On-line acquisition, analysis, and e-mailing of high-resolution exact-mass electron impact/chemical ionization mass spectrometry data acquired using an automated direct probe

A complete automation package has been developed for data acquisition, processing, interpreting, and e-mailing of high-resolution exact-mass electron impact (EI) and chemical ionization (CI) mass spectrometry data. A commercial high performance magnetic sector mass spectrometer equipped with a commercial programmable robotic direct probe was used. The software package contains a series of modules that automatically performs all the functions necessary for data reduction and reporting. In sequential order, these functions include downloading of sample information from a corporate database, creation of a sample list, acquisition of high-resolution exact-mass data, processing of the data, generation of an exact-mass report, e-mailing of the results to the requesting chemists, and finally shutting down of the instrument. The performance of the system was evaluated with nearly 500 samples. The system was found to be reliable and robust with a small average systematic mass error of −0.47 mmu and a standard deviation of 1.61 mmu.     

Data-controlled automation of liquid chromatography/tandem mass spectrometry analysis of peptide mixtures

The structural characterization of proteins and peptides isolated in minute quantities requires the most efficient use of available sample. A mass spectrometer data system was programmed to continuously evaluate incoming liquid chromatography/mass spectrometry data against a user-defined array of information. The resulting conclusions were used to automatically set and modify acquisition parameters in real time to collect collision-induced dissociation spectra for selected ions (tandem mass spectrometry). This approach has provided a mechanism to target specific subsets of masses in a complex mixture and/or to discriminate selectively against masses that are known or not of interest. Masses of contaminants or peptide masses derived from known proteins can be automatically recorded and removed from further consideration for collision-induced dissociation analysis. Once recorded, these “libraries” of masses can be used across multiple analyses. This technique directs the mass spectrometer data system to focus on the analysis of masses significant to the user, even if their signal intensities are well below the intensities of contaminating masses. When combined with a database search program to correlate tandem mass spectra to known protein sequences, the identity of the protein can be established unequivocally by using less than 100 fmol of sample.     

AutoScan: an automated workstation for rapid determination of mass and tandem mass spectrometry conditions for quantitative bioanalytical mass spectrometry

An automated flow injection analysis (FIA) mass spectrometry system (AutoScan) was developed to allow rapid unattended determination of optimal conditions during mass (ms) and tandem mass spectrometry (ms/ms) on new chemical entities (NCEs) arranged in 96-well plates. The 96-well plate is placed on the deck of a modified Gilson Multiprobe autosampler for injection into a PE Sciex API 2000 triple quadrupole mass spectrometer. A customized software interface is used to create the necessary scan experiments by associating each 96-well plate of NCEs to be scanned with an index file containing data on the identity of each analyte and its expected molecular weight. Analytes are injected four at a time into a custom injection manifold and conventional mass spectra are acquired in both polarities (+/-) using an alternating positive/negative Q1 scan function. The software determines the optimal polarity and definitive precursor ion for all analytes and uses the results to build the injection sequence for product ion scanning. The samples are automatically re-injected under MS/MS conditions, and product ion scans that loop among different collision energies are collected for each analyte. The resulting data are processed automatically and the optimal MS/MS transitions for each analyte are selected. A color-coded graphical interface facilitates data review. Any unusual ion transitions or transposition errors made during plate preparation are noted and corrected. Complete MS and MS/MS conditions are obtained for 96 compounds in about one hour and the resulting data are available for download as sample control injection sequence files.     

A linear time-of-flight mass analyzer for thermal ionization cavity mass spectrometry

In this paper we report the basic design characteristics, typical operating parameters, and isotope ratio performance of an orthogonal acceleration linear thermal ionization cavity time-of-flight mass spectrometer (TIC-TOFMS). The present system is capable of mass resolution of 750–850 (FWHM) over a wide range of masses, and can generate and analyze multi-element spectra from sub-μg samples (solids and solution residues) in <30–45 min. The optimum precision (1σ) of isotope ratios determined from 60–80 spectra (each the average of 600 individual spectra) is 0.2–0.4% R.S.D., and is limited by the instrument drift, dead time and the data acquisition and processing capabilities of the 8-bit digital oscilloscope used to collect the data. Isotope ratio accuracy (1σ, per mass unit) for major isotopes is typically <±1.0%.     

