Non-Direct Sequence Ions in the Tandem Mass Spectrometry of Protonated Peptide Amides—an Energy-Resolved Study

The fragmentation reactions of the MH⁺ ions of Leu-enkephalin amide and a variety of heptapeptide amides have been studied in detail as a function of collision energy using a QqToF beam type mass spectrometer. The initial fragmentation of the protonated amides involves primarily formation of b_n ions, including significant loss of NH₃ from the MH⁺ ions. Further fragmentation of these b_n ions occurs following macrocyclization/ring opening leading in many cases to b_n ions with permuted sequences and, thus, to formation of non-direct sequence ions. The importance of these non-direct sequence ions increases markedly with increasing collision energy, making peptide sequence determination difficult, if not impossible, at higher collision energies.

Reagent Cluster Anions for Multiple Gas-Phase Covalent Modifications of Peptide and Protein Cations

Multiple gas phase ion/ion covalent modifications of peptide and protein ions are demonstrated using cluster-type reagent anions of N-hydroxysulfosuccinimide acetate (sulfo-NHS acetate) and 2-formyl-benzenesulfonic acid (FBMSA). These reagents are used to selectively modify unprotonated primary amine functionalities of peptides and proteins. Multiple reactive reagent molecules can be present in a single cluster ion, which allows for multiple covalent modifications to be achieved in a single ion/ion encounter and at the ‘cost’ of only a single analyte charge. Multiple derivatizations are demonstrated when the number of available reactive sites on the analyte cation exceeds the number of reagent molecules in the anionic cluster (e.g., data shown here for reactions between the polypeptide [K₁₀ + 3H]³⁺ and the reagent cluster [5R_5Na – Na]^–). This type of gas-phase ion chemistry is also applicable to whole protein ions. Here, ubiquitin was successfully modified using an FBMSA cluster anion which, upon collisional activation, produced fragment ions with various numbers of modifications. Data for the pentamer cluster are included as illustrative of the results obtained for the clusters comprised of two to six reagent molecules.

Are Clusters Important in Understanding the Mechanisms in Atmospheric Pressure Ionization? Part 1: Reagent Ion Generation and Chemical Control of Ion Populations

It is well documented since the early days of the development of atmospheric pressure ionization methods, which operate in the gas phase, that cluster ions are ubiquitous. This holds true for atmospheric pressure chemical ionization, as well as for more recent techniques, such as atmospheric pressure photoionization, direct analysis in real time, and many more. In fact, it is well established that cluster ions are the primary carriers of the net charge generated. Nevertheless, cluster ion chemistry has only been sporadically included in the numerous proposed ionization mechanisms leading to charged target analytes, which are often protonated molecules. This paper series, consisting of two parts, attempts to highlight the role of cluster ion chemistry with regard to the generation of analyte ions. In addition, the impact of the changing reaction matrix and the non-thermal collisions of ions en route from the atmospheric pressure ion source to the high vacuum analyzer region are discussed. This work addresses such issues as extent of protonation versus deuteration, the extent of analyte fragmentation, as well as highly variable ionization efficiencies, among others. In Part 1, the nature of the reagent ion generation is examined, as well as the extent of thermodynamic versus kinetic control of the resulting ion population entering the analyzer region.

Fragmentation of clusters induced by collision with a solid surface: comparison of antimony and bismuth cluster ions

Mass-selected antimony cluster ions Sb _n ⁺ (n = 3-12) and bismuth cluster ions Bi _{ntn} ⁺ (n = 3-8) are allowed to collide with the surface of highly oriented pyrolytic graphite at energies up to 350 eV. The resulting fragment ions are analysed in a time-of-flight mass spectrometer. Two main fragmentation channels can be identified. At low impact energies both Sb _n ⁺ and Bi _n ⁺ cluster ions lose neutral tetramer and dimer units upon collision. Above about 150 eV impact energy Sb ₃ ⁺ becomes the predominant fragment ion of all investigated antimony clusters. The enhanced stability of these fragment clusters can be explained in the framework of the polyhedral skeletal electron pair theory. In contrast, Bi _n ⁺ cluster scattering leads to the formation of Bi ₃ ⁺ , Bi ₂ ⁺ and Bi+ with nearly equal abundances, if the collision energy exceeds 75 eV. The integral scattering yield is substantially higher in this case as compared to Sb _n ⁺ clusters.     

