Influence of internal standard charge state on the accuracy of mass measurements in orthogonal acceleration time-of-flight mass spectrometers

Accuracy of mass measurements performed in orthogonal acceleration time-of-flight (oa-TOF) mass spectrometers highly depends on the quality of the signal and the internal calibration. The use of two reference compounds which bracket the targeted unknown, give rise to ions with sufficient signal-to-noise ratio while avoiding detector saturation and produce signals of similar intensity as compared to the target is a common requirement which allow a 5 ppm accuracy on a routine basis. Ion charge state is demonstrated here to be an additional and particularly critical parameter. Using internal references of lower charge state than the target ion systematically yielded overestimated data. Errors measured for quadruply charged molecules were in the range 16-18 ppm when mass calibrants were singly charged ions while accuracy was below 5 ppm when references and target ions were in the same charge state. Magnitude of errors was found to increase with the difference in charge state. This phenomenon arises from the orthogonal acceleration of ions in the TOF analyzer, an interface implemented in all TOF mass spectrometers to accommodate continuous beam ionization sources. Copyright (c) 2007 John Wiley & Sons, Ltd.     

Closely spaced external standard: a universal method of achieving 5 ppm mass accuracy over the entire MALDI plate in axial matrix-assisted laser desorption/ionization time-of-flight mass spectrometry

Close deposition of the sample and external standard was used in axial matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOFMS) to achieve mass accuracy equivalent to that obtained with an internal standard across the entire MALDI plate. In this work, the sample and external standard were deposited by continuous deposition in separate traces, each approximately 200 micro m wide. The dependence of the mass accuracy on the distance between the sample and standard traces was determined across a MALDI target plate with dimensions of 57.5 mm x 57.0 mm by varying the gap between the traces from 100 micro m to 4 mm. During acquisition, two adjacent traces were alternately irradiated with a 200-Hz laser, such that the peaks in the resulting mass spectra combined the sample and external standard. Ion suppression was not observed even when the peptide concentrations in the two traces differed by more than two orders of magnitude. The five peaks from the external standard trace were used in a four-term mass calibration of the masses of the sample trace. The average accuracy across the whole plate with this method was 5 ppm when peaks of the sample trace had signal-to-noise ratios of at least 30 and the gap between the traces was approximately 100 micro m. This approach was applied to determining peptide masses of a reversed-phase liquid chromatographic (LC) separation of a tryptic digest of beta-galactosidase deposited as a long serpentine trace across the MALDI plate, with accuracy comparable to that obtainable using internal calibration. In addition, the eluent from reversed-phase LC separation of a strong cation-exchange fraction containing tryptic peptides from a yeast lysate along with the closely placed external standard was deposited on the MALDI plate. The data obtained in the MS and MS/MS modes on a MALDI-TOF/TOF mass spectrometer were combined and used in database searching with MASCOT. Since the significant score is a function of mass accuracy in the MS mode, database searching with high mass accuracy reduced the number of false positives and also added peptides which otherwise would have been eliminated at lower mass accuracy (false negatives).     

A dual electrospray ionization source combined with hexapole accumulation to achieve high mass accuracy of biopolymers in Fourier transform ion cyclotron resonance mass spectrometry

A dual electrospray ionization (ESI) source employed with hexapole accumulation and gated trapping provides a novel method of using an internal standard to achieve high mass accuracies in Fourier transform ion cyclotron resonance mass spectrometry. Two ESI emitters are sequentially positioned in front of the heated metal capillary inlet by a solenoid fitted to an XYZ micromanipulator; one emitter contains the analyte(s) of interest and the other an internal standard. A 5 V transistor-transistor logic pulse from the data station controls the solenoid by means of a solid-state relay so that matching of spectral peak intensities (i.e., analyte and internal standard intensities) can be accomplished by adjusting the hexapole accumulation time for each species. Polythymidine, d(pT)18, was used as the internal standard for all studies reported here. The absolute average error for an internally calibrated 15-mer oligonucleotide (theoretical monoisotopic mass = 4548.769 Da) was -1.1 ppm (external calibration: 41 ppm) with a standard deviation of +/-3.0 ppm (external calibration: +/-24 ppm) for a total of 25 spectra obtained at various hexapole accumulation time ratios. Linear least squares regression analysis was carried out and revealed a linear dependence of the magnitudes of the peak height ratios (analyte/internal standard) vs. hexapole accumulation time ratios (analyte/internal standard) which is described by the following equation: y = 0.45 x - 0.02. The fitted line had a %RSD of the slope of 28% with an R2 of 0.93. The applicability of this methodology was extended to a polymerase chain reaction product with a theoretical average molecular mass of 50,849.20 Da. With the internal standard, d(pT)18, an absolute average error of -8.9 ppm (external calibration: 44 ppm) based on five measurements was achieved with a standard deviation of 11 ppm (external calibration: +/-36 ppm), thus illustrating this method's use for characterizing large biomolecules such as those encountered in genomics and proteomics related research.     

