Scrambling of autoinducing precursor peptides investigated by infrared multiphoton dissociation with electrospray ionization and Fourier transform ion cyclotron resonance mass spectrometry

Two synthetic precursor peptides, H₂N-CVGIW and H₂N-LVMCCVGIW, involved in the quorum sensing of Lactobacillus plantarum WCFS1, were characterized by mass spectrometry (MS) with electrospray ionization and 7-T Fourier transform ion cyclotron resonance (ESI-FTICR) instrument. Cell-free bacterial supernatant solutions were analyzed by reversed-phase liquid chromatography with ESI-FTICR MS to verify the occurrence of both pentapeptide and nonapeptide in the bacterial broth. The structural characterization of both protonated peptides was performed by infrared multiphoton dissociation using a continuous CO₂ laser source at a wavelength of 10.6 μm. As their fragmentation behavior cannot be directly derived from the primary peptide structure, all anomalous fragments were interpreted as neutral loss of amino acids from the interior of both peptides, i.e., loss of V, G, VG and M, MC, V, CC, from H₂N-CVGIW and H₂N-LVMCCVGIW, respectively. Mechanisms of this scrambling are proposed. FTICR MS provides accurate masses of all fragment ions with very low absolute mass errors (<1.6 ppm), which facilitated the reliable assignment of their elemental compositions. The resolving power was more than sufficient to resolve closely isobaric product ions with routine subparts per million mass accuracies. Only the occurrence of pentapeptide was found in the cell-free culture of L. plantarum, grown in Waymouth’s medium broth, with a low content of 5.2?±?2.6 μM by external calibration. Most of it was present as oxidized H₂N-CVGIW, that is, the soluble disulfide pentapeptide with a level tenfold higher (i.e., 50?±?4 μM, n?=?3).

External accumulation of ions for enhanced electrospray ionization fourier transform ion cyclotron resonance mass spectrometry

Electrospray ionization (ESI) in combination with Fourier transform ion cyclotron resonance (FTICR) mass spectrometry provides for mass analysis of biological molecules with unrivaled mass accuracy, resolving power and sensitivity. However, ESI FTICR MS performance with on-line separation techniques such as liquid chromatography (LC) and capillary electrophoresis has to date been limited primarily by pulsed gas assisted accumulation and the incompatibility of the associated pump-down time with the frequent ion beam sampling requirement of on-line chromatographic separation. Here we describe numerous analytical advantages that accrue by trapping ions at high pressure in the first rf-only octupole of a dual octupole ion injection system before ion transfer to the ion trap in the center of the magnet for high performance mass analysis at low pressure. The new configuration improves the duty cycle for analysis of continuously generated ions, and is thus ideally suited for on-line chromatographic applications. LC/ESI FTICR MS is demonstrated on a mixture of 500 fmol of each of three peptides. Additional improvements include a fivefold increase in signal-to-noise ratio and resolving power compared to prior methods on our instrument.     

Combined infrared multiphoton dissociation and electron capture dissociation with a hollow electron beam in Fourier transform ion cyclotron resonance mass spectrometry

An electron injection system based on an indirectly heated ring-shaped dispenser cathode has been developed and installed in a 7 Tesla Fourier transform ion cyclotron resonance (FTICR) mass spectrometer. This new hardware design allows high-rate electron capture dissociation (ECD) to be carried out by a hollow electron beam coaxial with the ion cyclotron resonance (ICR) trap. Infrared multiphoton dissociation (IRMPD) can also be performed with an on-axis IR-laser beam passing through a hole at the centre of the dispenser cathode. Electron and photon irradiation times of the order of 100 ms are required for efficient ECD and IRMPD, respectively. As ECD and IRMPD generate fragments of different types (mostly c, z and b, y, respectively), complementary structural information that improves the characterization of peptides and proteins by FTICR mass spectrometry can be obtained. The developed technique enables the consecutive or simultaneous use of the ECD and IRMPD methods within a single FTICR experimental sequence and on the same ensemble of trapped ions in multistage tandem (MS/MS/MS or MS(n)) mass spectrometry. Flexible changing between ECD and IRMPD should present advantages for the analysis of protein digests separated by liquid chromatography prior to FTICRMS. Furthermore, ion activation by either electron or laser irradiation prior to, as well as after, dissociation by IRMPD or ECD increases the efficiency of ion fragmentation, including the w-type fragment ion formation, and improves sequencing of peptides with multiple disulfide bridges. The developed instrumental configuration is essential for combined ECD and IRMPD on FTICR mass spectrometers with limited access into the ICR trap.     