Carbon dots-based fluorescent probes for sensitive and selective detection of iodide

We report on a simple method for the determination of iodide in aqueous solution by exploiting the fluorescence enhancement that is observed if the complex formed between carbon dots and mercury ion is exposed to iodide. Fluorescent carbon dots (C-dots) were treated with Hg(II) ion which causes quenching of the emission of the C-dots. On addition of iodide, the Hg(II) ions are removed from the complex due to the strong interaction between Hg(II) and iodide. This causes the fluorescence to be restored and enables iodide to be determined in the 0.5 to 20 μM concentration range and with a detection limit of ~430 nM. The test is highly selective for iodide (over common other anions) and was used for the determination of iodide in urine.

Multipurpose Dissociation Cell for Enhanced ETD of Intact Protein Species

We describe and characterize an improved implementation of ETD on a modified hybrid linear ion trap-Orbitrap instrument. Instead of performing ETD in the mass-analyzing quadrupole linear ion trap (A-QLT), the instrument collision cell was modified to enable ETD. We partitioned the collision cell into a multi-section rf ion storage and transfer device to enable injection and simultaneous separate storage of precursor and reagent ions. Application of a secondary (axial) confinement voltage to the cell end lens electrodes enables charge-sign independent trapping for ion–ion reactions. The approximately 2-fold higher quadrupole field frequency of this cell relative to that of the A-QLT enables higher reagent ion densities and correspondingly faster ETD reactions, and, with the collision cell’s longer axial dimensions, larger populations of precursor ions may be reacted. The higher ion capacity of the collision cell permits the accumulation and reaction of multiple full loads of precursor ions from the A-QLT followed by FT Orbitrap m/z analysis of the ETD product ions. This extends the intra-scan dynamic range by increasing the maximum number of product ions in a single MS/MS event. For analyses of large peptide/small protein precursor cations, this reduces or eliminates the need for spectral averaging to achieve acceptable ETD product ion signal-to-noise levels. Using larger ion populations, we demonstrate improvements in protein sequence coverage and aggregate protein identifications in LC-MS/MS analysis of intact protein species as compared to the standard ETD implementation.

Fragmentation Reactions of Methionine-Containing Protonated Octapeptides and Fragment Ions Therefrom: An Energy-Resolved Study

The fragmentation reactions of the MH⁺ ions as well as the b₇, a₇, and a₇* ions derived therefrom have been studied in detail for the octapeptides MAAAAAAA, AAMAAAAA, AAAAMAAA, and AAAAAAMA. Ionization was by electrospray using a QqToF mass spectrometer, which allowed a study of the evolution of the fragmentation channels as a function of the collision energy. Not surprisingly, the product ion mass spectra for the b₇ ions are independent of the original precursor sequence, indicating macrocyclization and reopening to the same mixture of protonated oxazolones prior to fragmentation. The results show that this sequence scrambling results in a distinct preference to place the Met residue in the C-terminal position of the protonated oxazolones. The a₇ and a₇* ions also produce product ion mass spectra independent of the original peptide sequence. The results for the a₇ ions indicate that fragmentation occurs primarily from an amide structure analogous to that observed for a₄ ions (Bythell et al. in J Am Chem Soc 132:14766–14779, 2010). Clearly, the rearrangement reaction they have proposed applies equally well to a_n ions as large as a₇. The major fragmentation modes of the MH⁺ ions at low collision energies produce b₇, b_6, and b₅ ions. As the collision energy is increased further fragmentation of these primary products produces, in part, non-direct sequence ions, which become prominent at lower m/z values, particularly for the peptides with the Met residue near the N-terminus.