Increased throughput in quantitative bioanalysis using parallel-column liquid chromatography with mass spectrometric detection

The feasibility of quantitative bioanalysis by parallel-column liquid chromatography in conjunction with a conventional single-source electrospray mass spectrometer has been investigated using plasma samples containing a drug and its three metabolites. Within a single chromatographic run time, sample injections were made alternately onto each of two analytical columns in parallel at specified intervals, with a mass spectrometer data file opened at every injection. Thus, the mass spectrometer collected data from two sample injections into separate data files within a single chromatographic run time. Therefore, without sacrificing the chromatographic separation or the selected reaction monitoring (SRM) dwell time, the sample throughput was increased by a factor of two. Comparing the method validation results obtained using the two-column system with those obtained using the corresponding conventional single-column approach, the methods on the two systems were found to be equivalent in terms of accuracy and precision. The parallel-column system is simple and can be implemented using existing laboratory equipment with no additional capital outlays. A parallel-column system configured in this manner can be used not only for the within-a-run analysis of two samples containing two different sets of chemical entities, but also for the within-a-run analysis of two samples containing the same set of chemical entities.     

Quantitation of small molecules using high‐resolution accurate mass spectrometers – a different approach for analysis of biological samples

The quantitative capabilities of a linear ion trap high‐resolution mass spectrometer (LTQ‐Orbitrap™) were investigated using full scan mode bracketing the m/z range of the ions of interest and utilizing a mass resolution (mass/FWHM) of 15000. Extracted ion chromatograms using a mass window of ±5–10 mmu centering on the theoretical m/z of each analyte were generated and used for quantitation. The quantitative performance of the LTQ‐Orbitrap™ was compared with that of a triple quadrupole (API 4000) operating using selected reaction monitoring (SRM) detection. Comparable assay precision, accuracy, linearity and sensitivity were observed for both approaches. The concentrations of actual study samples from 15 Merck drug candidates reported by the two methods were statistically equivalent. Unlike SRM being a tandem mass spectrometric (MS/MS)‐based detection method, a high resolution mass spectrometer operated in full scan does not need MS/MS optimization. This approach not only provides quantitative results for compounds of interest, but also will afford data on other analytes present in the sample. An example of the identification of a major circulating metabolite for a preclinical development study is demonstrated. Copyright © 2009 John Wiley & Sons, Ltd.     

'Information-Based-Acquisition' (IBA) technique with an ion-trap/time-of-flight mass spectrometer for high-throughput and reliable protein profiling

Highly complex protein mixtures can be analyzed after proteolysis using liquid chromatography/mass spectrometry (LC/MS). In an LC/MS run, intense peptide ions originating from high-abundance proteins are preferentially analyzed using tandem mass spectrometry (MS(2)), so obtaining the MS(2) spectra of peptide ions from low-abundance proteins is difficult even if such ions are detected. Furthermore, the MS(2) spectra may produce insufficient information to identify the peptides or proteins. To solve these problems, we have developed a real-time optimization technique for MS(2), called the Information-Based-Acquisition (IBA) system. In a preliminary LC/MS run, a few of the most intense ions detected in every MS spectrum are selected as precursors for MS(2) and their masses, charge states and retention times are automatically registered in an internal database. In the next run, a sample similar to that used in the first run is analyzed using database searching. Then, the ions registered in the database are excluded from the precursor ion selection to avoid duplicate MS(2) analyses. Furthermore, real-time de novo sequencing is performed just after obtaining the MS(2) spectrum, and an MS(3) spectrum is obtained for accurate peptide identification when the number of interpreted amino acids in the MS(2) spectrum is less than five. We applied the IBA system to a yeast cell lysate which is a typical crude sample, using a nanoLC/ion-trap time-of flight (IT/TOF) mass spectrometer, repeating the same LC/MS run five times. The obtained MS(2) and MS(3) spectra were analyzed by applying the Mascot (Matrix Science, Boston, MA, USA) search engine to identify proteins from the sequence database. The total number of identified proteins in five LC/MS runs was three times higher than that in the first run and the ion scores for peptide identification also significantly increased, by about 70%, when the MS(3) spectra were used, combined with the MS(2) spectra, before being subjected to Mascot analysis.     