Determination of the activation energy for unimolecular dissociation of a non-covalent gas-phase peptide: Substrate complex by infrared multiphoton dissociation fourier transform ion cyclotron resonance mass spectrometry

The activation energy for the unimolecular dissociation of a non-covalent supramolecular complex between an Artificial Cationic Receptor A ([Gua-Val-Val-Val-Amide]+, in which Gua is guanidiniocarbonyl pyrrole) and an Anionic Tetrapeptide B ([N-Acetyl-Val-Val-Ile-Ala]-) has been determined by measurement of the dissociation rate constant as a function of infrared CO2 laser power density. Singly-charged quasimolecular [A + B + H]+ ions are isolated, stored in a Fourier transform ion cyclotron resonance (FT-ICR) mass spectrometer, and irradiated by IR photons. The rate constant for dissociation of the non-covalent complex is determined at five different laser power densities. A plot of the natural logarithm of the first-order rate constant versus the natural logarithm of the laser power density yields a straight line, the slope of which provides an approximate measure of the activation energy (Ea(laser)) for dissociation. Ea(laser) is calculated by a relationship derived earlier by Dunbar and with a newly proposed equation by Paech et al. The results of the two approaches deliver significantly different activation energy values for the unimolecular dissociation of the non-covalent complex. We obtain EaI(laser) = 0.67 eV (Dunbar approximation) and EaII(laser) = 1.12 eV (Paech et al. approximation). Differences between the two approaches are discussed with respect to non-covalent complexes.     

Collision-induced dissociation of ester enolate ions using fourier transform mass spectrometry

A series of ester enolates was investigated by the technique of collision-induced dissociation (CID) using a Fourier transform mass spectrometer. Two primary modes of fragmentation were observed which led to CID products characteristic of the acyl and alkoxyl moieties of the ester enolates. An investigation of the fragmentation mechanism revealed that the primary fragmentation mode appears to be a sensitive function of the structure and the proton affinities of the two possible product ions. In most cases the anion (ketenyl or alkoxide) with the lower proton affinity was observed as the threshold product, suggestive of a proton-bound dimer intermediate. Interesting secondary dissociations were observed to occur from the primary product ions, as alkoxide ions fragmented to enolate ions or other stabilized anions.     

Structural validation of saccharomicins by high resolution and high mass accuracy fourier transform-ion cyclotron resonance-mass spectrometry and infrared multiphoton dissociation tandem mass spectrometry

Exceptionally high mass resolving power and mass accuracy combined with tandem mass spectrometry (MSⁿ) capability make Fourier transform ion cyclotron resonance mass spectrometry a powerful tool for structure verification and determination of biological macromolecules. By means of local internal calibration and electron mass correction, mass accuracy better than ±0.5 ppm was achieved for two oligosaccharide antibiotics, Saccharomicins A and B, consistent with the proposed elemental compositions based upon NMR data. High resolution and high mass accuracy MS/MS data were obtained for both oligosaccharides by use of infrared multiphoton dissociation (IRMPD) with a 40 W continuous-wave CO₂ laser. The spectra were charge-state deconvolved by the “Z-score” algorithm to yield much simpler mass-only spectra. Sequences of 15 sugar residues could be confirmed from the charge state deconvolved accurate mass MS/MS spectra for Saccharomicins A and B, even without use of traditional prior permethylation. A fragment corresponding to an internal sugar loss rearrangement was observed by IRMPD and studied by collision activated dissociation MS⁴.     

