Tandem-trapped ion mobility spectrometry/mass spectrometry coupled with ultraviolet photodissociation.

RATIONALE: Tandem-ion mobility spectrometry/mass spectrometry methods have recently gained traction for the structural characterization of proteins and protein complexes. However, ion activation techniques currently coupled with tandem-ion mobility spectrometry/mass spectrometry methods are limited in their ability to characterize structures of proteins and protein complexes. METHODS: Here, we describe the coupling of the separation capabilities of tandem-trapped ion mobility spectrometry/mass spectrometry (tTIMS/MS) with the dissociation capabilities of ultraviolet photodissociation (UVPD) for protein structure analysis. RESULTS: We establish the feasibility of dissociating intact proteins by UV irradiation at 213 nm between the two TIMS devices in tTIMS/MS and at pressure conditions compatible with ion mobility spectrometry (2-3 mbar). We validate that the fragments produced by UVPD under these conditions result from a radical-based mechanism in accordance with prior literature on UVPD. The data suggest stabilization of fragment ions produced from UVPD by collisional cooling due to the elevated pressures used here ("UVnoD2"), which otherwise do not survive to detection. The data account for a sequence coverage for the protein ubiquitin comparable to recent reports, demonstrating the analytical utility of our instrument in mobility-separating fragment ions produced from UVPD. CONCLUSIONS: The data demonstrate that UVPD carried out at elevated pressures of 2-3 mbar yields extensive fragment ions rich in information about the protein and that their exhaustive analysis requires IMS separation post-UVPD. Therefore, because UVPD and tTIMS/MS each have been shown to be valuable techniques on their own merit in proteomics, our contribution here underscores the potential of combining tTIMS/MS with UVPD for structural proteomics.

Gas-phase metal ion chelation investigated with IRMPD spectroscopy: A brief review of Robert Dunbar's contributions.

With the passing of Prof. Robert C. Dunbar on 31 October 2017, the field of ion chemistry lost one of its modern heroes. Throughout his career in mass spectrometry, two of his main research interests involved the interaction of trapped ions with electromagnetic radiation and the chelation motifs of metal ions with organic ligands. The focus of his early career was on the fundamental processes that take place in molecules upon ultraviolet and infrared excitation. From 2003 to 2017, his scientific interests shifted to more structural questions, notably to resolving the structures and binding motifs of metal ion chelation complexes by application of infrared photodissociation spectroscopy. These experiments were carried out during numerous visits to the (Free Electron Laser for Infrared eXperiments) (FELIX) facility in the Netherlands and were complemented by extensive theoretical investigations by Rob. As a tribute to our friend, we present in this contribution a brief review of this work.

Influence of Experimental Conditions on the Ratio of 25-Hydroxyvitamin D3 Conformers for Validating a Liquid Chromatography/Ion Mobility-Mass Spectrometry Method for Routine Quantitation.

The utility of adding ion mobility (IM) to liquid chromatography/mass spectrometry (LC/MS) for quantitation of 25-hydroxyvitamin D3 (25OHD3) is evaluated. Sodiated 25OHD3 ions adopt both closed and open conformations, whereas the stereoisomer 3-epi-25-hydroxyvitamin D (epi25OHD), when sodiated, adopts only a closed gas-phase conformation. The unique open conformation for sodiated 25OHD3 permits unambiguous quantitation. Nonetheless, the ratio of open versus closed gas-phase conformations for sodiated 25OHD3 can vary with instrumental conditions; conversion from the open to the closed conformer is attributed to radio frequency (rf) heating within the ion accumulation trap. Ion heating becomes significant when space charge in the trap forces ions to larger radii where the rf field is higher. To avoid biasing quantitation, an isotopically labeled internal standard must be used to account for changes in conformer ratio. Thirty-three serum extract samples were evaluated by LC/IM-MS and were found to not be biased by changes in ion conformer ratios, permitting reliable quantitation of 25OHD3 without interference from the epimer.

Infrared ion spectroscopy: an analytical tool for the study of metabolites.

Vibrational ion spectroscopy techniques coupled with mass spectrometry are applied to standard metabolites as a proof-of-principle demonstration for the structural identification of unknown metabolites. The traditional room temperature infrared multiple photon dissociation (IRMPD) spectroscopy technique is shown to differentiate chemical moieties in isobaric and isomeric variants. These results are compared to infrared spectra of cryogenically cooled analyte ions, showing enhanced spectral resolution, and thus also improved differentiation between closely related molecules, such as isomers. The cryogenic spectroscopy is effected in a recently developed mass-selective cryogenic linear ion trap, which is capable of high sensitivity and the ability to measure the IR spectra of multiple analytes simultaneously.

