Minimizing Peak Coalescence: High-Resolution Separation of Isotope Peaks in Partially Deamidated Peptides by Matrix-Assisted Laser Desorption/Ionization Fourier Transform Ion Cyclotron Resonance Mass Spectrometry

An Enhanced Isotopic Fine Structure Method for Exact Mass Analysis in Discovery Metabolomics: FIA-CASI-FTMS

A major bottleneck in metabolomics is the annotation of a molecular formula as a first step to a tentative structure assignment of known and unknown metabolites. The direct observation of an isotopic fine structure (IFS) provides the ability to confidently assign an unknown's molecular formula out of a complex mass spectrum. However, the majority of mass spectrometers deployed for metabolomic studies do not have sufficient resolving power and high-fidelity isotope ratios in the mass range of interest to determine molecular formulas from IFS data. To increase the number of unknowns for which IFS can be determined, a segmented "boxcar" approach using a selection quadrupole as a broadband mass filter is used. In this longer, enhanced dynamic range discovery experiment, selected ions in a specific mass range are accumulated before detection by the analyzer cell. The mass filter window is then moved across the entire mass range resulting in a composite mass spectrum covering the m/z range of interest for phenomics research. The effectiveness of the FIA-CASI-FTMS workflow utilizing IFS for molecular formula assignment is realized with the implementation of the dynamically harmonized cell, which distinguishes the approach from other segmented workflows because of the analytical properties of the cell. The discovery approach was applied to a human plasma sample to confidently assign an unknown molecular formula as part of the quest to illuminate its metabolic "dark matter" via high-fidelity IFS ratio determinations. The FIA-CASI-FTMS workflow showed a 2.6-fold increase in both matching with the Human Metabolome Database and an increase in the IFS pattern.

Mass Defect-Based N,N-Dimethyl Leucine Labels for Quantitative Proteomics and Amine Metabolomics of Pancreatic Cancer Cells

Mass spectrometry-based stable isotope labeling has become a key technology for protein and small-molecule analyses. We developed a multiplexed quantification method for simultaneous proteomics and amine metabolomics analyses via nano reversed-phase liquid chromatography-tandem mass spectrometry (nanoRPLC-MS/MS), called mass defect-based N,N-dimethyl leucine (mdDiLeu) labeling. The duplex mdDiLeu reagents were custom-synthesized with a mass difference of 20.5 mDa, arising from the subtle variation in nuclear binding energy between the two DiLeu isotopologues. Optimal MS resolving powers were determined to be 240K for labeled peptides and 120K for labeled metabolites on the Orbitrap Fusion Lumos instrument. The mdDiLeu labeling does not suffer from precursor interference and dynamic range compression, providing excellent accuracy for MS¹-centric quantification. Quantitative information is only revealed at high MS resolution without increasing spectrum complexity and overlapping isotope distribution. Chromatographic performance of polar metabolites was dramatically improved by mdDiLeu labeling with modified hydrophobicity, enhanced ionization efficiency, and picomole levels of detection limits. Paralleled proteomics and amine metabolomics analyses using mdDiLeu were systematically evaluated and then applied to pancreatic cancer cells.

Automated Affinity Capture and On-Tip Digestion to Accurately Quantitate in Vivo Deamidation of Therapeutic Antibodies

Deamidation of therapeutic antibodies may result in decreased drug activity and undesirable changes in pharmacokinetics and immunogenicity. Therefore, it is necessary to monitor the deamidation levels [during storage] and after in vivo administration. Because of the complexity of in vivo samples, immuno-affinity capture is widely used for specific enrichment of the target antibody prior to LC-MS. However, the conventional use of bead-based methods requires large sample volumes and extensive processing steps. Furthermore, with automation difficulties and extended sample preparation time, bead-based approaches may increase artificial deamidation. To overcome these challenges, we developed an automated platform to perform tip-based affinity capture of antibodies from complex matrixes with rapid digestion and peptide elution into 96-well microtiter plates followed by LC-MS analysis. Detailed analyses showed that the new method presents high repeatability and reproducibility with both intra and inter assay CVs < 8%. Using the automated platform, we successfully quantified the levels of deamidation of a humanized monoclonal antibody in cynomolgus monkeys over a time period of 12 weeks after administration. Moreover, we found that deamidation kinetics between in vivo samples and samples stressed in vitro at neutral pH were consistent, suggesting that the in vitro stress test may be used as a method to predict the liability to deamidation of therapeutic antibodies in vivo.

