Electrospray ionization—Fourier transform ion cyclotron resonance mass spectrometry at 11.5 tesla: Instrument design and initial results

Initial results obtained using a new electrospray ionization (ESI) Fourier transform ion cyclotron resonance (FTICR) mass spectrometer operated at a magnetic field 11.5 tesla are presented. The new instrument utilized an electrostatic ion guide between the ESI source and FTICR trap that provided up to 5% overall transmission efficiency for light ions and up to 30% efficiency for heavier biomolecules. The higher magnetic field in combination with an enlarged FTICR ion trap made it possible to substantially improve resolving power and operate in a more robust fashion for large biopolymers compared to lower field instruments. Mass resolution up to 10⁶ has been achieved for intermediate size biopolymers such as bovine ubiquitin (8.6 kDa) and bovine cytochrome c (12.4 kDa) without the use of frequency drift correction methods. A mass resolution of 370,000 has been demonstrated for isotopically resolved molecular ions of bovine serum albumin (66.5 kDa). Comparative measurements were made with the same spectrometer using a lower field 3.5-tesla magnet allowing the performance gains to be more readily quantified. Further improvements in pumping capacity of the vacuum system and efficiency of ion transmission from the source are expected to lead to further substantial sensitivity gains.     

Primary to quaternary protein structure determination with electrospray ionization and magnetic sector mass spectrometry

Electrospray ionization with a forward-geometry magnetic sector mass spectrometer was used for collisionally activated dissociation studies of multiply charged polypeptides and for studying non-covalently bound protein systems. The high-resolution capabilities of a high-performance instrument allow the resolution of isotopic contributions for product ions and molecular ion species. Determination of product ion charge states by this method reduces difficulties in the interpretation of product ion mass spectra from multiply charged precursors, which are generated either in the atmospheric pressure/vacuum electrospray interface or in the collision chamber of the mass spectrometer. Extended tandem mass spectrometric experiments have the potential for sequencing larger polypeptides. However, evidence for isomerization of gas-phase product ions from substance P and substance P analogues was observed, complicating the interpretation of product ion spectra. Non-covalent complexes can also be studied by electrospray ionization magnetic sector MS. The higher m/z range of such an instrument is a major advantage for studying weakly bound systems, such as heme–protein systems (myoglobin, hemoglobin) and protein aggregates (concanavalin A), because of their tendency to form complex ions with relatively low charge states.     

Billionfold data increase from mass spectrometry instrumentation

The mass spectrometers of 1910–1950 gave 10–100 separately measurable mass values (resolution increments) in a single spectrum; the few other analytical methods then with this capability, such as emission spectroscopy, were not suitable for molecular characterization. The introduction of high-resolution mass spectra 40 years ago gave a 10² increase in resolution increments, while tandem mass spectrometry (MS²) 30 years ago promised a similar exponential gain. A key to the present realization of this was the discovery of Fourier-transform mass spectrometry 20 years ago, while electrospray ionization of large molecules 10 years ago greatly extended the upper mass limit of spectra. These improvements can now give 10⁵–10⁶ resolution increments in the mass spectrum of a large molecule. Extending this with MS² ions in any of > 10⁴ mass regions can be dissociated to produce a mass spectrum with these > 10⁵ resolution increments. With the several steps of MS ⁿ now achievable, this represents a > 10⁹ data gain since 1950. However, utilization of this amazing capability is in its infancy, presenting a tremendous challenge for our field.     

Top-down protein sequencing by CID and ECD using desorption electrospray ionisation (DESI) and high-field FTICR mass spectrometry

We report high resolution spectra for the medium molecular weight proteins myoglobin and cytochrome-c obtained using a custom desorption electrospray ionisation (DESI) source coupled to a Bruker Daltonics 12 T Apex Qe Fourier transform ion cyclotron resonance mass spectrometer (FTICR-MS). The DESI source was designed for accurate alignment and reproduction of critical geometric variables. A two axis motorised stage was included to enable automated rastering of the sample under the DESI plume. Spectra for the intact proteins have been obtained under single-acquisition conditions and a top-down analysis of cytochrome-c was performed using both collision induced dissociation (CID) and electron capture dissociation (ECD) of the isolated [M+15H]¹⁵⁺ charge state. The sequence coverage is comparable to that obtained using electrospray ionisation, demonstrating the utility of top-down protein analysis by DESI FTICR-MS.     