Combined infrared multiphoton dissociation and electron-capture dissociation using co-linear and overlapping beams in Fourier transform ion cyclotron resonance mass spectrometry

A novel set-up for Fourier transform ion cyclotron resonance mass spectrometry (FTICR) is reported for simultaneous infrared multiphoton dissociation (IRMPD) and electron-capture dissociation (ECD). An unmodified electron gun ensures complete, on-axis overlap between the electron and the photon beams. The instrumentation, design and implementation of this novel approach are described. In this configuration the IR beam is directed into the ICR cell using a pneumatically actuated mirror inserted into the ion-optical path. Concept validation was made using different combinations of IRMPD and ECD irradiation events on two standard peptides. The ability to perform efficient IRMPD, ECD and especially simultaneous IRMPD and ECD using lower irradiation times is demonstrated. The increase in primary sequence coverage, with the combined IRMPD and ECD set-up, also increases the confidence in peptide and protein assignments.     

Ion kinetic energy modulation for improved ion trapping in electrospray ionization fourier transform ion cyclotron resonance mass spectrometry

A new technique for manipulating the kinetic energy distribution of electrospray ions that arrive at a Fourier transform ion cyclotron resonance trapped-ion cell is presented. Narrow kinetic energy distributions can complicate the selection of appropriate trapping conditions for electrospray ions and introduce charge discrimination in resulting mass spectra. Modulation of the applied skimmer potential controllably broadens the kinetic energy distribution, which improves the reproducibility of acquired spectra and eliminates charge discrimination. Mass spectra of horse heart cytochrome c are presented to demonstrate the utility of the technique. For example, applied static skimmer potentials of 12 and 9 V yield charge state distributions ranging from [M+19H]⁺¹⁹ to [M+12H]⁺¹² and [M+15H]⁺¹⁵ to [M+7H]⁺⁷, respectively. A 12 ± 2 V, 100-Hz modulation of the skimmer potential yields an electrospray spectrum with charge states that range from [M+19H]⁺¹⁹ to [M+7H]⁺⁷, which is more representative of the source distribution.     

An investigation of the energetics of peptide ion dissociation by laser desorption chemical ionization fourier transform mass spectrometry

The energy dependence of competing fragmentation pathways of protonated peptide molecules is studied via laser desorption—chemical ionization in a Fourier transform ion cyclotron resonance spectrometer. Neutral peptide molecules are desorbed by the technique of substrate-assisted laser desorption, followed by post-ionization with a proton transfer reagent ion species. The chemical ionization reaction activates the protonated peptide molecules, which then fragment in accordance with the amount of excess energy that is deposited. Chemical ionization forms a protonated molecule with a narrower distribution of activation energy than can be formed by activation methods such as collision activated dissociation. Furthermore, the upper limit of the activation energy is well defined and is approximately given by the enthalpy of the chemical ionization reaction. Control over the fragmentation of peptide ions is demonstrated through reactions between desorbed peptide molecules with different reagent ion species. The fragmentation behavior of peptide ions with different internal energies is established by generation of a breakdown curve for the peptide under investigation. Breakdown curves are reported for the peptides Val-Pro, Val-Pro-Leu, Phe-Phe-Gly-Leu-Met NH₂, and Arg-Lys-Asp-Val-Tyr. The derived breakdown curve of Val-Pro has been fitted by using quasi-equilibrium Rice-Ramsperger-Kassel-Marcus theory to model the unimolecular dissociation of the protonated peptide to provide a better understanding of the mechanisms for the formation of fragment ions that originate from protonated peptides.     