Traveling Wave Ion Mobility Mass Spectrometry and Ab Initio Calculations of Phosphoric Acid Clusters

Positive and negative ion electrospray mass spectra obtained from 50 mM phosphoric acid solutions presented a large number of phosphoric acid clusters: [(H₃PO₄)_n?+?zH] ^z+ or [(H₃PO₄)_n – zH] ^z– , with n up to 200 and z up to 4 for positively charged clusters, and n up to 270 and z up to 7 for negatively charged cluster ions. Ion mobility experiments allowed very explicit separation of the different charge states. Because of the increased pressures involved in ion mobility experiments, dissociation to smaller clusters was observed both in the trap and transfer areas. Voltages along the ion path could be optimized so as to minimize this effect, which can be directly associated with the cleavage of hydrogen bonds. Having excluded the ion mobility times that resulted from dissociated ions, each cluster ion appeared at a single drift time. These drift times showed a linear progression with the number of phosphoric atoms for cluster ions of the same charge state. Cross section calculations were carried out with MOBCAL on DFT optimized geometries with different hydrogen locations and with three types of atomic charges. DFT geometry optimizations yielded roughly spherical structures. Our results for nitrogen gas interaction cross sections showed that values were dependent on the atomic charges definition used in the MOBCAL calculation. This pinpointed the necessity to define a clear theoretical framework before any comparative interpretations can be attempted with uncharacterized compounds.

Direct Analysis in Real Time Mass Spectrometry (DART-MS) of Ionic Liquids

Direct analysis in real time mass spectrometry (DART-MS) was used to analyze ionic liquids (ILs) containing either imidazolium or phosphonium cations combined with different types of inorganic and organic anions. Ionic liquids were directly inserted into the ionization source using a glass probe without dissolution into organic solvents. Mass spectra of the ILs were collected in both positive and negative mode with a linear ion-trap instrument. The intact cation of the compound was typically the dominant peak in positive mass spectra and cluster ion formation was present. Some individual anions were not readily observed in the negative mass spectra (based on the type of anion); however, the mass difference of adjacent cluster ions equal the mass of a complete IL and the anion mass could be verified by subtracting the known cation mass. The degree and intensity of the cluster ion formations was found to be dependent on the nature of the specific ILs as well as the DART temperature gas stream.

Negative ion tandem mass spectrometry of prenylated fungal metabolites and their derivatives

Liquid chromatography negative ion electrospray ionisation tandem mass spectrometry has been used for characterisation of naturally occurring prenylated fungal metabolites and synthetic derivatives. The fragmentation studies allow an elucidation of the decomposition pathways for these compounds. It could be shown, that the prenyl side chain is degraded by successive radical losses of C₅ units. Both the benzoquinones and the phenolic derivatives display significant key ions comprising the aromatic ring. In some cases, the formation of significant oxygen-free key ions could be evidenced by high-resolution MS/MS measurements. Furthermore, the different types of basic skeletons, benzoquinones and phenol type as well as cyclic prenylated compounds, can be differentiated by their MS/MS behaviour.

Sputtered metal cluster ions: Unimolecular decomposition and collision induced fragmentation

Cluster ions are produced by ion bombardment of thick metal targets and mass selected in a Wien filter. The unimolecular decomposition of Al _n ⁺ , Cu _n ⁺ , Mo _n ⁺ , W _n ⁺ , and Pb _n ⁺ is investigated under UHV conditions. The time evolution of the decay allows a glimpse into the cluster formation/fragmentation process. Highly excited metal cluster ions decompose mainly by evaporating single neutral atoms with rates reaching 100%. The collision induced fragmentation (CIF) of stable mass selected metal cluster ions in a low pressure Ar and O₂ gas target will be compared to the unimolecular decay.     

Resonance Activation and Collision-Induced-Dissociation of Ions Using Rectangular Wave Dipolar Potentials in a Digital Ion Trap Mass Spectrometer

Collision-induced dissociation (CID) of ions by resonance activation in a quadrupole ion trap is usually accomplished by resonance exciting the ions to higher kinetic energy, whereby the high kinetic energy ions collide with a bath gas, such as helium or argon, inside the trap and dissociate to fragments. A new ion activation method using a well-defined rectangular wave dipolar potential formed by dividing down the trapping rectangular waveform is developed and examined herein. The mass-selected parent ions are resonance excited to high kinetic energies by simply changing the frequency of the rectangular wave dipolar potential and dissociation proceeds. A relationship between the ion mass and the activation waveform frequency is also identified and described. This highly efficient (CID) procedure can be realized by simply changing the waveform frequency of the dipolar potential, which could certainly simplify tandem mass spectrometry analysis methods.

