Automated sub-ppm mass accuracy on an ESI-TOF for use with drug discovery compound libraries

An automated, routine method to obtain sub-ppm accurate mass data on a benchtop electrospray ionization time-of-flight (ESI-TOF) mass spectrometer is described. Standards in the mass range 114 to 734 Da were analyzed over a 5-day period to demonstrate intra- and interday precision and mean mass accuracy less than 1 ppm. One hundred drug discovery pharmaceutical compounds were used to demonstrate an absolute average mass accuracy of 0.47 +/- 0.31 ppm. This is in contrast to previous reports of accurate mass analysis using time-of-flight mass spectrometry (TOFMS) technology that operates within 3 to 5 ppm. The same 100 samples were also analyzed using Fourier transform mass spectrometry (FTMS) technology and yielded comparable results to the TOFMS analysis.     

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.     

Exact mass measurement on an electrospray ionization time-of-flight mass spectrometer: error distribution and selective averaging

An automated, accurate and reliable way of acquiring and processing flow injection data for exact mass measurement using a bench-top electrospray ionization time-of-flight (ESI-TOF) mass spectrometer is described. Using Visual Basic programs, individual scans were selected objectively with restrictions on ion counts per second for both the compound of interest and the mass reference peaks. The selected "good scans" were then subjected to two different data-processing schemes ("combine-then-center" and "center-then-average"), and the results were compared at various ion count limit settings. It was found that, in general, the average of mass values from individual scans is more accurate than the centroid mass value of the combined (same) scans. In order to acquire a large number of good scans in one injection (to increase the sampling size for statistically valid averaging), an on-line dilution chamber was added to slow down the typically rapid mass chromatographic peak decay in flow-injection analysis. This simple addition worked well in automation without the need for manual sample dilution. In addition, by dissolving the reference compound directly into the mobile phase, manual syringe filling can be eliminated. Twenty-seven samples were analyzed with the new acquisition and process routines in positive electrospray ionization mode. For the best method found, the percentage of samples with RMS error less than 5 ppm was 100% with repetitive injection data (6 injections per sample), and 95% with single injection data. Afterwards, 31 other test samples were run (with MW ranging from 310 to 3493 Da, 21 samples in ESI+ and 10 in ESI- mode) and processed with similar parameters and 100% of them were mass-calculated to RMS error less than 5 ppm also.     

Development of a simple and reliable accurate mass liquid chromatography/electrospray ionization mass spectrometry method for high-resolution accurate mass determinations of new drug entities on a triple quadrupole mass spectrometer

Accurate mass measurements are used to determine the elemental composition and formulae of molecules to confirm their identity or to assist in their characterization. Currently, the most widely used techniques for measuring exact masses employ magnetic sector instruments, Fourier transform ion cyclotron resonance mass spectrometers and lower resolution instruments such as time-of-flight (TOF) and quadrupole-TOF. This paper reports the accurate mass measurement using a triple quadrupole mass spectrometer. Indeed, the recently introduced triple quadrupole mass spectrometer, with unique enhanced mass-resolution capability, has demonstrated simple data acquisition methods and requires few experiments to measure exact masses with accuracy and determines elemental compositions of both protonated and deprotonated molecules. All the accurate mass measurements were performed using both positive and negative electrospray ionization in enhanced mass-resolution mode (peak width of 0.1 Th FWMH). Several new drug entities were investigated as simulated unknowns and analyzed by means of an accurate mass liquid chromatography/electrospray ionization mass spectrometry (AM-LC/ESI-MS) method. The accurate mass measurements resulted in only one proposed elemental composition for all tested compounds, using reasonable elemental limits and mass tolerance for the calculation. Moreover, all the experimentally determined accurate mass measurements gave satisfactory results in terms of accuracy (lower than 5 ppm).     

Determination of ammonia, ethanol and acetic acid in solution using membrane introduction mass spectrometry

Methods have been developed to allow applications of membrane introduction mass spectrometry (MIMS) to monitor solution phase components of fermentation broths using electron ionization. The solutions are transported by flow injection analysis (FIA) through a direct insertion membrane probe, fitted with a silicone membrane in the sheet configuration. Analytes of interest pass through the membrane and are ionized by electron implant ionization. The compounds monitored are ammonia, acetic acid, and ethanol, with ammonia being detected as the monochloramine derivative which is generated at pH 10 upon addition of hypochlorite. Quantitation is achieved using external standard solutions. The dynamic range for the quantification of ammonia is 2-8000 ppm, and for ethanol and acetic acid 10-1000 ppm. This method provides rapid detection of analytes of interest, on-line monitoring capabilities, and the advantage of electron ionization. The introduction of samples into the mass spectrometer is achieved readily and automatically, the response time is a few seconds, and there are no memory effects.     