Trapping and detection of ions generated in a high magnetic field electrospray ionization fourier transform ion cyclotron resonance mass spectrometer

The trapping and detection parameters employed with a Fourier transform ion cyclotron resonance (FTICR) mass spectrometer that is interfaced to a high magnetic field electrospray ionization (ES11 source are presented. ES1 occurs at atmospheric pressure in a 1.5-T field, and FTICR detection occurs 25 cm away at 3.0 T in either one of two cells separated by a conductance limit and maintained at pressure differentials of 5 × 10⁵ and 2 × 10⁷ torr, respectively. The continuous electrospray ion current traversing the high- and low-pressure cells is 350 and 100 pA, respectively. Retarding grid studies at the high-pressure cell indicate electrospray ion kinetic energies are controllable from less than an electronvolt to more than 10 eV. These kinetic energies are a function of desolvating capillary-skimmer assembly distance and the skimmer potential. Efficient accumulation of injected ions is accomplished only when the trap-plate potential matches the ion kinetic energy. If this condition is satisfied, the trapped ion cell fills to the ion space charge limit within a few hundred milliseconds. It is concluded that even at the high pressures used, the primary trapping mechanism cannot be solely collision dependent because the rate of ion accumulation is independent of background pressure. However, optimized FTICR excitation conditions for peptides and proteins in the mass range from 10³ to more than 10⁶ kDa are found to vary strongly with pressure; this is attributed to large mass- and charge-dependent differences in ion-molecule collision frequency.     

Mass and charge assignment for electrospray ions by cation adduction

The assignment of the mass (m) value from the m/z value for ions with a multiple number of charges (z) in electrospray mass spectra usually utilizes multiple peaks of the same m but different z values, or unit-mass—separated isotopic peaks of the same z value from high resolution spectra. The latter approach is also feasible with much less resolving power using adduct ions of much higher mass separation. The application of this to mixture spectra containing many masses, such as spectra from tandem mass spectrometry (MS/MS) ion dissociation, does not appear to have been pointed out previously. Thus, replacing two protons by one Cu²⁺ ion increases the mass by 61.5 Da, with this shift providing a mass scale for assignment of m and z from this pair of m/z values. The more common Na⁺ adduct peaks provide a 22.0 Da separation, of utility for 1000 resolving power only below approximately 10 kDa. Further, collisional dissociation lowers the degree of Cu²⁺ adduction in the resulting sequence-specific fragment ions much less than that of the corresponding Na⁺ adducts, making the Cu²⁺ adducts far more useful for m and z determination in MS/MS studies.     

Concentric tube vacuum chamber for high magnetic field,high-pressure ionization in a fourier transform ion cyclotron resonance mass spectrometer

A new differential pumping design for external source Fourier transform ion cyclotron resonance mass spectrometry is described. A network of concentric tubes of increasing diameter terminates at a series of conductance limits across which a pressure from atmosphere to low-10^?8 torr is achieved. This design permits high-pressure sources to be positioned within the solenoidal superconducting magnet less than 20 cm from the analyzer trapped ion cell. Ionization at high magnetic field offers the advantage of radial ion confinement and consequently delivers enhanced ion current to the trapped ion cell. Ion injection utilizing this vacuum chamber design is simpler than previously reported serial pumping stage designs because elaborate focusing optics to overcome the magnetic mirror effect are unnecessary. Two probe-mounted atmospheric pressure sources are described as evidence of the general applicability of the concentric tube vacuum chamber. An electrospray source that delivers several hundred picoamperes of ion current to the cell yields high-sensitivity spectra of proteins beyond 100 kDa. Improved pumping compared with a prototype concentric tube network configuration now permits mass resolution in excess of 20,000 for the [M + 4H]⁴⁺ ion of melittin. The resolution is sufficient to distinguish isotope peaks within a single charge state. A probe-mounted, pulsed-laser ablation source that permits cluster formation in the strong magnetic field is also demonstrated.     

Enhancement of the effective resolution of mass spectra of high-mass biomolecules by maximum entropy-based deconvolution to eliminate the isotopic natural abundance distribution

Although high-resolution Fourier transform ion cyclotron resonance mass spectrometry can resolve individual isotopic masses for biomolecules of more than 100 ku, its effective mass accuracy is limited by the distribution of naturally occurring rare isotopes (¹³C, ¹⁵N, ¹⁸O, ³⁴S, etc.). In this article, we compare least-squares and maximum entropy methods for deconvolution of the isotopic natural abundance distribution to narrow the mass spectral isotopic abundance envelope for greatly enhanced effective mass resolution. We apply both methods to yield deconvolved high-resolution deuterium distributions for peptides and proteins subjected to H/D exchange prior to electrospray Fourier transform ion cyclotron resonance mass analysis. In addition, we show that even unresolved isotopic envelopes from a quadrupole mass spectrometer can be narrowed for considerably improved resolution there as well.     