A high-performance matrix-assisted laser desorption/ionization orthogonal time-of-flight mass spectrometer with collisional cooling

A high-performance orthogonal time-of-flight (TOF) mass spectrometer was developed specifically for use in combination with a matrix-assisted laser desorption/ionization (MALDI) source. The MALDI source features an ionization region containing a buffer gas with variable pressure. The source is interfaced to the TOF section via a collisional focusing ion guide. The pressure in the source influences the rate of cooling and allows control of ion fragmentation. The instrument provides uniform resolution up to 18,000 FWHM (full width at half maximum). Mass accuracy routinely achieved with a single-point internal recalibration is below 2 ppm for protein digest samples. The instrument is also capable of recording spectra of samples containing compounds with a broad range of masses while using one set of experimental conditions and without compromising resolution or mass accuracy.     

Molecular weight determination of underivatized oligodeoxyribonucleotides by positive-ion matrix-assisted ultraviolet laser-desorption mass spectrometry

A Wiley-McLaren type time-of-flight mass spectrometer has been used for molecular weight measurements of several unprotected oligodeoxyribonucleotides using matrix-assisted UV laser desorption. Approximately 10 to 100 pmol of sample was required for recording their positive-ion mass spectra with a mass resolution in the range of 150 to 300 (Full width at half maximum) (FWHM). Little fragmentation was observed.     

Accurate mass measurement at enhanced mass-resolution on a triple quadrupole mass-spectrometer for the identification of a reaction impurity and collisionally-induced fragment ions of cabergoline

In this study, accurate mass measurements were made by electrospray ionization (ESI) on a triple quadrupole mass spectrometer operating in enhanced mass-resolution mode (peak width = 0.1 u FWMH), to give qualitative information relating to the pharmaceutical, cabergoline. Accurate mass determinations by ESI-MS were performed on a protonated impurity formed during cabergoline storage. The accurate mass measurement resulted in only one proposed elemental composition for the impurity, using reasonable elemental limits and mass tolerance for the calculation. This information was sufficient to propose a structure for the impurity where ESI-MS/MS proved consistent. The difference between the accurate mass measurement and the exact mass calculated for the proposed structure was 0.8 mmu, with a standard deviation of 0.7 mmu for replicate accurate mass determinations. Accurate mass determinations in ESI-MS/MS provided information on cabergoline fragment ions formed through collisionally-induced dissociation. Since the potential formation of isobaric ions exists for two major cabergoline fragment ions, accurate mass measurement allowed for the determination of the most probable fragment ion structures. The differences between the accurate mass measurements and exact masses calculated for the proposed fragment ions were 1.9 and 2.1 mmu, with standard deviations of 0.4 and 0.8 mmu, respectively, for replicate determinations.     

Enhanced resolution triple-quadrupole mass spectrometry for fast quantitative bioanalysis using liquid chromatography/tandem mass spectrometry: investigations of parameters that affect ruggedness

In order to increase sample analysis throughput, the use of fast liquid chromatography in quantitative bioanalysis based on liquid chromatography coupled with tandem mass spectrometry (LC/MS/MS) has become prevalent. Therefore, it is important to increase the specificity of such bioanalytical methods. This can be done by enhancing both the chromatographic and mass resolving power. Increasing the mass spectrometric resolving power to minimize interference from endogenous compounds in the biological matrix is the subject of this paper. We present the results of our experience with developing and validating SRM-based, enhanced resolution bioanalytical methods using a new triple-quadrupole mass spectrometer with enhanced resolution capability. We have shown that SRM bioanalytical methods using better than unit-mass resolution (Q1 FWHM = 0.2 Th, Q3 FWHM = 0.7 Th) can be developed which are as rugged as unit resolution methods (Q1 FWHM = 0.7 Th, Q3 FWHM = 0.7 Th). The enhanced resolution methods require more attention to detail than unit resolution methods. For instance, the mass setting for precursor ion selection is more critical because the mass peak is narrower. Because of this, enhanced resolution methods may be more easily influenced by temperature changes in the laboratory. We have shown that there is good correlation between the shift in the precursor ion mass and the ambient temperature. Other studies carried out to investigate the effects on mass peak shape and response (both in the SIM and SRM mode) as the result of varying the FWHM revealed some interesting results. For instance, the decrease in response with the decrease in the FWHM was larger using SRM compared to that using SIM. However, the decrease in both SRM and SIM response with decreasing FWHM was significantly smaller compared with the decrease obtained using an older generation instrument. We demonstrate that, at concentrations near the limit of detection, the signal specificity can be improved by using an enhanced resolution method. To compare the performance of an enhanced resolution method against a unit resolution method under optimized mass spectrometric conditions, we analyzed calibration standards and quality control samples using a lower limit of quantitation that could be easily achieved by either method. Under these conditions, the two methods were essentially the same, demonstrating that the enhanced resolution method is as accurate, precise and rugged as the unit resolution method. We propose system suitability procedures, based on precursor ion scan, product ion scan, SRM with fractional mass changes, or SIM with a narrow scan width, for the updating of the SRM set masses before the start of analysis. We also recommend that Q1 SRM masses be determined during and at the end of analysis in order to ascertain whether or not the precursor masses have shifted during the course of the analysis.     