Mass correlated acceleration in a reflectron MALDI TOF mass spectrometer: an approach for enhanced resolution over a broad mass range

Compared to continuous extraction, pulsed extraction (PE) of ions formed by matrix-assisted laser desorption/ionization (MALDI) in time-of-flight (TOF) mass spectrometers significantly improves mass resolution. Parameters such as extraction voltage, delay time, and correction pulse must be varied, however, to achieve optimum mass resolution over a broad mass range because the PE method is mass dependent. We previously reported a novel method, mass correlated acceleration (MCA), which we have now combined with a reflectron MALDI TOF mass spectrometer to further enhance mass resolution over a broader mass range. Unlike the PE method, MCA is not mass dependent and high resolution mass spectra can be achieved with a single tuning of instrument parameters. The ions may be brought into focus simultaneously, i.e., the multi-channel recording advantage can be more fully realized. The MCA dual-stage ion source design includes an extraction pulse region and an acceleration region that contains a time-dependent waveform correlated with mass. We demonstrate the validity of this novel technique with applications in peptide mixture analysis and protein digests of lysozyme and bovine serum albumin.     

Identification of glucuronide conjugates of ketobemidone and its phase I metabolites in human urine utilizing accurate mass and tandem time-of-flight mass spectrometry

The glucuronide conjugates of ketobemidone, norketobemidone and hydroxymethoxyketobemidone were identified in human urine post-intravenous administration of Ketogan Novum. The human urine was extracted on a mixed-mode solid-phase micro-column before analysis with liquid chromatography/electrospray ionization time-of-flight mass spectrometry (LC/ESI-TOF-MS) and tandem MS (MS/MS). Accurate mass and collision-induced dissociation product ion spectra were used for identification of the glucuronide conjugates. Two different TOF mass spectrometers were used and the accurate mass measurements were performed on three separate days with each instrument. The accuracy of the mass measurements was better than 2.1 ppm for two out of three conjugates and the inter-day relative standard deviation was within +/-0.00049%. The MS/MS fragmentation patterns of the conjugates were in accordance with those of the synthetic aglycones and included peaks originating from the [M + H](+) ion of the respective aglycone.     

Accurate mass measurements and ultrahigh-resolution: evaluation of different mass spectrometers for daily routine analysis of small molecules in negative electrospray ionization mode

Six mass spectrometers based on different mass analyzer technologies, such as time-of-flight (TOF), hybrid quadrupole-TOF (Q-TOF), orbitrap, Fourier transform ion cyclotron resonance (FT-ICR), and triple quadrupole (QqQ), installed at independent laboratories have been tested during a single day of work for the analysis of small molecules in negative electrospray ionization (ESI) mode. The uncertainty in the mass measurements obtained from each mass spectrometer has been determined by taking the precision and accuracy of replicate measurements into account. The present study is focused on calibration processes (before, after, and during the mass measurement), the resolving power of the mass spectrometers, and the data processing for obtaining elemental formulae. The mass range between m/z 100 and 600 has been evaluated with a mix of four standards. This mass range includes small molecules usually detected in food and environmental samples. Negative ESI has been tested as there is almost no data on accurate mass (AM) measurements in this mode. Moreover, it has been used because it is the ESI mode for analysis of many compounds, such as pharmaceutical, herbicides, and fluorinated compounds. Natural organic matter has been used to demonstrate the significance of ultrahigh-resolution in complex mixtures. Sub-millidalton accuracy and precision have been obtained with Q-TOF, FT-ICR, and orbitrap achieving equivalent results. Poorer accuracy and precision have been obtained with the QqQ used: 11 mDa root-mean-square error and 6–11 mDa standard deviation. Some advice and requirements for daily AM routine analysis are also discussed here.     