Fourier-transform electrospray instrumentation for tandem high-resolution mass spectrometry of large molecules

Department of Chemistry, Baker Laboratory, Cornell University, Ithaca, New York, USA Mass spectrometry instrumentation providing unit resolution and lo-ppm mass accuracy for molecules larger than 10 kDa was first reported in 1991. This instrumentation has now been improved with a 6.2-T magnet replacing that of 2.8 T, a more efficient vacuum system, ion injection with controlled ion kinetic energies, accumulated ion trapping with an open-cylindrical ion cell, acquisition of 2M data points, and updated electrospray apparatus. The resulting capabilities include resolving power of 5 × 10⁵ for a 29-kDa protein, less than l-ppm mass measuring error, and dissociation of protein molecular ions to produce dozens of fragment ions whose exact masses can be identified from their mass-to-charge ratio values and isotopic peak spacing.     

High-resolution accurate mass measurements of biomolecules using a new electrospray ionization ion cyclotron resonance mass spectrometer

A novel electrospray ionization/Fourier transform ion cyclotron resonance mass spectrometer based on a 7-T superconducting magnet was developed for high-resolution accurate mass measurements of large biomolecules. Ions formed at atmospheric pressure using electrospray ionization (ESI) were transmitted (through six differential pumping stages) to the trapped ion cell maintained below 10^?9 torr. The increased pumping speed attainable with cryopumping (> 10⁵ L/s) allowed brief pressure excursions to above 10^?4 torr, with greatly enhanced trapping efficiencies and subsequent short pumpdown times, facilitating high-resolution mass measurements. A set of electromechanical shutters were also used to minimize the effect of the directed molecular beam produced by the ES1 source and were open only during ion injection. Coupled with the use of the pulsed-valve gas inlet, the trapped ion cell was generally filled to the space charge limit within 100 ms. The use of 10–25 ms ion injection times allowed mass spectra to be obtained from 4 fmol of bovine insulin (M_r 5734) and ubiquitin (M_r 8565, with resolution sufficient to easily resolve the isotopic envelopes and determine the charge states. The microheterogeneity of the glycoprotein ribonuclease B was examined, giving a measured mass of 14,898.74 Da for the most abundant peak in the isotopic envelope of the normally glycosylated protein (i.e., with five mannose and two N-acetylglucosamine residues (an error of approximately 2 ppm) and an average error of approximately 1 ppm for the higher glycosylated and various H₃PO₄ adducted forms of the protein. Time-domain signals lasting in excess of 80 s were obtained for smaller proteins, producing, for example, a mass resolution of more than 700,000 for the 4⁺ charge state (m/z 1434) of insulin.     

Dynamics of ions of intact proteins in the Orbitrap mass analyzer

While allowing analysis of intact proteins without a theoretical upper mass limit, the Orbitrap mass analyzer demonstrates reduced resolving power as ion mass increases even at a constant mass-to-charge ratio. It is shown that this effect comes from the effects of ion scattering on background gas molecules. The main mechanisms causing decay of acquired transient appear to be fragmentation as well as accelerated dephasing of ion packets. Isotopic resolution of proteins including bovine serum albumin (MW 66.4 kDa) and transferrin (MW 78 kDa) has also been demonstrated. As a part of this study, detection of individual multiply-charged ions of myoglobin (MW 16.9 kDa) has been demonstrated. Quantized distribution of signal intensities for myoglobin ions well above the noise threshold was observed, with high mass accuracy and resolution of recorded individual ions used as an independent confirmation of correct assignment of signal to ions rather than to noise. The latter also allowed us to benchmark the sensitivity of image-current detection and explore in detail factors responsible for signal decay.     

Coupling electrospray corona discharge, charge reduction and ion mobility mass spectrometry: From peptides to large macromolecular protein complexes