Collision-induced reactions of size-selected molecular cluster anions

Collision-induced reactions of size-selected cluster anions, (CO₂) _n ^? and (N₂O)_nO^? with He and Kr atoms were studied at collision energies from 0.1 to 2.0 eV (center-of mass) by means of a tandem mass-spectrometer equipped with a pair of octapole ion guides. The dominant process was evaporation of the constituent molecules from the parent cluster ion. The absolute cross section for the evaporation was measured as functions of the size of the parent cluster ion and the collision energy. The reaction was explained by collisional excitation of the parent cluster ion followed by its unimolecular dissociation. The observed cross sections which correspond to those for the collisional excitation agree with those calculated in terms of charge-induced dipole and induced dipole-induced dipole interactions between the parent cluster ion and the target atom. The distributions of the product ions resulting from the unimolecular dissociation were reproduced by a simple calculation based on RRK theory. In the collision of (CO₂) _n ^? , the cross sections for (CO₂) ₁₀ ^? and (CO₂) ₁₄ ^? were significantly small and their abundances in the product ion distributions were particularly large. These findings indicate that (CO₂) ₁₀ ^? and (CO₂) ₁₄ ^? are stable species. On the other hand, stable species in (N₂O)_nO^? was found to be (N₂O)₅O^?.     

Kinetic and Thermodynamic Control of Protonation in Atmospheric Pressure Chemical Ionization

For p-(dimethylamino)chalcone (p-DMAC), the N atom is the most basic site in the liquid phase, whereas the O atom possesses the highest proton affinity in the gas phase. A novel and interesting observation is reported that the N- and O-protonated p-DMAC can be competitively produced in atmospheric pressure chemical ionization (APCI) with the change of solvents and ionization conditions. In neat methanol or acetonitrile, the protonation is always under thermodynamic control to form the O-protonated ion. When methanol/water or acetonitrile/water was used as the solvent, the protonation is kinetically controlled to form the N-protonated ion under conditions of relatively high infusion rate and high concentration of water in the mixed solvent. The regioselectivity of protonation of p-DMAC in APCI is probably attributed to the bulky solvent cluster reagent ions (S_nH⁺) and the analyte having different preferred protonation sites in the liquid phase and gas phase.

Implementation of Dipolar Resonant Excitation for Collision Induced Dissociation with Ion Mobility/Time-of-Flight MS

An ion mobility/time-of-flight mass spectrometer (IMS/TOF MS) platform that allows for resonant excitation collision induced dissociation (CID) is presented. Highly efficient, mass-resolved fragmentation without additional excitation of product ions was accomplished and over-fragmentation common in beam-type CID experiments was alleviated. A quadrupole ion guide was modified to apply a dipolar AC signal across a pair of rods for resonant excitation. The method was characterized with singly protonated methionine enkephalin and triply protonated peptide angiotensin I, yielding maximum CID efficiencies of 44 % and 84 %, respectively. The Mathieu q_x,y parameter was set at 0.707 for these experiments to maximize pseudopotential well depths and CID efficiencies. Resonant excitation CID was compared with beam-type CID for the peptide mixture. The ability to apply resonant waveforms in mobility-resolved windows is demonstrated with a peptide mixture yielding fragmentation over a range of mass-to-charge (m/z) ratios within a single IMS-MS analysis.

Inclusion Complexes of Ionic Liquids and Cyclodextrins: Are They Formed in the Gas Phase?

The interaction of imidazolium-based ionic liquids with α- and β-cyclodextrins was investigated by electrospray ionization mass spectrometry with variable collision induced dissociation energy and quantum chemical gas-phase calculations. The center-of-mass energy at which 50 % of a precursor ion decomposes (E_cm,1/2) was determined for the isolated [cyclodextrin + cation]⁺ or [cyclodextrin + anion]^– adduct ions of imidazolium-based ionic liquids with different alkyl chain lengths combined with a large set of anions, such as chloride, bromide, bis(trifluoromethylsulfonyl)imide, tetrafluoroborate, hexafluorophosphate, trifluoromethanesulfonate, methanesulfonate, dicyanamide, and hydrogensulfate. Moreover, both symmetric and asymmetric imidazolium cationic cores were evaluated. The relative interaction energies in the adduct ions were interpreted in terms of the influence of cation/anion structures and their inherent properties, such as hydrophobicity and hydrogen bond accepting ability, in the complexation process with the cyclodextrins. The trends observed in the mass spectral data together with quantum-chemical calculations suggest that in the gas phase, cations and anions will preferentially interact with the lower or upper rim of the cyclodextrin, respectively, as opposed to what has been reported in condensed phase where the formation of an inclusion complex between ionic liquid and cyclodextrin is assumed.

