unfolding curves of unsolvated Trp-cage ions are invariant with the acetonitrile content of the solution from which they are formed, possibly as a result of conformational relaxation during or after desolvation. This work demonstrates the power of combined solution and gas-phase studies and of single-point mutations to identify specific noncovalent interactions which contribute to protein-fold stability. The combination of experiment and simulation is particularly useful because these approaches yield complementary information which can be used to deduce the details of structural changes of proteins in the gas phase.

Shedding Light on Biomolecule Conformational Dynamics Using Fluorescence Measurements of Trapped Ions

Biomolecule conformational change has been widely investigated in solution using several methods; however, much less experimental data about structural changes are available for completely isolated, gas-phase biomolecules. Studies of conformational change in unsolvated biomolecules are required to complement the interpretation of mass spectrometry measurements and in addition, can provide a means to directly test theoretical simulations of biomolecule structure and dynamics independent of a simulated solvent. In this Feature Article, we review our recent introduction of a fluorescence-based method for probing local conformational dynamics in unsolvated biomolecules through interactions of an attached dye with tryptophan (Trp) residues and fields originating on charge sites. Dye-derivatized biomolecule ions are formed by electrospray ionization and are trapped in a variable-temperature quadrupole ion trap in which they are irradiated with either continuous or short pulse lasers to excite fluorescence. Fluorescence is measured as a function of temperature for different charge states. Optical measurements of the dye fluorescence include average intensity changes, changes in the emission spectrum, and time-resolved measurements of the fluorescence decay. These measurements have been applied to the miniprotein, Trp-cage, polyproline peptides and to a beta-hairpin-forming peptide, and the results are presented as examples of the broad applicability and utility of these methods. Model fits to Trp-cage fluorescence data measured as a function of temperature provide quantitative information on the thermodynamics of conformational changes, which are reproduced well by molecular dynamics. Time-resolved measurements of the fluorescence decays of Trp-cage and small polyproline peptides definitively demonstrate the occurrence of fluorescence quenching by the amino acid Trp in unsolvated biomolecules.

Effect of buffer gas on the fluorescence yield of trapped gas-phase ions

We investigated the dependence of three different gases, helium, argon, and nitrogen, on the fluorescence signal intensity of rhodamine 6G cations in the gas phase. The method is based on laser-induced fluorescence of ions trapped in a Fourier transform ion cyclotron mass spectrometer. We found that the use of helium results in the highest fluorescence signal, while no fluorescence was detected when using argon under the same conditions.

Conformational Change in Unsolvated Trp-cage Protein Probed by Fluorescence

We report the first direct measurements of the unfolding of a protein, Trp-cage, in the gas phase using laser-induced fluorescence of protein ions in a heated quadrupole ion trap. The changes in enthalpy and entropy associated with the observed conformational change are obtained by fitting a two-state model of protein unfolding to the fluorescence intensities plotted versus temperature. The enthalpy and entropy changes for the 2+ and 3+ charge states are greater than the values measured in solution and depend on charge state.

Photodissociation spectroscopy of trapped protonated tryptophan

We have coupled a quadrupole ion trap with a frequency doubled optical parametric oscillator laser. The photodissociation spectrum of the protonated tryptophan ion from 215 to 320 nm is reported. The yields of fragmentation on each mass channel as a function of the laser wavelength were obtained. We also report experiments involving multiple stages of laser induced dissociation and discuss possible structures for the fragmentation products.

Fast gas-phase hydrogen/deuterium exchange observed for a DNA G-quadruplex

The gas-phase hydrogen/deuterium (H/D) exchange kinetics of DNA G-quadruplexes has been investigated using Fourier transform ion cyclotron resonance mass spectrometry (FTICRMS). The quadruplex [(TGGGGT)4 . 3NH4+] undergoes very fast H/D exchange, in both the positive and in the negative ion modes, compared to DNA duplexes and other quadruplexes tested, and compared to the corresponding single-stranded TGGGGT. Substitution of NH4+ for K+ did not alter this fast H/D exchange, indicating that the hydrogens of the ammonium ions are not those exchanged. However, stripping of the interior cations of the quadruplex by source collision-induced dissociation (CID) in the positive ion mode showed that the presence of the inner cations is essential for the fast exchange to be possible. Molecular dynamics simulations show that the G-quadruplex is very rigid in the gas phase with NH4+ ions inside the tetrads. We suggest that the fast H/D exchange is favored by this rigid quadruplex conformation. This example illustrates that the concept that compact DNA structures exchange H for D slower than unfolded ones is a misconception.

Laser-induced fluorescence of trapped gas-phase molecular ions generated by internal source matrix-assisted laser desorption/ionization in a Fourier transform ion cyclotron resonance mass spectrometer

The combination of laser-induced fluorescence with mass spectrometry opens up new possibilities both for detection purposes and for structural studies of trapped biomolecular ions in the gas phase. However, this approach is experimentally very challenging, and only a handful of studies have been reported so far. In this contribution, a novel scheme for laser-induced fluorescence measurements of ions trapped inside a Fourier transform ion cyclotron resonance (FT-ICR) mass spectrometer will be introduced. It is based on an open FT-ICR cell design, continuous wave axial excitation of the fluorescence, orthogonal photon collection by fiber optics, and single photon counting detection. Rhodamine 6G ions generated by an internal matrix-assisted laser desorption/ionization source were used to develop and test the set-up. Due to photobleaching processes, the excitation laser power and the observation time window have to be carefully optimized. An ion tomography method was used to align the excitation laser. Potential applications for studying the gas-phase structure of fluorescent biomolecular ions and for investigating fluorescence resonance energy transfer of donor-acceptor pairs will be presented.

Optical detection methods for mass spectrometry of macroions

Detection of macroions has been a challenge in the field of mass spectrometry. Conventional ionization-based detectors, relying on production and multiplication of secondary electrons, are restricted to detection for charged particles of m/z < 1 x 10(6). While both energy-sensitive and charge-sensitive detectors have been developed recently to overcome the limitation, they are not yet in common use. Photon-sensitive detectors are suggested to be an alternative, with which detection of macroions (or charged particles) by either elastic light scattering (ELS) or laser-induced fluorescence (LIF) has been possible. In this article, we provide a critical review on the developments of novel optical detection methods for mass spectrometry of macroions, including both micron-sized and nano-sized synthetic polymers as well as high-mass biomolecules. Design and development of new spectrometers making possible observations of the mass spectra of macroions with sizes in the range of 10-10(3) nm or masses in the range of 1-10(6) MDa are illustrated. The potential and promise of this optical approach toward macroion detection with high efficiency are discussed in practical aspects.