We present the design and implementation of a home-built point-to-plane corona discharge probe, which rapidly and efficiently charge reduces biological ions generated by electrospray ionization (ESI). The molecules analysed ranged from small peptides such as Glu-fibrinopeptide B (1.5 kDa), small proteins such as myoglobin (16.9 kDa), polymers such as polyethylene glycol (PEG 10 k) which all showed intense singly charged ions; to large native multiprotein complexes such as GroEL (802 kDa) which show a broad range of charge-reduced species. The corona discharge probe operates at atmospheric pressure and was directly interfaced with a standard-ESI or nanoflow-ESI source of quadrupole ion mobility time-of-flight mass spectrometer. The corona discharge probe is completely modular and could potentially be mounted to any commercial or research grade mass spectrometer with an ESI source. The level of charge reduction is precisely controlled by the applied voltage and/or probe gas flow rate and when in operation, results in approximately a 50 % reduction in total ion current. We also present the combination of corona discharge and travelling wave ion mobility and assign helium collision cross-section values (Ω_He) to the charge reduced species of the native protein complex pyruvate kinase. It would appear that the Ω_He of the +20 charge state for pyruvate kinase is approximately 20 % smaller than the +35 charge state. Finally, we discuss the potential benefits and concerns of utilising charge reduced protein species as a means of extending the travelling wave collision cross-section calibration range over that which is already published.     

Electrospray ionization ion trap mass spectrometry of a tetrahedral supramolecular Ti4L4 cluster

The analysis of self-assembled supramolecular clusters held together by metal-ligand interactions is a relatively new area in mass spectrometry. These complexes may have molecular weights exceeding several kDa, are often highly charged and their composition is most sensitive to their chemical environment. Electrospray ionization appears to be the ionization technique of choice for their mass spectral characterization. The analysis (positive and negative ion detection mode) of the prototype compound [Ti₄L₄]^8? (L = a catechol-based tris-bidentate ligand; MW of cluster = 2293 u) using a Paul trap mass analyzer is reported. The combination of electrospray ionization and high resolution ion trap technology is a powerful tool which provides the unambiguous solution state characterization of this supramolecular cluster. The results are correlated with the known solid state structure of the cluster and reactions previously reported for mononuclear Ti(IV) catecholates.     

q value and parent energy optimization using a low-voltage ionization approach increases resolution in linear ion trap mass spectrometry

In this work, the isolation step in the linear ion trap was performed using different “q values” conditions at a low collision-induced dissociation (CID) energy leading to the parent ion resolution improvements, reasonably due to better ion energy distribution. According to the results, we obtained a greater resolution and mass accuracy operating in both traditional electrospray and low voltage ionization near the q value = 0.778 and with a CID energy of 10%. This effect was evaluated with low-molecular-mass compounds (skatole and arginine). The proposed optimization yielded a superior instrument performance without adding technological complexity to mass spectrometry analyses.     

Infrared, surface-assisted laser desorption ionization mass spectrometry on frozen aqueous solutions of proteins and peptides using suspensions of organic solids

Surface-assisted, laser desorption ionization (SALDI) time-of-flight mass spectra of proteins and peptides have been obtained from bulk frozen aqueous solutions by adding solid organic powders to the solutions before freezing. Abundant analyte ions were obtained with a 3.28 µm Nd:YAG/OPO laser. 20 compounds were evaluated as solid additives, and 16 yielded protein mass spectra. Successful solids included compounds like pyrene, aspartic acid, and polystyrene. The best results were obtained with nicotinic acid and indole-2-carboxylic acid, which yielded protein mass spectra anywhere on the sample and with every laser shot. Compared with ultraviolet-matrix-assisted laser desorption ionization on the same instrument, cryo-IR-SALDI had a comparable detection limit (≈1 µM), a lower mass resolution for peptides, and a higher mass resolution for large proteins. Approximately 2500 cryo-IR-SALDI mass spectra were obtained from a single spot on a 0.3-mm-thick frozen sample before the metal surface was reached. About 0.1 nL of frozen solution was desorbed per laser shot. The extent of protein charging varied between the SALDI solids used. With thymine, myoglobin charge states up to MH ₁₂ ⁺¹² were observed. It is tentatively concluded that observed ions are preformed in the frozen sample.     

Gaseous myoglobin ions stored at greater than 300 K

Multiply-charged myoglobin ions retaining the prosthetic heme group have been formed by electrospray, injected into a quadrupole ion trap, and stored for up to one second prior to mass analysis. Collisional activation experiments indicate that these ions readily fragment into the charged heme group and the complementary apomyoglobin ion. No fragmentation is observed, however, upon ion storage in the presence of a neutral bath gas at 1 × 10^?3 torr for up to one second. The significance of this observation is that these non-covalently-bound ions, in which both the heme group and the polypeptide carry charge, are kinetically stable for over one second at room temperature and, perhaps, at higher temperatures. This suggests that other biologically relevant ions derived using electrospray and bound by non-covalent interactions can be studied using the various tools available with ion storage mass spectrometers and by other techniques that employ relatively high pressure environments for the study of gaseous ions.     