Immobilized artificial membrane chromatography coupled with atmospheric pressure ionization mass spectrometry

Liquid chromatographic separations on monolayers of cell membrane phospholipids covalently immobilized to silica particles at high molecular density is used for mimicking solute partitioning into biological membranes that generally correlates with membrane transport. This technique called immobilized artificial membrane chromatography usually employs ultraviolet (UV) detection where a single compound is analyzed in a chromatographic run limiting thereby its throughput for drug discovery applications. For coupling with atmospheric pressure ionization mass spectrometry, the phosphate-buffered saline mobile phase was replaced with one that used ammonium acetate as a volatile buffer. While atmospheric pressure chemical ionization accommodated a purely aqueous effluent, interfacing with electrospray ionization required effluent splitting and the addition of an organic modifier (5%, v/v, acetonitrile). Neuropeptide FF antagonists as early-phase drug candidates were used for the comparative evaluation of the methods. Whereas electrospray ionization produced essentially no fragment ions, several compounds involved in our study yielded low-abundance molecular ions with atmospheric pressure chemical ionization. The use of mass spectrometry yielded data that correlated well with those obtained by the method employing UV detection. Both atmospheric pressure ionization methods permitted the simultaneous determination of the k'(IAM), capacity factors and, therefore, an increased-throughput ranking of potential new leads emerged from the drug discovery process based on affinity to artificial membranes.     

Investigation into accurate mass capability of matrix-assisted laser desorption/ionization time-of-flight mass spectrometry, with respect to radical ion species

Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOFMS) has been shown to be an effective technique for the characterization of organometallic, coordination, and highly conjugated compounds. The preferred matrix is 2-[(2E)-3-(4-tert-butylphenyl)-2-methylprop-2-enylidene]malononitrile (DCTB), with radical ions observed. However, MALDI-TOFMS is generally not favored for accurate mass measurement. A specific method had to be developed for such compounds to assure the quality of our accurate mass results. Therefore, in this preliminary study, two methods of data acquisition, and both even-electron (EE+) ion and odd-electron (OE+.) radical ion mass calibration standards, have been investigated to establish the basic measurement technique. The benefit of this technique is demonstrated for a copper compound for which ions were observed by MALDI, but not by electrospray (ESI) or liquid secondary ion mass spectrometry (LSIMS); a mean mass accuracy error of -1.2 ppm was obtained.     

Investigation of uremic analytes in hemodialysate and their structural elucidation from accurate mass maps generated by a multi‐dimensional liquid chromatography/mass spectrometry approach

Historically, structural elucidation of unknown analytes by mass spectrometry alone has involved tandem mass spectrometry experiments using electron ionization. Most target molecules for bioanalysis in the metabolome are unsuitable for detection by this previous methodology. Recent publications have used high‐resolution accurate mass analysis using an LTQ‐Orbitrap with the more modern approach of electrospray ionization to identify new metabolites of known metabolic pathways. We have investigated the use of this methodology to build accurate mass fragmentation maps for the structural elucidation of unknown compounds. This has included the development and validation of a novel multi‐dimensional LC/MS/MS methodology to identify known uremic analytes in a clinical hemodialysate sample. Good inter‐ and intra‐day reproducibility of both chromatographic stages with a high degree of mass accuracy and precision was achieved with the multi‐dimensional liquid chromatography/tandem mass spectrometry (LC/MS/MS) system. Fragmentation maps were generated most successfully using collision‐induced dissociation (CID) as, unlike high‐energy CID (HCD), ions formed by this technique could be fragmented further. Structural elucidation is more challenging for large analytes >270 Da and distinguishing between isomers where their initial fragmentation pattern is insufficiently different. For small molecules (<200 Da), where fragmentation data may be obtained without loss of signal intensity, complete structures can be proposed from just the accurate mass fragmentation data. This methodology has led to the discovery of a selection of known uremic analytes and two completely novel moieties with chemical structural assignments made. Copyright © 2009 John Wiley & Sons, Ltd.     