Fourier transform ion cyclotron resonance (FT ICR) mass spectrometry: Theory and simulations

Fourier transform ion cyclotron resonance (FT ICR) mass spectrometer offers highest resolving power and mass accuracy among all types of mass spectrometers. Its unique analytical characteristics made FT ICR important tool for proteomics, metabolomics, petroleomics, and investigation of complex mixtures. Signal acquisition in FT ICR MS takes long time (up to minutes). During this time ion-ion interaction considerably affects ion motion and result in decreasing of the resolving power. Understanding of those effects required complicated theory and supercomputer simulations but culminated in the invention of the ion trap with dynamic harmonization which demonstrated the highest resolving power ever achieved. In this review we summarize latest achievements in theory and simulation of FT ICR mass spectrometers.

A novel Fourier transform ion cyclotron resonance mass spectrometer with improved ion trapping and detection capabilities

A novel Fourier transform ion cyclotron resonance (FT-ICR) mass spectrometer has been developed for improved biomolecule analysis. A flared metal capillary and an electrodynamic ion funnel were installed in the source region of the instrument for improved ion transmission. The transfer quadrupole is divided into 19 segments, with the capacity for independent control of DC voltage biases for each segment. Restrained ion population transfer (RIPT) is used to transfer ions from the ion accumulation region to the ICR cell. The RIPT ion guide reduces mass discrimination that occurs as a result of time-of-flight effects associated with gated trapping. Increasing the number of applied DC bias voltages from 8 to 18 increases the number of ions that are effectively trapped in the ICR cell. The RIPT ion guide with a novel voltage profile applied during ion transfer provides a 3- to 4-fold increase in the number of ions that are trapped in the ICR cell compared with gated trapping for the same ion accumulation time period. A novel ICR cell was incorporated in the instrument to reduce radial electric field variation for ions with different z-axis oscillation amplitudes. With the ICR cell, called trapping ring electrode cell (TREC), we can tailor the shape of the trapping electric fields to reduce dephasing of coherent cyclotron motion of an excited ion packet. With TREC, nearly an order of magnitude increase in sensitivity is observed. The performance of the instrument with the combination of RIPT, TREC, flared inlet, and ion funnel is presented.

Restrained ion population transfer: a novel ion transfer method for mass spectrometry

Fourier transform ion cyclotron resonance (FTICR) mass spectrometers function such that the ion accumulation event takes place in a region of higher pressure outside the magnetic field which allows ions to be thermally cooled before being accelerated toward the ICR cell where they are decelerated and re-trapped. This transfer process suffers from mass discrimination due to time-of-flight effects. Also, trapping ions with substantial axial kinetic energy can decrease the performance of the FTICR instrument compared with the analysis of thermally cooled ions located at the trap center. Therefore, it is desirable to limit the energy imparted to the ions which results in lower applied trap plate potentials and reduces the spread in axial kinetic energy. The approach presented here for ion transfer, called restrained ion population transfer or RIPT, is designed to provide complete axial and radial containment of an ion population throughout the entire transfer process from the accumulation region to the ICR cell, eliminating mass discrimination associated with time-of-flight separation. This was accomplished by use of a number of quadrupole segments arranged in series with independent control of the direct current (DC) bias voltage applied to each segment of the quadrupole ion guide. The DC bias voltage is applied in such a way as to minimize the energy imparted to the ions allowing transfer of ions with low kinetic energy from the ion accumulation region to the ICR cell. Initial FTICR mass spectral data are presented that illustrate the feasibility of RIPT. A larger m/z range for a mixture of peptides is demonstrated compared with gated trapping. The increase in ion transfer time (3 ms to 130 ms) resulted in an approximately 11% decrease in the duty cycle; however this can be improved by simultaneously transferring multiple ion populations with RIPT. The technique was also modeled with SIMION 7.0 and simulation results that support our feasibility studies of the ion transfer process are presented.

Applications of mass spectrometry for the structural characterization of recombinant protein pharmaceuticals

Therapeutic proteins produced using recombinant DNA technologies are generally complex, heterogeneous, and subject to a variety of enzymatic or chemical modifications during expression, purification, and long-term storage. The use of mass spectrometry (MS) for the evaluation of recombinant protein sequence and structure provides detailed information regarding amino acid modifications and sequence alterations that have the potential to affect the safety and activity of therapeutic protein products. General MS approaches for the characterization of recombinant therapeutic protein products will be reviewed with particular attention given to the standard MS tools available in most biotechnology laboratories. A number of recent examples will be used to illustrate the utility of MS strategies for evaluation of recombinant protein heterogeneity resulting from post-translational modifications (PTMs), sequence variations generated from proteolysis or transcriptional/translational errors, and degradation products which are formed during processing or final product storage. Specific attention will be given to the MS characterization of monoclonal antibodies as a model system for large, glycosylated, recombinant proteins. Detailed examples highlighting the use of MS for the analysis of monoclonal antibody glycosylation, deamidation, and disulfide mapping will be used to illustrate the application of these techniques to a wide variety of heterogeneous therapeutic protein products. The potential use of MS to support the selection of cell line/clone selection and formulation development for therapeutic antibody products will also be discussed.