Development and Characterization of A Linear Matrix-assisted Laser Desorption Ionization Mass Spectrometer

Matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) is an important analytical technique for biological macromolecules, such as proteins, peptides and nucleic acid, especially in the field of microbial identification. On the basis of previous study, a linear MALDI-TOF MS was been designed and assembled for biological applications. The instrument comprised a vacuum system, a vacuum fast sample introduction system, an optical system, a time-of-flight mass analyzer, an ion source, a data acquisition system and an electronic control system. The ion source adopted two-stage source acceleration, delayed extraction and dynamic pulse focusing technique. The time-of-flight distance of field-free drift region was about 1 m. The optical system adopted a solid-state laser with adjustable frequency of 1–2000 Hz and spots of 20–100 μm. The angle of incidence laser was controlled at 5°. A series of experiments were carried out to further evaluate the instrument performances. It could not only analyze the samples more than 199 kDa, but also achieve isotope resolution at 1000–3000 Da and up to 900 (FWHM) at 5000–17000 Da. The minimum detectable concentration of gramicidin was 10 amol μL^?1, absolute sensitivity reached up to 2.56 amol. Independent detection of saliva samples from different targets showed that the instrument had higher producibility. We identified Escherichia coli and Shigella spp., which are two common bacteria but difficult to be differentiated by mass spectrometry, showing its potential identification for clinical microorganism. In summary, this instrument can play a role on clinical examination in the near future.     

带羟乙基侧臂三脚架多胺Cu(Ⅱ)配合物切割肌红蛋白所得片断的质谱指认

采用电喷雾质谱和串联质谱以及聚丙烯酰胺凝胶电泳技术研究了[CuL(H₂O)](BF₄)₂(L为2-[二(2-氨乙酸)氨基]乙醇)与马心肌红蛋白的键合作用和水解切割。聚丙烯酰胺凝胶电泳研究显示在中性及60 ℃条件下，切割效率与[CuL(H₂O)]²⁺的浓度和温育时间密切相关。电喷雾质谱和串联质谱分析显示，[CuL(H₂O)]²⁺通过与肌红蛋白的氨基酸His36，His93，His116和Arg139侧链的结合，并在羟乙基侧臂的促进下，选择性地水解了肽键Phe33-Thr34，Gln91-Ser92，Ala94-Thr95，His116-Ser117和Asn140-Asp141。     

Development of quadrupole mass spectrometers using rapid prototyping technology

In this report, we present a prototype design of a quadrupole mass filter (QMF) with hyperbolic electrodes, fabricated at the University of Liverpool using digital light processing (DLP), a low-cost and lightweight 3D rapid prototyping (RP) technique. Experimental mass spectra are shown for H₂⁺, D₂⁺, and He⁺ ions to provide proof of principle that the DLP mass filter is working as a mass analyzer in the low-mass range (1 to 10 amu). The performance of the DLP QMF has also been investigated for individual spectral peaks. Numerical simulations of the instrument were performed by coupling CPO and Liverpool QMS-2 programs to model both the ion source and mass filter, respectively, and the instrument is shown to perform as predicted by theory. DLP thus allows miniaturization of mass spectrometers at low cost, using hyperbolic (or other) geometries of mass analyzer electrodes that provide optimal ion manipulation and resolution for a given application. The potential of using RP fabrication techniques for developing miniature and microscale mass analyzers is also discussed.     

Matrix-assisted ionization vacuum for protein detection,fragmentation and PTM analysis on a high resolution linear ion trap-orbitrap platform

Matrix-assisted ionization vacuum (MAIV) is a novel ionization technique that generates multiply charged ions in vacuum without the use of laser ablation or high voltage. MAIV can be achieved in intermediate-vacuum and high-vacuum matrix-assisted laser desorption/ionization (MALDI) sources and electrospray ionization (ESI) sources without instrument modification. Herein, we adapt MAIV onto the MALDI-LTQ-Orbitrap XL platform for biomolecule analysis. As an attractive alternative to MALDI for in solution and in situ analysis of biomolecules, MAIV coupling to high resolution and accurate mass (HRAM) MS instrument has successfully expanded the mass detection range and improved the fragmentation efficiency due to the generation of multiply charged ions. Additionally, the softness of MAIV enables potential application in labile post-translational modification (PTM) analysis. In this study, proteins as large as 18.7 kDa were detected with up to 18 charges; intact peptides with labile PTM were well preserved during the ionization process and characterized MS/MS; peptides and proteins in complex tissue samples were detected and identified both in liquid extracts and in situ. Moreover, we demonstrated that this method facilitates MS/MS analysis with improved fragmentation efficiency compared to MALDI-MS/MS.