Probing the Structures of Solvent-Complexed Ions Formed in Electrospray Ionization Using Cryogenic Infrared Photodissociation Spectroscopy.

The gas-phase infrared photodissociation (IRPD) spectra of solvent-tagged small biomolecules are studied in a cryogenic ion trap at 17 K. In this study para-aminobenzoic acid (PABA) and tyramine molecules are noncovalently tagged with water or acetonitrile in the electrospray ionization (ESI) source. The complexes are then cooled in the cryogenic trap prior to spectroscopic measurements. These molecules provide two putative sites for solvent attachment: the protonated amine (NH3+) and the OH groups. Comparisons of the experimental IR spectra to theoretical spectra obtained with density functional theory show that the NH3+ site is mainly favored. Evidence for the formation of both NH3-bound and OH-bound conformers is found only in tyramine, despite having similar solution- and gas-phase energetics to that of PABA. Since the structures cannot interconvert in the gas phase, this suggests an isomerization during the electrospray process.

Effects of ESI conditions on kinetic trapping of the solution-phase protonation isomer of p-aminobenzoic acid in the gas phase.

The effects of electrospray ionization (ESI) solvent and source temperature on the relative abundance of the preferred solution-phase (N-protonated; i.e. amine) versus preferred gas-phase (O-protonated; i.e., acid) isomers of p-aminobenzoic acid (PABA) were investigated. When PABA was electrosprayed from protic solvents (i.e., methanol/water), the infrared multiple photon dissociation (IRMPD) spectrum recorded was consistent with that for O-protonation, according to both calculations and previous studies. When aprotic solvent (i.e., acetonitrile) was used, a different spectrum was recorded and was assigned to the N-protonated isomer. As the amine is the preferred protonation site in solution, this suggests that an isomerization takes place under certain conditions. Photodissociation at the diagnostic band for the O-protonated isomer (NH2 stretching mode) was used to quantify the relative contributions of each isomer to ion signal as a function of ESI conditions. For mixtures of methanol and acetonitrile, the relative contribution of the O-protonated gas-phase structure increased as a function of methanol content. Yet, substituting methanol for water resulted in a marked decrease of isomerization to the O-protonated structure. The source temperature (i.e., temperature of a heated desolvation capillary) was found to play a key role in determining the extent of isomerization, with higher temperatures yielding increased presence of gas-phase structures. These results are consistent with a protic bridge mechanism, in which the ESI droplet temperatures, dependent on endothermic desolvation and radiative heating from the capillary, may determine the isomerization yield.

Supercharging Proteins: How Many Charges Can a Protein Carry?

Very highly charged proteins, so-called "supercharged" ions, can lose (excess) protons to background gases like N2 . It is remarkable that such extremely acidic species can be generated in electrospray ionization, in the presence of not just N2 but also much higher-basicity solvents. What mechanism(s) can explain such high charging, and what is the ultimate limit?

H2SO4 and SO3 transfer reactions in a sulfopeptide-basic peptide complex.

We report on the intermolecular transfer of sulfuric acid (H2SO4) and sulfur trioxide (SO3) from an acidic sulfopeptide (sSE) to a basic peptide (R3); this is achieved by subjecting a noncovalent complex of sSE + R3 to collisional activation in a quadrupole ion trap. The product ions resulting from the sulfo-group transfers were characterized by MS(3) experiments. Peak assignments were additionally supported by isotope-labeling and energy-resolved collision induced dissiciation (CID) experiments. The observed reactions and their potential implications for proteomics and post-translational modification discovery experiments are discussed.

Peptide fragmentation products in mass spectrometry probed by infrared spectroscopy.

Vibrational spectroscopy offers detailed insights, by virtue of diagnostic infrared bands, into the chemical structures and moieties which are formed during peptide fragmentation inside mass spectrometers. Over the past few years, IRMPD spectroscopy has led to a greatly improved understanding of the chemistry that takes place during collision-induced dissociation (CID) of protonated peptides. For instance, the rearrangement chemistry of b- and a-type ions, which is relevant in sequence scrambling pathways, has been directly confirmed with the technique. In this chapter, we provide a brief background on peptide fragmentation chemistry, and give an overview of areas where vibrational spectroscopy has been successfully implemented, such as CID of protonated and de-protonated peptides. We also discuss the potential of the technique for elucidating lesser-studied radical dissociation processes, such as electron capture dissociation (ECD), electron transfer dissociation (ETD), and laser photodissociation.

Differentiating sulfopeptide and phosphopeptide ions via resonant infrared photodissociation.