New methodical and instrumental developments in laser ablation inductively coupled plasma mass spectrometry

Many tasks in bulk analysis, micro analysis and depth profile analysis can be solved advantageously by laser ablation inductively coupled plasma mass spectrometry (Laser ICP-MS) in particular, when both the chemical and elemental distributions in the sample are to be determined. However, the analyst has to take into account that the analytical precision and accuracy of the Laser ICP-MS is influenced decisively by signal standardization, the homogeneity of the samples as well as calibration standards and the mass-spectrometric measuring mode, which is usually sequential when performed with scanning mass spectrometers such as quadrupol- or sector-based instruments. Using the ablated mass as standard, an excellent level of the analytical precision and accuracy (relative standard deviation R.S.D.<0.5%) has been obtained for homogeneous sample materials such as alloys. For inhomogeneous samples, such as pressed pellets, a statistical test is described, which is based upon the auto-correlation function to characterize the sample inhomogeneity. The application of the test allows us to calculate the representative mass for the quantitative analysis at previously defined analytical precision. In the instrumental part of the paper a new type of an ICP—time-of-flight (TOF) mass spectrometer—is described, constructed and built up in our laboratory. For fast signal counting an application-specific integrated circuit (ASIC) was developed, which permits a time resolution of 1 ns. The analytical performance of the TOF when used in combination with an ICP is demonstrated in terms of resolution, ion extraction rate, detection limits and dynamic range. The determination of ³⁹K⁺ and ⁴⁰Ca⁺ at trace level can be realized in a cool plasma condition (high central gas flow) only with a small interference by ⁴⁰Ar⁺. Detection limits of 23 elements were measured with typical values in the lower nanograms per liter range. The ion extraction rates, measured for a sample mass of 1 ng in terms of counts per second divided by the relative isotope abundance, are one order of magnitude higher than those obtained with a quadrupol-based instrument.     

Sub parts-per-million mass measurement accuracy of intact proteins and product ions achieved using a dual electrospray ionization quadrupole fourier transform ion cyclotron resonance mass spectrometer

High mass measurement accuracy (MMA) is demonstrated for intact proteins and subsequent collision-induced dissociation product ions using internal calibration. Internal calibration was accomplished using a dual electrospray ionization source coupled with a hybrid quadrupole Fourier transform ion cyclotron resonance (Q-FT-ICR) mass spectrometer. Initially, analyte ions generated via the first electrospray (ESI) emitter are isolated and dissociated in the external quadrupole. This event is followed by a simultaneous switch to the calibrant ion ESI emitter and a disablement of the isolation and activation of the external quadrupole such that a broad m/z range of calibrant ions are accumulated before injecting the analyte/calibrant ion mixture into the ICR cell. Two different internal calibrant solutions were utilized in these studies to evaluate this approach for the top-down characterization of melittin and ubiquitin. While external calibration of protein fragments resulted in absolute MMA greater than 16 ppm, internal standardization significantly improved upon the MMA of both the intact proteins and their products ions which ranged from -2.0 ppm to 1.1 ppm, with an average of -0.9 ppm. This method requires limited modification to ESI-FT-ICR mass spectrometers and is applicable for both positive and negative ionization modes.     

A modified internal lock-mass method for calibration of the product ions derived from sustained off-resonance irradiation collision-induced dissociation using a Fourier transform mass spectrometer

A modified internal lock-mass calibration method is introduced for improving the mass measurement accuracy of the product ion spectra derived from sustained off-resonance irradiation collision-induced dissociation (SORI-CID) Fourier transform ion cyclotron resonance (FTICR) mass spectrometry. This method involves an initial external calibration of the Fourier transform mass spectrometer to obtain the initial A- and B-terms for the equation (f(i) = A/(m/z)(i) + B). The A-term is adjusted by using an empirical relationship between the up-shift of the A-term and the pulse-gas duration, whereas the B-term is adjusted by using the mass of the unfragmented precursor ion from the SORI-CID mass spectrum of the unknown sample as internal lock-mass. These adjusted A- and B-terms are then used to provide exact mass SORI-CID calibration for the unknown sample. The modified internal lock-mass method achieved average mass measurement accuracy of approximately 3 ppm which is significantly better than that of the conventional internal lock-mass calibration ( approximately 9 ppm) and is approaching that of the internal calibration ( approximately 2 ppm) and requires no addition of internal calibrant or instrumental modifications.     