Realistic modeling of ion cloud motion in a Fourier transform ion cyclotron resonance cell by use of a particle-in-cell approach

Using a 'Particle-In-Cell' approach taken from plasma physics we have developed a new three-dimensional (3D) parallel computer code that today yields the highest possible accuracy of ion trajectory calculations in electromagnetic fields. This approach incorporates coulombic ion-ion and ion-image charge interactions into the calculation. The accuracy is achieved through the implementation of an improved algorithm (the so-called Boris algorithm) that mathematically eliminates cyclotron motion in a magnetic field from digital equations for ion motion dynamics. It facilitates the calculation of the cyclotron motion without numerical errors. At every time-step in the simulation the electric potential inside the cell is calculated by direct solution of Poisson's equation. Calculations are performed on a computational grid with up to 128 x 128 x 128 nodes using a fast Fourier transform algorithm. The ion populations in these simulations ranged from 1000 up to 1,000,000 ions. A maximum of 3,000,000 time-steps were employed in the ion trajectory calculations. This corresponds to an experimental detection time-scale of seconds. In addition to the ion trajectories integral time-domain signals and mass spectra were calculated. The phenomena observed include phase locking of particular m/z ions (high-resolution regime) inside larger ion clouds. A focus was placed on behavior of a cloud of ions of a single m/z value to understand the nature of Fourier transform ion cyclotron resonance (FTICR) resolution and mass accuracy in selected ion mode detection. The behavior of two and three ion clouds of different but close m/z was investigated as well. Peak coalescence effects were observed in both cases. Very complicated ion cloud dynamics in the case of three ion clouds was demonstrated. It was found that magnetic field does not influence phase locking for a cloud of ions of a single m/z. The ion cloud evolution time-scale is inversely proportional to magnetic field. The number of ions needed for peak coalescence depends quadratically on the magnetic field.

Long-lived electron capture dissociation product ions experience radical migration via hydrogen abstraction

To explore the mechanism of electron capture dissociation (ECD) of linear peptides, a set of 16-mer peptides were synthesized with deuterium labeled on the alpha-carbon position of four glycines. The ECD spectra of these peptides showed that such peptides exhibit a preference for the radical to migrate to the alpha-carbon position on glycine via hydrogen (or deuterium) abstraction before the final cleavage and generation of the detected product ions. The data show c-type fragment ions, ions corresponding to the radical cation of the c-type fragments, c*, and they also show c*-1 peaks in the deuterated peptides only. The presence of the c*-1 peaks is best explained by radical-mediated scrambling of the deuterium atoms in the long-lived, metastable, radical intermediate complex formed by initial electron capture, followed by dissociation of the complex. These data suggest the presence of at least two mechanisms, one slow, one fast. The abundance of H* and -CO losses from the precursor ion changed upon deuterium labeling indicating the presence of a kinetic isotope effect, which suggests that the values reported here represent an underestimation of radical migration and H/D scrambling in the observed fragments.

Observation of Increased Ion Cyclotron Resonance Signal Duration through Electric Field Perturbations

Ion motion in Fourier transform ion cyclotron resonance mass spectrometry (FTICR-MS) is complex and the subject of ongoing theoretical and experimental studies. Two predominant pathways for the loss of ICR signals are thought to include damping of cyclotron motion, in which ions lose kinetic energy and radially damp toward the center of the ICR cell, and dephasing of ion coherence, in which ions of like cyclotron frequency become distributed out of phase at similar cyclotron radii. Both mechanisms result in the loss of induced ion image current in FTICR-MS measurements and are normally inseparable during time-domain signal analysis. For conventional ICR measurements which take advantage of ion ensembles, maximization of the ion population size and density can produce the desired effect of increasing phase coherence of ions during cyclotron motion. However, this approach also presents the risk of coalescence of ion packets of similar frequencies. In general, ICR researchers in the past have lacked the tools necessary to distinguish or independently control dephasing and damping mechanisms for ICR signal loss. Nonetheless, the ability to impart greater phase coherence of ions in ICR measurements will allow significant advances in FTICR-MS research by improving the current understanding of ICR signal loss contributions of dephasing and damping of ion ensembles, increasing overall time-domain signal length, and possibly, resulting in more routine ultrahigh resolution measurements. The results presented here demonstrate the ability to employ a high density electron beam to perturb electric fields within the ICR cell during detection of cyclotron motion, in an approach we call electron-promoted ion coherence (EPIC). As such, EPIC reduces ICR signal degradation through loss of phase coherence, and much longer time-domain signals can be obtained. Our results demonstrate that time-domain signals can be extended by more than a factor of 4 with the implementation of EPIC, as compared to conventional experiments with otherwise identical conditions. The application of EPIC has also been observed to reduce the appearance of peak coalescence. These capabilities are not yet fully optimized nor fully understood in terms of the complex physics that underlies the enhancement. However, the enhanced time-domain signals can result in improved resolution in frequency-domain signals, and as such, this result is important for more efficient utilization of FTICR-MS. High resolution and accurate mass analysis are prime motivating factors in the application of advanced FTICR technology. We believe the approach presented here and derivatives from it may have significant benefit in future applications of advanced FTICR technology.