The post-translational modifications sulfation and phosphorylation pose special challenges to mass spectral analysis due to their isobaric nature and their lability in the gas phase, as both types of peptides dissociate through similar channels upon collisional activation. Here, we present resonant infrared photodissociation based on diagnostic sulfate and phosphate OH stretches, as a means to differentiate sulfated from phosphorylated peptides within the framework of a mass spectrometry platform. The approach is demonstrated for a number of tyrosine-containing peptides, ranging from dipeptides (YG, pYG, and sYG) over tripeptides (GYR, GpYR, and GsYR), to more biologically relevant enkephalin peptides (YGGFL, pYGGFL, and sYGGFL). In all cases, the diagnostic ranges for sulfate OH stretches are established as 3580-3600 cm(-1) and can thus be distinguished from other characteristic hydrogen stretches, such as carboxylic acid OH, alcohol OH, and phosphate OH stretches.

Reaction of the C3(X(1)Σg (+)) carbon cluster with H2S(X(1)A1), hydrogen sulfide: photon-induced formation of C3S, tricarbon sulfur.

In this paper we report on the neutral-neutral reaction of the C3 carbon cluster with H2S in solid inert argon at 12 K, conditions that mimic, in part, the surfaces of interstellar grains. In the first step of the reaction, a C3•H2S complex is formed via an almost barrierless entrance addition mechanism. This complex, stabilized by an estimated 7.45 kJ/mol (CCSD(T)/aug-cc-pVTZ//B3LYP/6-311++G(d,p) level), is formed by the interaction of a terminal carbon of C3 with a hydrogen in H2S. This con-covalent complex displays a band at 2044.1 cm(-1) observed via Fourier transform infrared absorption spectroscopy. With the help of the MP2/aug-ccpVDZ level method, this band is assigned to the CC asymmetric vibration mode. When the complex is exposed to UV-visible photons (hν < 5.5 eV) the tricarbon sulfur C3S molecule is identified, based on the appearance of a characteristic CC stretching band at 2047.5 cm(-1). Calculated ground-state potential energy surfaces also confirm the concomitant formation of molecular H2. This facile reaction pathway involves an attainable transition state of 174.4 kJ/mol. Conversely, competing lower-energy reaction pathways that would lead to the generation of H2C3S (propadienethione), or C2H2 (acetylene) and CS, involve much more complex, multi-stage pathways, and are not observed experimentally.

Metal cation binding to gas-phase pentaalanine: divalent ions restructure the complex.

Ion-neutral complexes of pentaalalanine with several singly- and doubly charged metal ions are examined using conformation analysis by infrared multiple photon dissociation (IRMPD) spectroscopy and density functional theory (DFT) computations. The infrared spectroscopy in the 1500-1800 cm(-1) region is found to be conformationally informative; in particular, the frequency of the C═O stretching mode of the terminal carboxyl group is diagnostic for hydrogen bonding of the terminal hydroxyl. The doubly charged alkaline earth metal ions (Ca(2+) and Ba(2+)) enforce a highly structured chelation shell around the metal ion, with six strongly bound Lewis-basic chelation sites, and no hydroxyl hydrogen bonding. With the more weakly binding alkali metal ions (Na(+), K(+), and Cs(+)), structures with intramolecular hydrogen bonds are more favorable, leading to dominance of conformations with lower degrees of metal ion chelation. The favored coordination mode correlates with ionic charge and binding strength but is not related to the ionic radius of the metal ion.

Crown complexation of protonated amino acids: influence on IRMPD spectra.

We report infrared multiple photon dissociation (IRMPD) spectra for a series of crown-adducted, protonated amino acids, generated by electrospray ionization. The tight chelation of 18-crown-6 on the protonated NH(3)(+) moiety results in a considerable red shift of the NH(3)(+) stretch modes, notably the antisymmetric NH(3)(+) stretch. This is rationalized by a distortion of the NH(3)(+) normal mode potential energy surface, as verified by quantum chemical calculations. On the other hand, the local oscillator modes, such as the carboxylic acid OH stretch, indole NH stretch, and phenol OH stretches, remain well-resolved and are subject to minor and predictable blue shifts of 5-15 cm(-1). Other chemically diagnostic modes, such as the guanidine NH stretch and alcohol OH stretches, also have discernible band positions. Crucially, some of these diagnostic band positions have little to no overlap with one another and can hence be readily distinguished. In addition, the complexes are often found to efficiently photodissociate by neutral loss of 18-crown-6, particularly for higher-basicity amino acids. This in principle opens the door on multiplexing the IRMPD experiment, where the IR spectra of multiple precursors are recorded simultaneously.

Screening for phosphorylated and nonphosphorylated peptides by infrared photodissociation spectroscopy.