External ion accumulation of low molecular weight poly(ethylene glycol) by electrospray ionization fourier transform mass spectrometry

The combination of electrospray ionization (ESI) with Fourier transform mass spectrometry (FTMS) is a powerful tool in characterizing synthetic polymers. ESI permits the generation of intact, multiply charged high mass ions, whereas FTMS provides high mass resolution and correspondingly improved mass accuracy. However, under “nonideal” empirically determined operating conditions, a mass discrimination effect occurs as a function of accumulation time that can result in significant differences for calculated average mass values (M_n, M_w) and polydispersities. A multidimensional tuning process to eliminate the deleterious effects of mass bias is demonstrated for several sodiated poly(ethylene glycol) samples containing oligomers with masses covering a 600–3350 Da mass regime. In addition, experiments are performed in order to elucidate the possible mechanism(s) that cause the mass discrimination effect. It is proposed that extended collisions (reactive and nonreactive) occur in the hexapole to alter the energy (and velocity) distributions of the ions before injection into the trap. By choosing higher skimmer potentials, ions over a narrower energy “window” are preselected in the hexapole and exhibit lower overall mass bias effects.     

Speciation of nitrogen containing aromatics by atmospheric pressure photoionization or electrospray ionization fourier transform ion cyclotron resonance mass spectrometry

We determine the elemental compositions of aromatic nitrogen model compounds as well as a petroleum sample by atmospheric pressure photoionization (APPI) and electrospray Ionization (ESI) with a 9.4 Tesla Fourier transform ion cyclotron resonance (FT-ICR) mass spectrometer. From the double-bond equivalents calculated for the nitrogen-containing ions from a petroleum sample, we can infer the aromatic core structure (pyridinic versus pyrrolic nitrogen heterocycle) based on the presence of M(+.) (odd-electron) versus [M+H](+) (even-electron) ions. Specifically, nitrogen speciation can be determined from either a single positive-ion APPI spectrum or two ESI (positive- and negative-ion) spectra. APPI operates at comparatively higher temperature than ESI and also produces radical cations that may fragment before detection. However, APPI fragmentation of aromatics can be eliminated by judicious choice of instrumental parameters.     

Atmospheric pressure ionization permanent magnet fourier transform ion cyclotron resonance mass spectrometry

A new Fourier transform ion cyclotron resonance mass spectrometer based on a permanent magnet with an atmospheric pressure ionization source was designed and constructed. A mass resolving power (full-width-at-half-maximum) of up to 80,000 in the electron ionization mode and 25,000 in the electrospray mode was obtained. Also, a mass measurement accuracy at low-ppm level has been demonstrated for peptide mixtures in a mass range of up to 1200 m/z in the isotopically resolved mass spectra.     

Tamdem quadrupole fourier transform mass spectrometry

Tandem quadrupole Fourier transform mass spectrometry is shown to be a practical technique for the determination of molecular weights. Samples in the mass range up to 6000 daltons can be routinely analyzed at the 0.1–1.0 pmol level. Ions indicative of molecular weight are generated by particle bombardment, transmitted to and trapped inside a superconducting magnetic field and mass analyzed. Additional structural information is obtained by exposing the trapped ions to photons generated by an argon fluoride excimer laser to effect laser photodissociation. Sequence analysis of oligopeptides fractionated by liquid chromatography is discussed. Application of the technique to the structural chacterization of proteins isolated by two-dimensional gel electrophoresis is also demonstrated.     

Collision-induced dissociation pathways of anabolic steroids by electrospray ionization tandem mass spectrometry

Anabolic steroids are structurally similar compounds, and their product-ion spectra obtained by tandem mass spectrometry under electrospray ionization conditions are quite difficult to interpret because of poly-ring structures and lack of a charge-retaining center in their chemical structures. In the present study, the fragmentation of nine anabolic steroids of interest to the racing industry was investigated by using triple quadrupole mass spectrometer, Fourier transform ion cyclotron resonance (FT-ICR) mass spectrometer, and a linear ion trap instrument. With the aid of an expert system software (Mass Frontier version 3.0), accurate mass measurements, and multiple stage tandem mass spectrometric (MS(n)) experiments, fragmentation pathways were elucidated for boldenone, methandrostenolone, tetrahydrogestrinone (THG), trenbolone, normethandrolone and mibolerone. Small differences in the chemical structures of the steroids, such as an additional double-bond or a methyl group, result in significantly different fragmentation pathways. The fragmentation pathways proposed in this paper allow interpretation of major product ions of other anabolic steroids reported by other researchers in a recent publication. The proposed fragmentation pathways are helpful for characterization of new steroids. The approach used in this study for elucidation of the fragmentation pathways is helpful in interpretation of complicated product-ion spectra of other compounds, drugs and their metabolites.     