Numerical Modeling of Ion Transport in an ESI-MS System

Gas and ion transport in the capillary-skimmer subatmospheric interface of a mass spectrometer, which is typically utilized to separate unevaporated micro-droplets from ions, was studied numerically using a two-step approach spanning multiple gas dynamic regimes. The gas flow in the heated capillary and in the interface was determined by solving numerically the Navier-Stokes equation. The capillary-to-skimmer gas/ion flow was modeled through the solution of the full Boltzmann equation with a force term. The force term, together with calculated aerodynamic drag, determined the ion motion in the gap between the capillary and skimmer. Three-dimensional modeling of the impact of the voltage applied to the Einzel lens on the transmission of doubly charged peptide ions through the skimmer orifice was compared with experimental data obtained in the companion study. Good agreement between measured and computed signals was observed. The numerical results indicate that as many as 75% of the ions that exit from the capillary are lost on the conical surface of the skimmer or capillary outer surface because of the electrostatic force and plume divergence.

Synthesis and application of head-to-head-type styrene dimers bearing two fluoroalkyl end-groups

Head-to-head-type styrene and substituted styrene dimers bearing two fluoroalkyl end-groups have been efficiently synthesized by a simple reaction of perfluoroalkyl iodide with styrene under radical conditions as a mixture of meso and racemic forms. The meso form obtained from the mixture by recrystallization gave a crystal suitable for X-ray diffraction study and the crystal structure was found to be based on π-stacking of benzene rings and aggregation of fluoroalkyl chains. Dynamic light scattering measurements showed that meso-styrene dimers bearing two fluoroalkyl end-groups can form the nanometer size-controlled self-assemblies through the intermolecular π-stacking of benzene rings and aggregation of end-capped fluoroalkyl groups in methanol.

The Effective Temperature of Ions Stored in a Linear Quadrupole Ion Trap Mass Spectrometer

The extent of internal energy deposition into ions upon storage, radial ejection, and detection using a linear quadrupole ion trap mass spectrometer is investigated as a function of ion size (m/z 59 to 810) using seven ion-molecule thermometer reactions that have well characterized reaction entropies and enthalpies. The average effective temperatures of the reactants and products of the ion-molecule reactions, which were obtained from ion-molecule equilibrium measurements, range from 295 to 350 K and do not depend significantly on the number of trapped ions, m/z value, ion trap q _z value, reaction enthalpy/entropy, or the number of vibrational degrees of freedom for the seven reactions investigated. The average of the effective temperature values obtained for all seven thermometer reactions is 318?±?23 K, which indicates that linear quadrupole ion trap mass spectrometers can be used to study the structure(s) and reactivity of ions at near ambient temperature.

Energy Dependence of HCD on Peptide Fragmentation: Stepped Collisional Energy Finds the Sweet Spot

An understanding of the process of peptide fragmentation and what parameters are best to obtain the most useful information is important. This is especially true for large-scale proteomics where data collection and data analysis are most often automated, and manual interpretation of spectra is rare because of the vast amounts of data generated. We show herein that collisional cell peptide fragmentation, in this case higher collisional dissociation (HCD) in the Q Exactive, is significantly affected by the normalized energy applied. Both peptide sequence and energy applied determine what ion fragments are observed. However, by applying a stepped normalized collisional energy scheme and combining ions from low, medium, and high collision energies, we are able to increase the diversity of fragmentation ions generated. Application of stepped collision energy to HEK293T lysate demonstrated a minimal effect on peptide and protein identification in a large-scale proteomics dataset, but improved phospho site localization through increased sequence coverage. Stepped HCD is also beneficial for tandem mass tagged (TMT) experiments, increasing intensity of TMT reporters used for quantitation without adversely effecting peptide identification.