Development and validation of an isotope-dilution electrospray ionization tandem mass spectrometry method with an on-line sample clean-up device for the quantitative analysis of the benzene exposure biomarker S-phenylmercapturic acid in human urine

An isotope-dilution electrospray ionization tandem mass spectrometry (ESI-MS/MS) method with an on-line sample clean-up device, for the quantitative analysis of human urine for the benzene exposure biomarker S-phenylmercapturic acid (SPMA), was developed and validated. The sample clean-up system was constructed from an autosampler, a reversed-phase C18 trap cartridge, a two-position switching valve, and controlling computer software and hardware. The sample clean-up system was interfaced via 1/20 splitting to the ESI source of a triple-quadrupole mass spectrometer using negative ion mode and multiple reaction monitoring for SPMA and the isotope-labeled internal standard. A strategy was adopted to acquire pooled blank urine matrix and quality control samples spiked with standards. Validated procedures and data on method specificity, detection limits, standard curves, precision and recovery, sample storage stability, and inter-laboratory comparison are presented. The analytical system was fully automated. No tedious manual sample clean-up procedures are required. With the selectivity and the sensitivity provided by ESI-MS/MS detection, the analytical system can be used for high-throughput and accurate determination of SPMA levels in human urine samples, as a biomarker for environmental as well as occupational benzene exposure.     

High-speed gradient parallel liquid chromatography/tandem mass spectrometry with fully automated sample preparation for bioanalysis: 30 seconds per sample from plasma

In this work, a high-throughput and high-performance bioanalytical system is described that is capable of extracting and analyzing 1152 plasma samples within 10 hours. A Zymark track robot system interfaced with a Tecan Genesis liquid handler was used for simultaneous solid-phase extraction of four 96-well plates in a fully automated fashion. The extracted plasma samples were injected onto four parallel monolithic columns for separation via a four-injector autosampler. The use of monolithic columns allowed for fast and well-resolved separations at a considerably higher flow rate without generating significant column backpressure. This resulted in a total chromatographic run cycle time of 2 min on each 4.6 x 100 mm column using gradient elution. The effluent from the four columns was directed to a triple quadrupole mass spectrometer equipped with an indexed four-probe electrospray ionization source (Micromass MUX interface). Hence, sample extraction, separation, and detection were all performed in a four-channel parallel format that resulted in an overall throughput of about 30 s per sample from plasma. The performance of this system was evaluated by extracting and by analyzing twelve 96-well plates (1152) of human plasma samples spiked with oxazepam at different concentrations. The relative standard deviation (RSD) of analyte sensitivity (slope of calibration curve) across the four channels and across the 12 plates was 5.2 and 6.8%, respectively. An average extraction recovery of 77.6% with a RSD of 7.7% and an average matrix effect of 0.95 with a RSD of 5.2% were achieved using these generic extraction and separation conditions. The good separation efficiency provided by this system allowed for rapid method development of an assay quantifying the drug candidate and its close structural analog metabolite. The method was cross-validated with a conventional liquid chromatography/tandem mass spectrometry (LC/MS/MS) assay.     

337 nm matrix-assisted laser desorption/ionization of single aerosol particles.