Automated high resolution mass spectrometry for the synthetic chemist

Exact mass measurement at high resolution is an important tool alongside other spectroscopic methods to help confirm the structure of a novel compound prepared by the synthetic chemist. Exact mass measurement is used in the pharmaceutical industry to confirm the expected empirical formula of a product when problems have been experienced using elemental analysis. Because of the amount of manual intervention necessary when acquiring exact mass measurements, especially when using probe ionization techniques such as fast atom bombardment ionization or electron ionization, this method has been seen to be time consuming and labor intensive for the mass spectrometrist. An automated high resolution mass spectrometric method has been developed at Pfizer Central Research which has streamlined exact mass measurement. The method, which uses electrospray ionization on a double focusing mass spectrometer, is described. The samples are analyzed using a flow injection technique, with sodiated polyethylene glycol present in the mobile phase to provide mass reference peaks. The data are acquired and processed using a macro developed “in house.” This automated technique can process 15–20 samples an hour including data processing and report generation, using very small amounts of compound (∼25 μg), but more importantly it can be left to run unattended overnight. This allows the instrument to be used for more complex experiments during the day when it is important to have a mass spectrometrist present. The results presented here demonstrate that this method gives exact mass measurements within an acceptable limit of 5 ppm, and the variation on one sample, injected 10 times, is not excessively high (−1.8 to +1.6 mDa).     

Atmospheric pressure ionization–tandem mass spectrometry of the phenicol drug family

In this work, the mass spectrometry behaviour of the veterinary drug family of phenicols, including chloramphenicol (CAP) and its related compounds thiamphenicol (TAP), florfenicol (FF) and FF amine (FFA), was studied. Several atmospheric pressure ionization sources, electrospray (ESI), atmospheric pressure chemical ionization and atmospheric pressure photoionization were compared. In all atmospheric pressure ionization sources, CAP, TAP and FF were ionized in both positive and negative modes; while for the metabolite FFA, only positive ionization was possible. In general, in positive mode, [M + H]⁺ dominated the mass spectrum for FFA, while the other compounds, CAP, TAP and FF, with lower proton affinity showed intense adducts with species present in the mobile phase. In negative mode, ESI and atmospheric pressure photoionization showed the deprotonated molecule [M–H]^?, while atmospheric pressure chemical ionization provided the radical molecular ion by electron capture. All these ions were characterized by tandem mass spectrometry using the combined information obtained by multistage mass spectrometry and high‐resolution mass spectrometry in a quadrupole‐Orbitrap instrument. In general, the fragmentation occurred via cyclization and losses or fragmentation of the N‐(alkyl)acetamide group, and common fragmentation pathways were established for this family of compounds. A new chemical structure for the product ion at m/z 257 for CAP, on the basis of the MS³ and MS⁴ spectra is proposed. Thermally assisted ESI and selected reaction monitoring are proposed for the determination of these compounds by ultra high‐performance liquid chromatography coupled to tandem mass spectrometry, achieving instrumental detection limits down to 0.1 pg. Copyright © 2013 John Wiley & Sons, Ltd.     

Parallel high-throughput accurate mass measurement using a nine-channel multiplexed electrospray liquid chromatography ultraviolet time-of-flight mass spectrometry system

A nine-channel multiplexed electrospray (MUX) liquid chromatography ultraviolet time-of-flight mass spectrometry (LC/UV/TOFMS) system has been used to simultaneously measure accurate masses of eluting components from eight parallel gradient LC columns. Accuracies better than 5 and 10 ppm were achieved for 50 and 80% of samples, respectively, from a single batch analysis of ten plates (960 samples) of a Fmoc-Asp(OtBu)-OH and reserpine mixture. Combinatorial library compounds were analyzed using this parallel high-throughput system in both positive and negative modes to rigorously verify expected products and identify side products. A mass accuracy of 10 ppm root mean square (RMS) is routinely obtained for combinatorial library samples from this high-throughput accurate mass LC/MS system followed by automated data processing. This mass accuracy is critical in revealing combinatorial synthesis problems that would be missed by unit mass measurement.     

Isotopic pattern and accurate mass determination in urine drug screening by liquid chromatography/time-of-flight mass spectrometry

An efficient method was developed for toxicological drug screening in urine by liquid chromatography coupled with electrospray ionization time-of-flight mass spectrometry. The method relies on a large target database of exact monoisotopic masses representing the elemental formulae of reference drugs and their metabolites. Mass spectral identification is based on matching measured accurate mass and isotopic pattern (SigmaFit) of a sample component with those in the database. Data post-processing software was developed for automated reporting of findings in an easily interpretable form. The mean and median of SigmaFit for true-positive findings were 0.0066 and 0.0051, respectively. The mean and median of mass error absolute values for true-positive findings were 2.51 and 2.17 ppm, respectively, corresponding to 0.65 and 0.60 mTh. For routine screening practice, a SigmaFit tolerance of 0.03 and a mass tolerance of 10 ppm were chosen. Ion abundance differences from urine extracts did not affect the accuracy of the automatically acquired SigmaFit or mass values. The results show that isotopic pattern matching by SigmaFit is a powerful means of identification in addition to accurate mass measurement.     