We present an infrared laser-based mass spectrometric strategy to differentiate peptides that are phosphorylated (i.e., containing pS, pT, or pY) from those that are nonphosphorylated (i.e., containing S, T, or Y), and those peptides that have none of these moieties (i.e., containing neither pS, pT, pY nor S, T, Y). This is demonstrated for a series of tripeptides and for two larger octapeptides, showing that the diagnostic phosphate OH stretch (indicative for pS, pT, or pY) can be distinguished from the alcohol OH stretch (indicative for S, T, or Y). In addition, the infrared multiple photon dissociation (IRMPD) spectra of multiple peptide analytes are recorded simultaneously in a multiplexed fashion. This is achieved by complexing each peptide precursor with a noncovalently bound 18-crown-6 ether, which is detached upon resonant infrared photon absorption.

Defying entropy: forming large head-to-tail macrocycles in the gas phase.

Spectral fingerprints: Collision-induced dissociation (CID) of protonated peptides in the gas phase results in linear fragment ions with a five-membered oxazolone ring on their C-terminal side. Infrared spectroscopy confirms that smaller fragments adopt oxazolone structures. Conversely, in mid-sized and larger fragments an isomerization to "head-to-tail" macrocycles is observed (see picture).

Mechanistic insights into intramolecular phosphate group transfer during collision induced dissociation of phosphopeptides.

We report on the rearrangement chemistry of model phosphorylated peptides during collision-induced dissociation (CID), where intramolecular phosphate group transfers are observed from donor to acceptor residues. Such "scrambling" could result in inaccurate modification localization, potentially leading to misidentifications. Systematic studies presented herein provide mechanistic insights for the unusually high phosphate group rearrangements presented some time ago by Reid and coworkers (Proteomics 2013, 13 [6], 964-973). It is postulated here that a basic residue like histidine can play a key role in mediating the phosphate group transfer by deprotonating the serine acceptor site. The proposed mechanism is consistent with the observation that fast collisional activation by collision-cell CID and higher-energy collisional dissociation (HCD) can shut down rearrangement chemistry. Additionally, the rearrangement chemistry is highly dependent on the charge state of the peptide, mirroring previous studies that less rearrangement is observed under mobile proton conditions.

Radical Rearrangement Chemistry in Ultraviolet Photodissociation of Iodotyrosine Systems: Insights from Metastable Dissociation, Infrared Ion Spectroscopy, and Reaction Pathway Calculations.

We report on the ultraviolet photodissociation (UVPD) chemistry of protonated tyrosine, iodotyrosine, and diiodotyrosine. Distonic loss of the iodine creates a high-energy radical at the aromatic ring that engages in hydrogen/proton rearrangement chemistry. Based on UVPD kinetics measurements, the appearance of this radical is coincident with the UV irradiation pulse (8 ns). Conversely, sequential UVPD product ions exhibit metastable decay on ca. 100 ns timescales. Infrared ion spectroscopy is capable of confirming putative structures of the rearrangement products as proton transfers from the imine and ß-carbon hydrogens. Potential energy surfaces for the various reaction pathways indicate that the rearrangement chemistry is highly complex, compatible with a cascade of rearrangements, and that there is no preferred rearrangement pathway even in small molecular systems like these. Graphical Abstract.

Operation and Performance of a Mass-Selective Cryogenic Linear Ion Trap.

We report on the performance of a cryogenic 2D linear ion trap (cryoLIT) that is shown to be mass-selective in the temperature range of 17-295 K. As the cryoLIT is cooled, the ejection voltages during the mass instability scan decrease, which results in an effective mass shift to lower m/z relative to room temperature. This is attributed to a decrease in trap radius caused by thermal contraction. Additionally, the cryoLIT generates reproducible mass spectra from day-to-day, and is capable of performing stored waveform inverse Fourier transform (SWIFT) mass isolation of fragile N2-tagged ions for the purpose of background-free infrared dissociation spectroscopy. Graphical Abstract ᅟ.

Amine vs. carboxylic acid protonation in ortho-, meta-, and para-aminobenzoic acid: An IRMPD spectroscopy study.

Infrared multiple photon dissociation (IRMPD) spectroscopy and computational chemistry are applied to the ortho-, meta-, and para- positional isomers of aminobenzoic acid to investigate whether the amine or the carboxylic acid are the favored sites of proton attachment in the gas phase. The NH and OH stretching modes yield distinct patterns that establish the carboxylic acid as the site of protonation in para-aminobenzoic acid, as opposed to the amine group in ortho- and meta-aminobenzoic acid, in agreement with computed thermochemistries. The trends for para- and meta-substitutions can be rationalized simplistically by inductive effects and resonant stabilization, and will be discussed in light of computed charge distributions based from electrostatic potentials. In ortho-aminobenzoic acid, the close proximity of the amine and acid groups allow a simultaneous interaction of the proton with both groups, thus stabilizing and delocalizing the charge more effectively, and compensating for some of the resonance stabilization effects.