Matrix-assisted laser desorption/ionization (MALDI) mass spectra were obtained from single particles injected directly into a time-of-flight mass spectrometer. Aerosol particles were generated at atmospheric pressure using a piezoelectric single-particle generator or a pneumatic nebulizer and introduced into the mass spectrometer through a series of narrow-bore tubes. Particles were detected by light scattering that was used to trigger a 337 nm pulsed nitrogen laser and the ions produced by laser desorption were mass separated in a two-stage reflectron time-of-flight mass spectrometer. MALDI mass spectra of single particles containing bradykinin, angiotensin II, gramicidin S, vitamin B(12) or gramicidin D were obtained at mass resolutions greater than 400 FWHM. For the piezoelectric particle generator, the efficiency of particle delivery was estimated to be approximately 0.02%, and 50 pmol of sample were consumed for each mass spectrum. For the pneumatic nebulizer, mass spectra could be obtained from single particles containing less than 100 amol of analyte, although the sample consumption for a typical mass spectrum was over 400 pmol.     

Fast liquid chromatography coupled to electrospray tandem mass spectrometry peptide sequencing for cross-species protein identification

Using a parallel microcolumn switching liquid chromatography set-up coupled to a quadrupole time-of-flight mass spectrometer, a rapid liquid chromatography/mass spectrometric (LC/MS) protein identification method is presented. Without prior sample clean-up up to 300 protein digest samples a day can be processed. Using data-directed acquisition, up to 10 fragmentation analyses for each protein sample can be acquired in the same chromatographic run that can be used for database searching. Using internal peptide sequence information, protein databases and the various nucleic acid databases can both be queried for cross-species identification of the protein sample. The method was evaluated and put into force to generate data for a tobacco cell culture protein database.     

Polarization induced electrospray ionization mass spectrometry for the analysis of liquid,viscous and solid samples

In this study, a polarization‐induced electrospray ionization mass spectrometry (ESI‐MS) was developed. A micro‐sized sample droplet was deposited on a naturally available dielectric substrate such as a fruit or a stone, and then placed close to (~2 mm) the orifice of a mass spectrometer applied with a high voltage. Taylor cone was observed from the sample droplet, and a spray emitted from the cone apex was generated. The analyte ion signals derived from the droplet were obtained by the mass spectrometer. The ionization process is similar to that in ESI although no direct electric contact was applied on the sample site. The sample droplet polarized by the high electric field provided by the mass spectrometer initiated the ionization process. The dielectric sample loading substrate facilitated further the polarization process, resulting in the formation of Taylor cone. The mass spectral profiles obtained via this approach resembled those obtained using ESI‐MS. Multiply charged ions dominated the mass spectra of peptides and proteins, whereas singly charged ions dominated the mass spectra of small molecules such as amino acids and small organic molecules. In addition to liquid samples, this approach can be used for the analysis of solid and viscous samples. A small droplet containing suitable solvent (5–10 µl) was directly deposited on the surface of the solid (or viscous) sample, placed close the orifice of mass spectrometer applied with a high voltage. Taylor cone derived from the droplet was immediately formed followed by electrospray processes to generate gas‐phase ions for MS analysis. Analyte ions derived from the main ingredients of pharmaceutical tablets and viscous ointment can be extracted into the solvent droplet in situ and observed using a mass spectrometer. Copyright © 2015 John Wiley & Sons, Ltd.     

Utility of three types of mass spectrometers for determining elemental compositions of ions formed from chromatographically separated compounds