Mass-correlated pulsed extraction: Theoretical analysis and implementation with a linear matrix-assisted laser desorption/ionization time of flight mass spectrometer

The pulsed extraction (PE) of ions produced by matrix-assisted laser desorption/ionization in time-of-flight mass spectrometers greatly improves mass resolution but, unfortunately, this method is mass dependent. Here we report an approach to expand the capabilities of the PE method so as to provide uniform focusing conditions over a wide mass range. Along with an extraction pulse, an additional pulse is applied to correct the mass dependency of the standard PE method. We describe the algorithm for derivation of this correction pulse waveform, where the first-order focusing conditions are valid all along the mass region of interest. Experimental verification of this method for correction of ion velocities demonstrated better mass resolution than standard PE over a wide mass range.     

Linear time-of-flight mass spectrometers: Postsource pulse focusing conditions and mass scale

The condition to cancel aberrations that result from initial ion velocities and length of ionization process by postsource pulse focusing in linear time-of-flight mass spectrometers is derived. The ion arrival time distribution as a function of ion mass is given, which permits mass scale calibration. Simple formulas allow calculation of the voltage needed for postsource pulse focusing and the limits of the mass range where the focusing action is felt. The theory is illustrated for a specific instrument case.     

Fragmentation of (LiF)(n)Li(+) clusters in the acceleration region of TOF spectrometers

The binary decay of ionized clusters in the extraction region of time-of-flight (TOF) spectrometers is analyzed. The dynamics of the fragments is studied and an analytical expression for the TOF peak shape is deduced; simulations are performed for linear spectrometers of different configurations. The questions addressed refer to the design of TOF spectrometers to improve their accuracy in the determination of metastable-state mean lives, the identification of precursor masses and the investigation of desorption mechanisms. As an illustration, the method is applied to the decay of positive ion clusters (LiF)(n)Li(+) for both spontaneous and collision-induced fragmentation processes. No clear evidence of delayed emission is found. The bumps observed in the TOF spectrum are due to tertiary ions emitted by the LiF target sputtered by secondary ions produced in the grid, a process that increases with higher target bias. The main cluster fragmentation observed is (LiF)(3)Li(+*) decaying preferentially into (LiF)Li(+); the data are compatible with a spontaneous decay of metastable clusters with mean lives of 20-30 ns.     

Atmospheric pressure ionization time-of-flight mass spectrometry coupled with fast liquid chromatography for quantitation and accurate mass measurement of five pharmaceutical drugs in human plasma

The quantitative determination and accurate mass measurement of five tricyclic amine pharmaceutical drugs (doxepin, desipramine, imipramine, amitriptyline and trimipramine) fortified in human plasma within a per sample run time of 18 s was accomplished by atmospheric pressure ionization (API) time-of-flight (TOF) mass spectrometry using a turboIonspray liquid chromatography/mass spectrometry (LC/MS) interface coupled with high-performance liquid chromatography (HPLC). The relatively short HPLC separation (18 s) was achieved using a short C18 column (15 x 2.1 mm i.d.) with a high aqueous mobile phase maintained at a flow-rate of 1.4 ml min(-1). An acquisition speed of 0.2 s per spectrum accommodates these fast separation conditions. This method employs a one-step liquid-liquid extraction procedure to isolate the five tricyclic amines from biological matrix components The overall extraction recovery was 75% for desipramine and >90% for the other four tricyclic amines. The lower level of quantitation was 1-2 ng ml(-1) for each compound. The calibration curve was linear from 2 to 100 ng ml(-1) for desipramine and from 1 to 50 ng ml(-1) for the other four tricyclic amines. A deuterated internal standard, imipramine-d3, was used for all five tricyclic amines. Acceptable intra- and inter-assay precision (1.0-17.7%) and accuracy (0.2-14.5%) were obtained. The linear dynamic range was extended to 200 based on a software upgrade for correcting ion current detection saturation. The accurate masses of the five tricyclic amines were determined by on-line LC/TOFMS analyses of biological extracts using two-point internal mass calibration. This was done by infusing a reference standard, Jeffamine D230, post-column into the HPLC effluent. All results showed a mass error not greater than 9 ppm for all the target compounds. These results were obtained from both synthetic mixtures when as little as 100 pg were injected or extracts of spiked human plasma samples with analytical concentration as low as 5 ng ml(-1). The factors influencing accurate mass measurements are discussed.     