Shotgun sequencing small oligonucleotides by nozzle-skimmer dissociation and electrospray ionization mass spectrometry

Nozzle-skimmer dissociation in combination with de novo sequencing was investigated as an approach for increasing the throughput of oligonucleotide analysis attainable by electrospray ionization mass spectrometry. An experimental method allowing for the sequential generation of precursor and fragment ion data during direct infusion of sample was developed. These data can then be used with readily available de novo sequencing software to characterize small oligonucleotides. When this approach was applied to mixtures of oligonucleotides, it was found that de novo sequencing becomes limited due to spectral congestion and overlapping oligonucleotide m/z dissociation product values. Self-packed C(18) microspray emitters were investigated as a means of reducing spectral complexity. It was found that such emitters allow for the analysis of oligonucleotide mixtures with minimal component overlap, and these emitters provide additional benefits of pre- concentrating and desalting the sample. These developments can provide a route for the more rapid characterization of ribonucleic acid endonuclease digestion mixtures.     

Signal suppression in electrospray ionization Fourier transform mass spectrometry of multi-component samples

The high resolution, mass range and sensitivity of Fourier transform mass spectrometry (FTMS) suggest that it could be a valuable tool for the quantitative analysis of biomolecules. To determine the applicability of electrospray ionization combined with FTMS to the quantitation of biomolecules in multi-component samples, mixtures of varying compositions and concentrations of cytochrome c, angiotensin II, insulin and chicken egg white lysozyme were examined. The instrument used has an electrospray source with a hexapole trap to accumulate ions for injection into an ion cyclotron resonance mass analyzer. Linear responses for single component samples of angiotensin II and insulin were in the range 0.031-3 microM and those of both cytochrome c and lysozyme were between 0.031 and 1 microM. In examining various mixtures of the proteins with angiotensin II, it was found that the presence of the large molecules suppresses the signal of the smaller molecules. This is suggested to be a result of ion-ion interactions producing selective ion loss from either the hexapole trap or the ion cyclotron resonance mass analyzer trap. More massive, more highly charged ions can collisionally transfer large amounts of translational energy to smaller, less highly charged ions, ejecting the smaller ions from the trap. Mass discrimination effects resulting from the trapping voltage were also examined. It was found that relative signal intensities of ions of different masses depend on trapping voltage for externally produced ions. The effect is most significant for spectra including masses that differ by 30% or more. This suggests that for quantitation all samples and standards be run at a constant trapping potential.     

Ions generated from uranyl nitrate solutions by electrospray ionization (ESI) and detected with fourier transform ion-cyclotron resonance (FT-ICR) mass spectrometry

Electrospray ionization (ESI) of uranyl nitrate solutions generates a wide variety of positively and negatively charged ions, including complex adducts of uranyl ions with methoxy, hydroxy, and nitrate ligands. In the positive ion mode, ions detected by Fourier transform ion cyclotron resonance (FT-ICR) mass spectrometry are sensitive to instrumental tuning parameters such as quadrupole operating frequency and trapping time. Positive ions correspond to oligomeric uranyl nitrate species that can be characterized as having a general formula of [(UO(2))(n)(A)(m)(CH(3)OH)(s)](+) or [(UO(2))(n)(O)(A)(m)(CH(3)OH)(s)](+) with n = 1-4, m = 1-7, s = 0 or 1, and A = OH, NO(3), CH(3)O or a combination of these, although the formation of NO(3)-containing species is preferred. In the negative ion mode, complexes of the form [(UO(2))(NO(3))(m)](-) (m = 1-3) are detected, although the formation of the oxo-containing ions [(UO(2))(O)(n)(NO(3))(m)](-) (n = 1-2, m = 1-2) and the hydroxy-containing ions [(UO(2))(OH)(n)(NO(3))(m)](-) (n = 1-2, m = 0-1) are also observed. The extent of coordinative unsaturation of both positive and negative ions can be determined by ligand association/exchange and H/D exchange experiments using D(2)O and CD(3)OD as neutral reaction partners in the gas-phase. Positive ions are of varying stability and reactivity and may fragment extensively upon collision with D(2)O, CD(3)OD and N(2) in sustained off-resonance irradiation/collision-induced dissociation (SORI-CID) experiments. Electron-transfer reactions, presumably occurring during electrospray ionization but also in SORI-CID, can result in reduction of U(VI) to U(V) and perhaps even U(IV).     

