Intercomparison study on accurate mass measurement of small molecules in mass spectrometry

The results from an intercomparison of accurate mass measurement of a small molecule (molecular weight 475 Da) across a broad range of mass spectrometers are reported. The intercomparison was designed to evaluate the relative capabilities and the optimum methodology of the diverse range of mass spectrometers currently used to record accurate mass measurements. The data will be used as a basis for developing guidance on accurate mass measurement. The need for guidance has resulted from the continued growth in the use of accurate mass measurements for assignment of elemental formula in the chemical and biochemical industries. This has been fuelled by a number of factors and includes the rapid pace of instrument development, which has enabled accurate mass measurements to be made in a less costly, yet robust fashion. The data from the intercomparison will allow us to compare those protocols that produced excellent accuracy and precision with those that produced poorer accuracy and/or precision for each type of mass spectrometer. The key points for best practice will then be established from this comparison for each type of mass spectrometer and accurate mass measurement technique. A compound was sent to the participating laboratories (in the UK, Europe, and USA), the identity of which was not revealed. Each laboratory was asked to record a minimum of five repeat mass measurements of the molecular species using their local protocols and their preferred ionization technique or techniques. To the best of our knowledge there were no interfering (unresolved) ions that originated from the sample. A questionnaire was also completed with the experimental work. The information from the questionnaires was used to evaluate the protocols used to record the measurements. Forty-five laboratories have reported their results. To summarize the performance of mass spectrometers in the intercomparison, magnetic sector field mass spectrometers used in peak matching mode and FTMS reported the highest mean mass measurement accuracy (88 and 83%, respectively, achieved < or =1 ppm). Magnetic sector field mass spectrometers used in voltage scanning produced 60% of the mean mass measurements with accuracy < or =1 ppm. Magnetic sector field mass spectrometers used in magnet scanning modes, quadrupole-TOF and TOF instruments generally achieved mean mass measurement accuracy between 5 and 10 ppm. The two low resolution triple quadrupoles used in the inter-comparison produced mean mass measurement accuracy of <2 ppm. The precision of the data from each instrument and experiment type is an important consideration when evaluating their relative capabilities. Using both the precision and accuracy, it will be possible to define the uncertainty associated with the elemental formulae derived from accurate mass measurements. Therefore, a thorough statistical evaluation of the data is underway and will be presented in a subsequent publication.     

A discussion on mass resolution in secondary ion mass spectrometry

Mass resolution is a very important parameter for mass spectrometry. It is necessary to compare the mass resolution between the newly developed TOF-SIMS and the conventionally high-performance magnetic SIMS. However, the definitions of mass resolution for these two types of instruments are quite different. Whether it is possible to compare mass resolution and how to do such comparison is a challenge. This problem was raised officially during the 2012 ISO/TC 201 meeting at Tampa, Florida, the United States and the long-term cooperation with ISO started afterwards. The definition of mass resolution is one of the most important and fundamental problems for mass spectrometry and should attract significant attention. Here, some detail discussions on mass resolution as well as the related experimental studies in the past few years, including the collaborations with ISO/TC 201/SC6 and SC1 are summarized. This summary covers the common problem for almost all the current existing and still used definitions of mass resolution. A reasonable new definition for mass resolution considering the peak shape or resolution function has been proposed, which has also been confirmed by using experimental studies of the mass resolution comparison between TOF and magnetic SIMS. This study lays a foundation for the future mass resolution comparisons between different mass spectrometry.     

High mass accuracy and high mass resolving power FT-ICR secondary ion mass spectrometry for biological tissue imaging

Biological tissue imaging by secondary ion mass spectrometry has seen rapid development with the commercial availability of polyatomic primary ion sources. Endogenous lipids and other small bio-molecules can now be routinely mapped on the sub-micrometer scale. Such experiments are typically performed on time-of-flight mass spectrometers for high sensitivity and high repetition rate imaging. However, such mass analyzers lack the mass resolving power to ensure separation of isobaric ions and the mass accuracy for elemental formula assignment based on exact mass measurement. We have recently reported a secondary ion mass spectrometer with the combination of a C₆₀ primary ion gun with a Fourier transform ion cyclotron resonance mass spectrometer (FT-ICR MS) for high mass resolving power, high mass measurement accuracy, and tandem mass spectrometry capabilities. In this work, high specificity and high sensitivity secondary ion FT-ICR MS was applied to chemical imaging of biological tissue. An entire rat brain tissue was measured with 150 μm spatial resolution (75 μm primary ion spot size) with mass resolving power (m/Δm _50%) of 67,500 (at m/z 750) and root-mean-square measurement accuracy less than two parts-per-million for intact phospholipids, small molecules and fragments. For the first time, ultra-high mass resolving power SIMS has been demonstrated, with m/Δm _50%?>?3,000,000. Higher spatial resolution capabilities of the platform were tested at a spatial resolution of 20 μm. The results represent order of magnitude improvements in mass resolving power and mass measurement accuracy for SIMS imaging and the promise of the platform for ultra-high mass resolving power and high spatial resolution imaging.