High-throughput one-bead-one-compound approach to peptide-encoded combinatorial libraries: MALDI-MS analysis of single TentaGel beads

The identification of pharmacologically promising compounds (lead compounds) from combinatorial libraries is frequently limited by the throughput of the analytical technique employed. Fourier transform mass spectrometry (FTMS) offers high sensitivity, mass accuracy (m/Deltam > 500 000), and sequencing capabilities. A rapid and efficient method for high-throughput analysis of single beads from peptide-encoded combinatorial libraries with matrix-assisted laser desorption/ionization (MALDI) mass spectrometry is presented. Encoding peptides on single beads are identified and structurally characterized by MALDI time-of-flight (TOF) and ultrahigh-resolution MALDI Fourier transform ion cyclotron resonance (FT-ICR) mass spectrometry. A strategy of on-probe sample preparation is developed to minimize handling of the beads.

Determination of the nature of naphthenic acids present in crude oils using nanospray Fourier transform ion cyclotron resonance mass spectrometry: the continued battle against corrosion

Recent research has shown that the corrosivity of naphthenic acids is related to their molecular mass and that the "total acid number" (TAN), traditionally used as an indicator of the naphthenic acid content of an oil, is not as reliable as first believed. The presence of naphthenic acids in crude oils leads to the corrosion of oil refinery equipment, with the oil industry incurring costs that will ultimately be passed on to the consumer. With regard to these concerns, mass spectrometry has been increasingly applied to the investigation of the naphthenic acid content of crude oils. To ascertain the nature of the species present, however, it is necessary to utilize an ionization technique that does not result in fragmentation, ensuring the detection only of molecular species which provide useful information about the sample constitution. In the following investigation, negative ion mode nanospray Fourier transform ion cyclotron resonance (FTICR) mass spectrometry has been applied to the analysis of crude oil samples, providing insight into the different acidic species that were present. Use of the negative ion mode to allow the selective observation of the naphthenic acids and the inherent high mass accuracy and ultrahigh resolution of FTICR mass spectrometry ensure that this technique is very well suited to the characterization of naphthenic acids within a crude oil sample. Determination of the nature of the naphthenic acids present provides vital information, such as the acids' sizes and composition, which may be used in the battle against corrosion and also used to fingerprint samples from different oil fields.

Direct detection and quantitation of He@C60 by ultrahigh-resolution Fourier transform ion cyclotron resonance mass spectrometry

In this paper, we report negative ion microelectrospray Fourier-transform ion cyclotron resonance (FT-ICR) mass spectrometry of C60 samples containing approximately 1% 3He@C60 or 4He@C60. Resolving He@C60- and 4He@C60- from C60 containing 3 or 4 13C instead of 12C atoms is technically challenging, because the target species are present in low relative abundance and are very close in mass. Nevertheless, we achieve baseline resolution of 3He@C60- from 13C3(12C57-) and 4He@C60- from 13C4(12C56-) in single-scan mass spectra obtained in broadband mode without preisolation of the ions of interest. The results constitute the first direct mass spectrometric observation of endohedral helium in a fullerene sample at this (low) level of incorporation. The results also demonstrate the feasibility of determining the extent of He incorporation from the FT-ICR mass spectral peak heights. The present measurements are in agreement with those obtained by the pyrolysis method [1-3]. Although limited in sensitivity, the mass spectral method is faster and easier than pyrolysis.