Advanced Mass Calibration and Visualization for FT-ICR Mass Spectrometry Imaging

Mass spectrometry imaging by Fourier transform ion cyclotron resonance (FT-ICR) yields hundreds of unique peaks, many of which cannot be resolved by lower performance mass spectrometers. The high mass accuracy and high mass resolving power allow confident identification of small molecules and lipids directly from biological tissue sections. Here, calibration strategies for FT-ICR MS imaging were investigated. Sub-parts-per-million mass accuracy is demonstrated over an entire tissue section. Ion abundance fluctuations are corrected by addition of total and relative ion abundances for a root-mean-square error of 0.158?ppm on 16,764 peaks. A new approach for visualization of FT-ICR MS imaging data at high resolution is presented. The ??Mosaic Datacube?? provides a flexible means to visualize the entire mass range at a mass spectral bin width of 0.001?Da. The high resolution Mosaic Datacube resolves spectral features not visible at lower bin widths, while retaining the high mass accuracy from the calibration methods discussed.     

Optimization of mass spectrometers using the adaptive particle swarm algorithm

Optimization of mass spectrometers using the adaptive particle swarm algorithm (APSA) is described along with implementations for ion optical simulations and various time-of-flight (TOF) instruments. The need for in situ self optimization is addressed through discussion of the reflectron TOF mass spectrometer (RTOF) on the European Space Agency mission Rosetta. In addition, a tool for optimization of laboratory mass spectrometers is presented and tested on two different instruments. After the application of APSA optimization, a substantial increase in performance for mass spectrometers that have manually been tuned for several weeks or months is demonstrated.     

Quantification and application of a liquid chromatography–tandem mass spectrometric method for the determination of WKYMVm peptide in rat using solid‐phase extraction

A liquid chromatographic–electrospray ionization–time‐of‐flight/mass spectrometric (LC‐ESI‐TOF/MS) method was developed and applied for the determination of WKYMVm peptide in rat plasma to support preclinical pharmacokinetics studies. The method consisted of micro‐elution solid‐phase extraction (SPE) for sample preparation and LC‐ESI‐TOF/MS in the positive ion mode for analysis. Phenanthroline (10 mg/mL) was added to rat blood immediately for plasma preparation followed by addition of trace amount of 2 m hydrogen chloride to plasma before SPE for stability of WKYMVm peptide. Then sample preparation using micro‐elution SPE was performed with verapamil as an internal standard. A quadratic regression (weighted 1/concentration²), with the equation y = ax² + bx + c was used to fit calibration curves over the concentration range of 3.02–2200 ng/mL for WKYMVm peptide. The quantification run met the acceptance criteria of ±25% accuracy and precision values. For quality control samples at 15, 165 and 1820 ng/mL from the quantification experiment, the within‐run and the between‐run accuracy ranged from 92.5 to 123.4% with precision values ≤15.1% for WKYMVm peptide from the nominal values. This novel LC‐ESI‐TOF/MS method was successfully applied to evaluate the pharmacokinetics of WKYMVm peptide in rat plasma.     

Improved mass accuracy for higher mass peptides by using SWIFT excitation for MALDI-FTICR mass spectrometry

Stepwise-external calibration has previously been shown to produce sub part-per-million (ppm) mass accuracy for the MALDI-FTICR/MS analyses of peptides up to m/z 2500. The present work extends these results to ions up to m/z 4000. Mass measurement errors for ions of higher mass-to-charge are larger than for ions below m/z 2500 when using conventional chirp excitation to detect ions. Mass accuracy obtained by using stored waveform inverse Fourier transform (SWIFT) excitation was evaluated and compared with chirp excitation. Analysis of measurement errors reveals that SWIFT excitation provides smaller deviations from the calibration equation and better mass accuracy than chirp excitation for a wide mass range and for widely varying ion populations.     