Improved mass accuracy for tandem mass spectrometry

With the emergence of top-down proteomics, the ability to achieve high mass measurement accuracy on tandem MS/MS data will be beneficial for protein identification and characterization. (FT-ICR) Fourier transform ion cyclotron resonance mass spectrometers are the ideal instruments to perform these experiments with their ability to provide high resolution and mass accuracy. A major limitation to mass measurement accuracy in FT-ICR instruments arises from the occurrence of space charge effects. These space charge effects shift the cyclotron frequency of the ions, which compromises the mass measurement accuracy. While several methods have been developed that correct these space charge effects, they have limitations when applied to MS/MS experiments. It has already been shown that additional information inherent in electrospray spectra can be used for improved mass measurement accuracy with the use of a computer algorithm called DeCAL (deconvolution of Coulombic affected linearity). This paper highlights a new application of the strategy for improved mass accuracy in tandem mass analysis. The results show a significant improvement in mass measurement accuracy on complex electron capture dissociation spectra of proteins. We also demonstrate how the improvement in mass accuracy can increase the confidence in protein identification from the fragment masses of proteins acquired in MS/MS experiments.     

Hybrid mass spectrometers for tandem mass spectrometry

Mass spectrometers that use different types of analyzers for the first and second stages of mass analysis in tandem mass spectrometry (MS/MS) experiments are often referred to as "hybrid" mass spectrometers. The general goal in the design of a hybrid instrument is to combine different performance characteristics offered by various types of analyzers into one mass spectrometer. These performance characteristics may include mass resolving power, the ion kinetic energy for collision-induced dissociation, and speed of analysis. This paper provides a review of the development of hybrid instruments over the last 30 years for analytical applications.     

Dynamic range of mass accuracy in LTQ orbitrap hybrid mass spectrometer

Using a novel orbitrap mass spectrometer, the authors investigate the dynamic range over which accurate masses can be determined (extent of mass accuracy) for short duration experiments typical for LC/MS. A linear ion trap is used to selectively fill an intermediate ion storage device (C-trap) with ions of interest, following which the ensemble of ions is injected into an orbitrap mass analyzer and analyzed using image current detection and fast Fourier transformation. Using this technique, it is possible to generate ion populations with intraspectrum intensity ranges up to 10(4). All measurements (including ion accumulation and image current detection) were performed in less than 1 s at a resolving power of 30,000. It was shown that 5-ppm mass accuracy of the orbitrap mass analyzer is reached with >95% probability at a dynamic range of more than 5000, which is at least an order of magnitude higher than typical values for time-of-flight instruments. Due to the high resolving power of the orbitrap, accurate mass of an ion could be determined when the signal was reliably distinguished from noise (S/Np-p)>2...3).     

Flow injection of the lock mass standard for accurate mass measurement in electrospray ionization time-of-flight mass spectrometry coupled with liquid chromatography

A method of flow injection of the lock mass for accurate mass measurement using electrospray ionization time-of-flight mass spectrometry is described. The reference compound is introduced in the chromatographic effluent via a six-port valve placed post-column, prior to the split connector. Flow injection is performed in such a way that the reference elution peak is superimposed in the total ion current and partially overlaps that of the investigated analyte, allowing independent ionization of the two compounds and thus accurate mass measurement with no ion suppression effects. Different lock mass molecules can be injected in a single analytical run to target various analytes. The performance of this methodology is demonstrated in both isocratic and gradient liquid chromatography modes. The molecular ion of the flow-injected lock mass could also be used as a reference for mass measurement of the in-source fragments of the analytes. Good mass accuracy, within 4 mDa of the theoretical values, was obtained.     