Broadband detection electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry to reveal enzymatically and chemically induced deamidation reactions within peptides

Among the numerous forms of chemical degradation of peptides or proteins, deamidation is one of the alterations observed most frequently. In this irreversible reaction, a glutamine or an asparagine side chain is hydrolyzed to glutamic acid or aspartic acid, respectively (conversion of NH2 to OH). Besides its influence in the deterioration of biotechnological and food products, deamidation represents a defined posttranslational modification reaction with respect to proteomics. Here mass spectrometric techniques play a leading role in determining posttranslational modifications. However, not all mass spectrometers are able to resolve signal differences of 0.0193 Da (mass difference of 12CO vs 13CNH) for singly charged molecules, the mass difference between the first isotopic signal of an asparagine/glutamine-containing peptide and the monoisotopic signal of the corresponding partially deamidated aspartate/glutamate derivative. To detect partial deamidation within peptides, advantage has been taken of the ability of Fourier transform ion cyclotron resonance mass spectrometry to perform very high mass resolution. In this work, we investigated up to triply charged ions produced by electrospray ionization using direct infusion. Although the special heterodyne detection mode enables higher mass resolution than the routinely used broadband detection, often only a small mass window can be investigated. Using broadband detection, we were able to resolve ions with a difference of m/z 0.0064 to detect partially deamidated peptides formed either enzymatically or under acidic and basic conditions.

Broad-band ion accumulation with an internal source MALDI-FTICR-MS

A new method is described which allows a broad mass range of ions from multiple MALDI events to be accumulated in an FIICR analyzer cell prior to detection. Signal intensity and signal-to-noise ratio are observed to grow in direct proportion to the number of laser shots, providing a substantial improvement to the analysis of low-level samples compared to more commonly used signal-averaging methods. In addition, calibrant ions desorbed from a separate sample spot can be added to the analyzer cell after an analyte population has been accumulated, providing an internal mass standard without the necessity of mixing calibrant and analyte. This method provides excellent mass accuracy by eliminating mass errors due to space charge effects.

Electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry

The basic principles and recent advances in electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry are reviewed. A brief history of electrospray ionization is provided, along with a complete technical description of the technique, electrospray ionization variations, and advantages. Next, the fundamental principles of Fourier transform ion cyclotron resonance mass spectrometry are covered, including ion cyclotron motion, ion cyclotron resonance excitation, and image current detection. Instrumentation and methods used to couple these techniques are then described. Topics include ion source configuration, ion transport through a strong magnetic field gradient, and ion trapping methods. The article concludes with selected applications that highlight the strengths of electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry.

Differential non-destructive image current detection in a fourier transform quadrupole ion trap

Dual-detector differential non-destructive Fourier transform detection in a quadrupole ion trap is shown to improve signal intensity and reduce noise compared with spectra recorded using a single detector. A larger area detector in each end-cap electrode is machined to fit its hyperbolic shape and so minimize field imperfections on the z-axis. Argon, acetophenone and bromobenzene spectra were recorded to allow a comparison between single- and dual-detector (differential) modes of detection and to demonstrate the improvement achieved with differential detection. Copyright 1999 John Wiley & Sons, Ltd.

Counting individual sulfur atoms in a protein by ultrahigh-resolution Fourier transform ion cyclotron resonance mass spectrometry: experimental resolution of isotopic fine structure in proteins

A typical molecular ion mass spectrum consists of a sum of signals from species of various possible isotopic compositions. Only the monoisotopic peak (e.g., all carbons are 12C; all nitrogens are 14N, etc.) has a unique elemental composition. Every other isotope peak at approximately integer multiples of approximately 1 Da higher in nominal mass represents a sum of contributions from isotope combinations differing by a few mDa (e.g., two 13C vs. two 15N vs. one 13C and one 15N vs. 34S, vs. 18O, etc., at approximately 2 Da higher in mass than the monoisotopic mass). At sufficiently high mass resolving power, each of these nominal-mass peaks resolves into its isotopic fine structure. Here, we report resolution of the isotopic fine structure of proteins up to 15.8 kDa (isotopic 13C,15N doubly depleted tumor suppressor protein, p16), made possible by electrospray ionization followed by ultrahigh-resolution Fourier transform ion cyclotron resonance mass analysis at 9.4 tesla. Further, a resolving power of m/Deltam50% approximately 8,000,000 has been achieved on bovine ubiquitin (8.6 kDa). These results represent a 10-fold increase in the highest mass at which isotopic fine structure previously had been observed. Finally, because isotopic fine structure reveals elemental composition directly, it can be used to confirm or determine molecular formula. For p16, for example, we were able to determine (5.1 +/- 0.3) the correct number (five) of sulfur atoms solely from the abundance ratio of the resolved 34S peak to the monoisotopic peak.