Viscosalines B1,2 and E1,2: Challenging New 3‐Alkyl Pyridinium Alkaloids from the Marine Sponge Haliclona viscosa

Four new 3‐alkyl pyridinium alkaloids, the viscosalines B₁ ( 1 a ), B₂ ( 1 b ), E₁ ( 2 a ), and E₂ ( 2 b ), were isolated from the Arctic sponge Haliclona viscosa. The structure elucidation of these isomeric compounds was challenging due to ambiguous fragments that derive during “standard” mass spectrometric fragmentation experiments. The final structure elucidation relied on the use of a combination of synthesis, liquid chromatography, and mass spectrometry. Three different mass spectrometers were used to differentiate between the synthetic structural isomers: a time‐of‐flight (TOF) mass spectrometer and two ion‐trap mass spectrometers with different ion‐transfer technologies (i.e., skimmer versus funnel optics). Although at first none of the spectrometers returned spectra that permitted structure elucidation, all three mass spectrometers provided analysis that successfully differentiated between the isomers after thorough method optimization. The use of in‐source collision‐induced dissociation (CID) with the ion trap and TOF instrument returned the most interesting results. The mode of fragmentation of the viscosalines under different experimental conditions is described herein. After successful optimization of the mass spectrometric method applied, the chromatographic method was improved to distinguish the previously inseparable isomers. Finally, both the liquid chromatography and mass spectrometric methods were applied to the natural products and the results compared to those from the synthetic compounds.     

Ideal velocity focusing in a reflectron time-of-flight mass spectrometer

A single-stage ion mirror in a time-of-flight (TOF) mass spectrometer (MS) can perform first order velocity focusing of ions initially located at a start focal plane while second order velocity focusing can be achieved using a double-stage reflectron. The situation is quite different when an ion source extraction field is taken into account. In this case which is common in any practical matrix-assisted laser desorption/ionization (MALDI) TOF-MS a single-stage reflectron, for example, cannot perform velocity focusing at all. In this paper an exact, analytic solution for an electric field inside a one-dimensional reflectron has been found to achieve universal temporal focusing of ions having an initial velocity distribution. The general solution is valid for arbitrary electric field distributions in the upstream (from the ion source to the reflectron) and downstream (from the reflectron to an ion detector) regions and in a decelerating part of the reflectron of a reflectron TOF mass spectrometer. The results obtained are especially useful for designing MALDI reflectron TOF mass spectrometers in which the initial velocity distribution of MALDI ions is the major limiting factor for achieving high mass resolution. Using analytical expressions obtained for an arbitrary case, convenient working formulas are derived for the case of a reflectron TOF-MS with a dual-stage extraction ion source. The special case of a MALDI reflectron TOF-MS with an ion source having a low acceleration voltage (or large extraction region) is considered. The formulas derived correct the effect of the acceleration regions in a MALDI ion source and after the reflectron before detecting ions.     

An improved calibration method for the matrix-assisted laser desorption/ionization-Fourier transform ion cyclotron resononance analysis of 15N-metabolically- labeled proteome digests using a mass difference approach

High mass measurement accuracy of peptides in enzymatic digests is critical for confident protein identification and characterization in proteomics research. Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR-MS) can provide low or sub-ppm mass accuracy and ultrahigh resolving power. While for ESI-FT-ICR-MS, the mass accuracy is generally 1 ppm or better, with matrix-assisted laser desorption/ionization (MALDI)-FT-ICR-MS, the mass errors can vary from sub-ppm with internal calibration to over 100 ppm with conventional external calibration. A novel calibration method for (15)N-metabolically labeled peptides from a batch digest of a proteome is described which corrects for space charge induced frequency shifts in FT-ICR spectra without using an internal calibrant. This strategy utilizes the information from the mass difference between the (14)N/(15)N peptide peak pairs to correct for space charge induced mass shifts after data collection. A procedure for performing the mass correction has been written into a computer program and has been successfully applied to high-performance liquid chromatography-MALDI-FT- ICR-MS measurement of (15)N-metabolic labeled proteomes. We have achieved an average measured mass error of 1.0 ppm and a standard deviation of 3.5 ppm for 900 peptides from 68 MALDI-FT-ICR mass spectra of the proteolytic digest of a proteome from Methanococcus maripaludis.