Identification of the 'wrong' active pharmaceutical ingredient in a counterfeit Halfan drug product using accurate mass electrospray ionisation mass spectrometry,accurate mass tandem mass spectrometry and liquid chromatography/mass spectrometry

Methodology is presented for identifying an unknown active (pharmaceutical) ingredient (AI) in a counterfeit drug product. A range of mass spectrometric techniques, i.e., accurate mass mass spectrometry, tandem mass spectrometry (MS/MS) and liquid chromatography/mass spectrometry (LC/MS), has been employed to determine the AI in a counterfeit Halfan suspension, an antimalarial drug. In particular, use of LockSpray accurate mass MS/MS allowed identification of parts of the molecule from fragments, hence limiting the number of possible elemental compositions for the nominal mass of 278 found for the AI in the counterfeit product. The analysis of the isotope pattern observed for the protonated molecule further reduced the number of possible elemental compositions. A literature search for readily commercially available compounds of molecular formula C(12)H(14)N(4)O(2)S suggested that the AI was either sulfamethazine or sulfisomidine. An LC/MS separation of those two compounds and reference MS/MS spectra obtained for sulfamethazine and sulfisomidine led to the conclusion that the AI in the counterfeit Halfan suspension is sulfamethazine, which is an antibacterial agent.     

The use of mass defect in modern mass spectrometry

Mass defect is defined as the difference between a compound's exact mass and its nominal mass. This concept has been increasingly used in mass spectrometry over the years, mainly due to the growing use of high resolution mass spectrometers capable of exact mass measurements in many application areas in analytical and bioanalytical chemistry. This article is meant as an introduction to the different uses of mass defect in applications using modern MS instrumentation. Visualizing complex mass spectra may be simplified with the concept of Kendrick mass by plotting nominal mass as a function of Kendrick mass defect, based on hydrocarbons subunits, as well as slight variations on this theme. Mass defect filtering of complex MS data has been used for selectively detecting compounds of interest, including drugs and their metabolites or endogenous compounds such as peptides and small molecule metabolites. Several strategies have been applied for labeling analytes with reagents containing unique mass defect features, thus shifting molecules into a less noisy area in the mass spectrum, thus increasing their detectability, especially in the area of proteomics. All these concepts will be covered to introduce the interested reader to the plethora of possibilities of mass defect analysis of high resolution mass spectra. Copyright © 2012 John Wiley & Sons, Ltd.     

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.     

Sample preparation for high throughput accurate mass analysis by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry

An automated sample preparation for high throughput accurate mass determinations by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOFMS) has been developed. Sample preparation was performed with an automated workstation and automated mass analyses were performed with a commercial MALDI-TOF mass spectrometer. The method was tested with a 41-sample library. MALDI-TOFMS was found to give the needed sensitivity, accurate mass measurement, and soft ionization necessary for structure confirmation, even of mixtures. A mass accuracy of 5 ppm or less was obtained in over 80% of known compound measurements. A mass accuracy better than 10 ppm was obtained for all measurements of known compounds. Analyses of parallel synthesis products resulted in 77% of the measurements with a mass accuracy of 5 ppm or better.     

A general method for quantitative measurement of molecular mass distribution by mass spectrometry

A method is presented to test whether the conversion of the mass spectrum of a polydisperse analyte to its molecular mass distribution is quantitative. Mixtures of samples with different average molecular masses, coupled with a Taylor’s expansion mathematical formalism, were used to ascertain the reliability of molecular mass distributions derived from mass spectra. Additionally, the method describes how the molecular mass distributions may be corrected if the degree of mass bias is within certain defined limits. This method was demonstrated on polydisperse samples of C₆₀ fullerenes functionalized with ethylpyrrolidine groups measured by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry; however, it is applicable to any polydisperse analyte and mass spectrometric method as long as spectrum resolution allows individual oligomers to be identified. Mass spectra of the derivatized fullerenes taken in positive ion mode were shown to give an accurate measurement of the molecular mass distribution while those taken in negative ion mode were not. Differences in the mechanisms for ion formation are used to explain the discrepancy.     