Compatibility of electron ionization and soft ionization methods in gas chromatography/orthogonal time‐of‐flight mass spectrometry

Orthogonal acceleration time‐of‐flight (oa‐TOF) mass spectrometry (MS) was coupled to gas chromatography (GC) to measure ion yields (ratio of ion counts to number of neutrals entering the ion source) and signal‐to‐noise (S/N) in the electron ionization (EI) mode (hard ionization) as well as in the soft ionization modes of chemical ionization (CI), electron capture negative ion chemical ionization (NICI) and field ionization (FI). Mass accuracies of the EI and FI modes were also investigated. Sixteen structurally diverse volatile organic compounds were chosen for this study. The oa‐TOF mass analyzer is highly suited for FI MS and provided an opportunity to compare the sensitivity of this ionization method to the more conventional ionization methods. Compared to the widely used quadrupole mass filter, the oa‐TOF platform offers significantly greater mass accuracy and therefore the possibility of determining the empirical formula of analytes. The findings of this study showed that, for the instrument used, EI generated the most ions with the exception of compounds able to form negative ions readily. Lower ion yields in the FI mode were generally observed but the chromatograms displayed greater S/N and in many cases gave spectra dominated by a molecular ion. Ion counts in CI are limited by the very small apertures required to maintain sufficiently high pressures in the ionization chamber. Mass accuracy for molecular and fragment ions was attainable at close to manufacturer's specifications, thus providing useful information on molecular ions and neutral losses. The data presented also suggests a potentially useful instrumental combination would result if EI and FI spectra could be collected simultaneously or in alternate scans during GC/MS. Copyright © 2009 John Wiley & Sons, Ltd.     

Automated peak tracking for comprehensive impurity profiling in orthogonal liquid chromatographic separation using mass spectrometric detection

The presence and quantity of impurities in pharmaceutical drugs can have a significant impact on their quality and safety. With the continuous pressure for increased industry productivity, there is urgent need for a systematic and comprehensive drug impurity profiling strategy. We report here our development of the fully automated Comprehensive Orthogonal Method Evaluation Technology (COMET) system. The system includes five columns, seven orthogonal HPLC methods, and hyphenated UV-MS detections, which provides automated generic impurities screening for any drug sample. An automated MS peak tracking approach by program-based mass spectral interpretation is devised to unambiguously track impurities among all orthogonal HPLC methods. The program passes electro-spray ionization mass spectra (ESI-MS) through four sequential decision-making mass ion tests and determines molecular weights for every peak. The system reduces the time required to obtain impurity profile from weeks to days, while the automated MS peak tracking takes only minutes to interpret all MS spectral data of interest. Up-to-date, impurity contents of 56 in-development drug candidate samples have all been successfully illustrated by COMET, which contained more than 500 chemical entities. The program is able to track more than 80% of the compounds automatically with majority of the failure due to insufficient ionization for some impurities by ESI. This system is well suited for efficient drug development and ensuring the quality and safety of drug products.     

The automation of a commercial Fourier transform mass spectrometer to provide a quick and robust method for determining exact mass for the synthetic chemist

Automation of a commercially available Fourier transform ion cyclotron resonance (FT-ICR) mass spectrometer for the routine analysis of the synthetic products from high-speed chemistry is described. The automation includes software written by the instrument manufacturer and in-house developed software; allowing electronic submission of samples from the chemist and e-mailing of results back to the chemist. The use of samples of relatively high concentration (ca 1 mg x mL(-1)) is possible due to the protocol that has been developed, which includes dilution by the autosampler during sample injection. Though high concentrations are used for speed and convenience the amount of sample consumed is still small ca 15 microg per injection. The results from this method have been shown to be both accurate (average error +/- 0.91 ppm) and precise (-0.70 ppm to 2.26 ppm). The system is capable of analysing up to 800 samples per 24 hours. As high speed chemistry becomes more highly utilised within discovery the number of samples requiring accurate mass analysis will rise, and the method we have described will prevent high resolution mass spectrometry becoming the bottleneck in new chemical entity production. The accuracy and precision demonstrated by this method allows high confidence levels in assigned molecular formulae for expected compounds and reduces the number of possible formulae to consider when working with a compound that is not the desired product of a given reaction.     