Infrared multiphoton dissociation spectroscopic analysis of peptides and oligosaccharides by using fourier transform ion cyclotron resonance mass spectrometry with a midinfrared free-electron laser

The fragmentation of peptides and oligosaccharides in the gas phase was investigated by means of electrospray ionization Fourier transform ion cyclotron resonance (FTICR) mass spectrometry coupled with dissociation by a laser-cleavage infrared multiphoton dissociation (IRMPD) technique. In this technique, an IR free-electron laser is used as a tunable source of IR radiation to cause cleavage of the ionized samples introduced into the FTICR cell. The gas-phase IRMPD spectra of protonated peptides (substance P and angiotensin II) and two sodiated oligosaccharides (sialyl Lewis X and lacto-N-fucopentaose III) were obtained over the IR scan range of 5.7-9.5 microm. In the IRMPD spectra for the peptide, fragment ions are observed as y/b-type fragment ions in the range 5.7-7.5 microm, corresponding to cleavage of the backbone of the parent amino acid sequence, whereas the spectra of the oligosaccharides have major peaks in the range 8.4-9.5 microm, corresponding to photoproducts of the B/Y type.     

Isotope pattern evaluation for the reduction of elemental compositions assigned to high-resolution mass spectral data from electrospray ionization fourier transform ion cyclotron resonance mass spectrometry

The number of possible chemical formulae assigned to an accurate determined mass was significantly reduced by comparing spectral and theoretical isotope patterns based on mass measurement obtained with an ultrahigh-resolution electrospray ionization Fourier transform ion cyclotron resonance mass spectrometer (ESI-FTICR-MS) at high field intensity (7 T). Reduction is performed by rating congruency between experimental and theoretical pattern intensity and mass, and filtering out compositions with insufficient user-definable results. The methods used for isotope pattern simulation, peak searching, and comparison will be briefly described and evaluated on molecule ion signals of 25 compounds (300-1000 Da) applying a mass accuracy of +/-5 ppm, a set of eight elements with constant constraints (C0-200H0-1000N0-15O0-15S0-2Cl0-2Br0-2Ru0-1), natural isotope abundances and experimental resolution (full width at half maximum).     

Electron capture dissociation implementation progress in fourier transform ion cyclotron resonance mass spectrometry

Successful electron capture dissociation (ECD) Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS) applications to peptide and protein structural analysis have been enabled by constant progress in implementation of improved electron injection techniques. The rate of ECD product ion formation has been increased to match the liquid chromatography and capillary electrophoresis timescales, and ECD has been combined with infrared multiphoton dissociation in a single experimental configuration to provide simultaneous irradiation, fast switching between the two techniques, and good spatial overlap between ion, photon, and electron beams. Here we begin by describing advantages and disadvantages of the various existing electron injection techniques for ECD in FT-ICR MS. We next compare multiple-pass and single-pass ECD to provide better understanding of ECD efficiency at low and high negative cathode potentials. We introduce compressed hollow electron beam injection to optimize the overlap of ion, photon, and electron beams in the ICR ion trap. Finally, to overcome significant outgassing during operation of a powerful thermal cathode, we introduce nonthermal electron emitter-based electron injection. We describe the first results obtained with cold cathode ECD, and demonstrate a general way to obtain low-energy electrons in FT-ICR MS by use of multiple-pass ECD.