Comparison of conventional and enhanced mass resolution triple-quadrupole mass spectrometers for discovery bioanalytical applications

A new triple-quadrupole mass spectrometry (MS) system with enhanced resolution capabilities has recently become available. In order to evaluate the performance of this new instrument for drug discovery assays, both the linearity and the limit of detection were compared in the positive electrospray ionization (ESI) mode with those of a conventional triple-quadrupole instrument supplied by the same manufacturer. For these studies, spiked mouse plasma standard samples were split and assayed by each instrument, which allowed for a direct comparison of the two systems. In the unit mass resolution mode, the new mass spectrometer was found to be at least ten-fold more sensitive than the conventional instrument. The sensitivity of the new mass spectrometer under the enhanced mass resolution mode was found to be even better by another factor of two. For the test compound, the linear dynamic range was found to be 0.05-5000 ng/mL for the new instrument as compared with 2.5-5000 ng/mL for the conventional mass spectrometer.     

Spectral counting robust on high mass accuracy mass spectrometers

Mass spectrometry is central to shotgun proteomics, an application that seeks to quantify as much of the total protein complement of a biological sample as possible. The high mass accuracy, resolution, capacity and scan rate of modern mass spectrometers have greatly facilitated this endeavor. The sum of MS to MS/MS transitions in tandem mass spectrometry, the spectral count (SC), of a peptide has been shown to be a reliable estimate of its relative abundance. However, when using SCs, optimal MS configurations are crucial in order to maximize the number of low abundant proteins quantified while keeping the estimates for the highly abundant proteins within the linear dynamic range. In this study, LC/MS/MS analysis was performed using an LTQ‐OrbiTrap on a sample containing many highly abundant proteins. Tuning the LTQ‐OrbiTrap mass spectrometer to minimize redundant MS/MS acquisition and to maximize resolution of the proteome by accurately measured m/z ratios resulted in an appreciable increase in quantified low abundant proteins. An exclusion duration of 90 s and an exclusion width of 10 ppm were found best of those tested. The spectral count of individual proteins was found to be highly reproducible and protein abundance ratios were not affected by the different settings that were applied. We conclude that on a high mass accuracy instrument spectral counting is a robust measure of protein abundance even for samples containing many highly abundant proteins and that tuning dynamic exclusion parameters appreciably improves the number of proteins that can be reliably quantified. Copyright © 2010 John Wiley & Sons, Ltd.     

Application of fractional mass for the identification of peptide-oligonucleotide cross-links by mass spectrometry

A method has been developed to identify oligonucleotide-peptide heteroconjugates by accurate mass measurements using MS. The fractional mass (the decimal fraction mass value following the monoisotopic nominal mass) for peptides and oligonucleotides is different due to their differing molecular compositions. This property has been used to develop the general conditions necessary to differentiate peptides and oligonucleotides from oligonucleotide-peptide heteroconjugates. Peptides and oligonucleotides generated by the theoretical digestion of various proteins and nucleic acids were plotted as nominal mass versus fractional mass. Such plots reveal that three nucleotides cross-linked to a peptide produce enough change in the fractional mass to be recognized from non-cross-linked peptides at the same nominal mass. Experimentally, a Cytochrome c digest was spiked with an oligonucleotide-peptide heteroconjugate and conditions for analyzing the sample using liquid chromatography (LC)-MS were optimized. Upon analysis of this mixture, all detected masses were plotted on a fractional mass plot and the heteroconjugate could be readily distinguished from non-cross-linked peptides. The method developed here can be incorporated into a general proteomics-like scheme for identifying protein-nucleic acid cross-links, and this method is equally applicable to characterizing cross-links generated from protein-DNA and protein-RNA complexes.     

Enhanced mass resolution tandem mass spectrometry method for 2,3,7,8-tetrachlorodibenzo-p-dioxin detection with ion trap mass spectrometry using high damping gas pressure

Damping gas flow was optimized for 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) determination using ion trap mass spectrometer. A tandem mass spectrometry (MS-MS) method with better than unit-mass resolution (mass width, 0.3 u) was developed at a damping gas flow of 1.5 ml/min and a collision-induced dissociation (CID) voltage of 3.30 V. The relative standard deviation (R.S.D.) at the enhanced resolution was 2.9% in 24 h of consecutive injections. The detection limit was significantly improved because the efficiency of both precursor ion trapping and fragmentation increased with the damping gas flow. Product ion yield was 4.5 times higher and limit of detection was 3.2 times lower than at the default flow (0.3 ml/min and 1.65 V).     