Using accurate mass electrospray ionization-time-of-flight mass spectrometry with in-source collision-induced dissociation to sequence peptide mixtures

Although data-dependent LC-MS-MS with database searching has become au courant for identifying proteins, the technique is constrained by duty-cycle inefficiency and the inability of most tandem mass analyzers to accurately measure peptide product ion masses. In this work, a novel approach is presented for simultaneous peptide fragmentation and accurate mass measurement using in-source collision-induced dissociation (CID) on electrospray ionization (ESI)-time-of-flight (TOF) MS. By employing internal mass reference compounds, mass measurement accuracy within +/-5 ppm for tryptic peptide precursors and +/-10 ppm for most sequence-specific product ions was consistently achieved. Analysis of a complex solution containing several digested protein standards did not adversely affect instrument performance.     

Investigation of collision‐induced dissociations involving odd‐electron ion formation under positive electrospray ionization conditions using accurate mass

Collision induced dissociation (CID) has been extensively used for structure elucidation. CID in the electrospray ionization (ESI) and atmospheric pressure chemical ionization (APCI) modes has been found to generate mostly even‐electron fragment ions while it has been occasionally reported to form odd‐electron free radical ions. However, the structural requirements and the fragmentation mechanisms for free‐radical CIDs have not been well characterized in the literature. For this purpose, we studied a series of aromatic and non‐aromatic compounds such as sulfonamides, N‐aryl amides, tert‐butyl‐substituted aromatic compounds, aryl alkyl ethers, and O‐alkyl aryl oximes using the LTQ? and LTQ Orbitrap? linear ion trap mass spectrometers. The accurate measurement of the fragment ion masses established the unambiguous assignment of the fragment structures resulting from the test compounds. Our results showed that free radical fragmentation is structure dependent and is to a large extent correlated with the neighboring groups in the structures that stabilize the newly formed free radical ions. Copyright © 2010 John Wiley & Sons, Ltd.     

微波等离子体常压解吸电离质谱法快速检测化学药剂中的活性成分

构建了一种新型电离源--微波等离子体常压解吸电离源, 等离子体由微波等离子体炬产生, 工作气体为Ar气, 微波频率为2450 MHz, 该离子源可在大气压下产生稳定的等离子体. 将该电离源与具有大气压接口的Corsair API-TOF型飞行时间质谱仪结合, 实现了化学药剂中单一或多种主要活性成分的快速分析, 在手动进样条件下, 检测速度可达每小时360次. 在微波等离子体环境下, 活性物质成盐时母体化合物上结合的酸性物质可被直接除掉, 谱图中主要离子为母体化合物的准分子离子[M+H]⁺, 便于识别. 微波等离子体常压解吸电离质谱法无需化学试剂, 具有实时、 快速及无污染等特点, 为药剂研发及化学工业提供了一种新的检测技术.     

Chemical ionization and electron impact mass spectrometry of some organophosphonate compounds

The application of gas chromatography chemical ionization mass spectrometry to the determination of a variety of alkyl alkylphosphonates, phosphonofluoridates, phosphonothiolates and an amidophosphorocyanidate is described. Comparison is made between the electron ionization and chemical ionization mass spectrometry of these compounds. Chemical ionization mass spectrometry is shown to enhance the capability for identification, especially when a limited sample is available. Results indicate that methane is highly useful for obtaining protonated molecular ions and association ions (formed by the transfer of a reactant ion to a sample molecule) as well as meaningful fragment ions. Ionizing ethylene and isobutane gives protonated molecular ions as base peaks for all of the compounds studied, including those where a lower abundance of the [MH]₊ ion is found via methane chemical ionization mass spectrometry. Ethylene is superior to isobutane on the basis of its effectiveness for serving as both a carrier and a reagent gas and gives better sensitivity. Although not an intrinsic part of this present study, analytical sensitivities in the subnanogram range were found.     

The development of an NMR chemical shift prediction application with the accuracy necessary to grade proton NMR spectra for identity

We have developed an NMR chemical shift prediction system that enables high throughput automatic grading of NMR spectra. In support of high throughput synthetic efforts for our drug discovery program, a rapid and accurate analysis for identity was needed. The system was designed and implemented to take advantage of the NMR assignments that had been tabulated on internally generated research compounds. The system has been operational for four years and has been used in conjunction with an internally written grading program to successfully analyze several hundred thousand samples based only on their 1D ¹H spectrum. A focused test of the system's accuracy on 1006 molecules demonstrated the ability to estimate the proton chemical shift with an average error of +/?0.16 ppm. This level of chemical shift accuracy allows for reliable structure confirmation by automated analysis using only proton NMR. Copyright © 2009 John Wiley & Sons, Ltd.