Tandem mass spectrometric accurate mass performance of time-of-flight and Fourier transform ion cyclotron resonance mass spectrometry: a case study with pyridine derivatives

The interpretation of mass spectra is a key process during compound identification, and the combination of tandem mass spectrometry (MS/MS) with high-accuracy mass measurements may deliver crucial information on the identity of a compound. Obtaining accurate mass data of fragment ions in MS/MS reveals the particular problem of mass calibration when a lockmass, which is frequently used to obtain accurate masses in MS, is absent. An alternative technique is to recalibrate the MS/MS spectrum using a reference MS/MS spectrum acquired under the same conditions. We have tested and validated this approach using a hybrid quadrupole/orthogonal acceleration reflectron-type time-of-flight (TOF) mass spectrometer. The results were compared with those obtained under similar conditions on a Fourier transform ion cyclotron resonance (FT-ICR) instrument. We found that the mass accuracy observed with such an "external" recalibration on the TOF instrument in MS/MS is identical to what can be obtained on a similar instrument operating in one-dimensional MS mode using the lockmass technique. However, mass accuracy in both cases is one order of magnitude inferior to that obtained using FTMS, and also inferior to that observed using sector field MS when operated at comparable resolution. Nevertheless, for small (<200 Da) molecules, this mass accuracy was still sufficient to have the "true" elemental composition identified as the first hit in about 70% of all cases. It was possible to elucidate the fragmentation mechanism of eight azaheterocycles containing a pyridine moiety, where the accurate mass data from the TOF instrument allowed distinction between two alternative fragmentation pathways.     

High mass accuracy in-source collision-induced dissociation tandem mass spectrometry and multi-step mass spectrometry as complementary tools for fragmentation studies of quaternary ammonium herbicides

Fragmentation studies using both an ion-trap mass analyzer and a hybrid quadrupole time-of-flight (Q-TOF) mass spectrometer were performed in order to establish the fragmentation pathways of organic molecules. A general strategy combining MSn data (n = 1-4) in an ion-trap analyzer with tandem mass spectrometry and in-source collision-induced dissociation tandem mass spectrometry (CID MS/MS) in a Q-TOF instrument was applied. The MSn data were used to propose a tentative fragmentation pathway following genealogical relationships. When several assignments were possible, MS/MS and in-source CID MS/MS (Q-TOF) allowed the elemental compositions of the fragments to be confirmed. Quaternary ammonium herbicides (quats) were used as test compounds and their fragmentation pathways were established. The elemental composition of the fragments was confirmed using the TOF analyzer with relative errors <0.0023 Da. Some fragments previously reported in the literature were reassigned taking advantage of the high mass resolution and accuracy of the Q-TOF instrument, which made it possible to solve losses where nitrogen was involved.     

Polynomial mass bias functions for the internal standardization of isotope ratio measurements by multi-collector inductively coupled plasma mass spectrometry

The development and application of a calibration strategy for routine isotope ratio analysis by multi-collector inductively coupled plasma mass spectrometry (ICP-MS) is described and assessed. Internal standardization was used to account for the mass dependant determinate error (mass bias). The general solution for polynomial isotope ratio mass bias functions for use with internal standardization and isotope ratio measurements by multi-collector inductively coupled plasma mass spectrometry was derived. The resulting linear isotope ratio mass bias function was demonstrated to be mathematically consistent and experimentally realistic for the analysis of acidified aqueous solutions of analyte and internal standard elements (clean solutions) by multi-collector inductively coupled plasma mass spectrometry.     

Generation of mass tags by the inherent electrochemistry of electrospray for protein mass spectrometry

We present herein a review of our work on the on-line electrochemical generation of mass tags toward cysteine residues in peptides and proteins. Taking advantage of the inherent electrochemical nature of electrospray generated from a microfabricated microspray emitter, selective probes for cysteine were developed and tested for on-line nonquantitative mass tagging of peptides and proteins. The nonquantitative aspect of the covalent tagging thus allows direct counting of free cysteines in the mass spectrum of a biomolecule through additional adduct peaks. Several substituted hydroquinones were investigated in terms of electrochemical properties, and their usefulness for on-line mass tagging during microspray experiments were assessed with L-cysteine, peptides, and intact proteins. Complementarily, numerical simulations were performed to properly understand the respective roles of mass transport, kinetics of electrochemical-chemical reactions, and design of the microspray emitter in the mass tagging overall efficiency. Finally, the on-line electrochemical tagging of cysteine residues was applied to the analysis of tryptic peptides of purified model proteins for protein identification through peptide mass fingerprinting.