Concentration factors of 1000 and more reveal dozens of compounds in extracts of water supplies. Library mass spectra for most of these compounds are not available, and alternative means of identification are needed. Determination of the elemental compositions of the ions in mass spectra makes feasible searches of commercial and chemical literature that often lead to compound identification. Instrumental capabilities that constrain the utility of a mass spectrometer for determining ion compositions for compounds that elute from a chromatographic column are scan speed, mass accuracy, linear dynamic range, and resolving power. Mass peak profiling from selected ion recording data (MPPSIRD) performed with a double-focusing mass spectrometer provides the best combination of these capabilities. This technique provides unique ion compositions for ions of higher mass from compounds eluting from a gas chromatograph than can be obtained by orthogonal acceleration time-of-flight (oa-TOF) or Fourier transform ion cyclotron resonance mass spectrometry. Multiple compositions are usually possible for an ion with a mass exceeding 150 Da within the error limits of the mass measurement. The correct composition is selected based on measured exact masses of the mass peak profiles resulting from isotopic ions higher in mass by 1 and 2 Da and accurate measurement of the summed abundances of these isotopic ions relative to the monoisotopic ion. A profile generation model (PGM) automatically determines which compositions are consistent with measured exact masses and relative abundances. The utility of oa-TOF and double-focusing mass spectrometry using ion composition elucidation (MPPSIRD plus the PGM) are considered for determining ion compositions of two compounds found in drinking water extracts and a third compound from a monitoring well at a landfill. Published in 2002 by John Wiley & Sons, Ltd.     

Software (MSPECTRA) for automatic interpretation of triacylglycerol molecular mass distribution spectra and collision induced dissociation product ion spectra obtained by ammonia negative ion chemical ionization mass spectrometry

Rapid analysis of molecular mass distributions of triacylglycerol (TAG) mixtures and regioisomeric structures of selected molecular mass species is possible using ammonia negative ion chemical ionization mass spectrometry utilizing sample introduction by direct exposure probe. However, interpretation of spectra and calculation of results is time consuming, thus lengthening the total analysis time. To facilitate result calculation a software package (MSPECTRA 1.3) was developed and applied to automatic processing of triacylglycerol molecular mass distribution spectra and collision induced dissociation (CID) product ion spectra. The program is capable of identifying triacylglycerol molecular mass species possessing different ACN:DB (acyl carbon number:number of double bonds) ratios on the basis of m/z values of [M - H](-) ions. In addition to such identification the program also corrects spectra for abundances of naturally occurring (13)C isotopes and calculates relative proportions of triacylglycerol molecular species in the analyzed samples. If several replicate spectra are processed simultaneously the program automatically calculates an average and standard deviation of relative proportions of molecular species. In the case of CID spectra the program identifies fatty acid fragment ions [RCO(2)](-) and the corresponding [M - H - RCO(2)H - 100](-) ions, and calculates the relative proportions of ions in both groups. These proportions are then used automatically to calculate the fatty acid combinations comprising the parent triacylglycerol molecule and the regiospecific positions of fatty acids. Processing of several replicate product ion spectra simultaneously produces averaged proportions of regioisomers comprising the parent triacylglycerol molecular species and the standard deviation of the analysis. The performance of the program was tested by analyzing triacylglycerol samples of human milk, human milk substitutes, human chylomicron and cocoa butter, and by comparing results obtained by automated processing of the data with manually calculated results.     

Algorithms for automatic interpretation of high resolution mass spectra

Automated interpretation of high-resolution mass spectra in a reliable and efficient manner represents a highly challenging computational problem. This work aims at developing methods for reducing a high-resolution mass spectrum into its monoisotopic peak list, and automatically assigning observed masses to known fragment ion masses if the protein sequence is available. The methods are compiled into a suite of data reduction algorithms which is called MasSPIKE (Mass Spectrum Interpretation and Kernel Extraction). MasSPIKE includes modules for modeling noise across the spectrum, isotopic cluster identification, charge state determination, separation of overlapping isotopic distributions, picking isotopic peaks, aligning experimental and theoretical isotopic distributions for estimating a monoisotopic peak's location, generating the monoisotopic mass list, and assigning the observed monoisotopic masses to possible protein fragments. The method is tested against a complex top-down spectrum of bovine carbonic anhydrase. Results of each of the individual modules are compared with previously published work.     

Novel multichannel plasma-source mass spectrometer

A novel mass spectrometer system for elemental analysis is described. The instrument combines an inductively coupled plasma (ICP) ion source with a Mattauch-Herzog mass spectrometer and multichannel ion detector. Ion detection is simultaneous and an elemental mass spectrum (20–230 μ) can be acquired in <10 ms. The instrument can be used with either Ar or He plasma sources. The speed of the system makes it well suited for acquisition of fast (10–100-ms duration) transient signals, such as those generated by pulsed laser ablation sample introduction. Preliminary system performance characteristics, which include detection limits, stability, and measurement accuracy, obtained with an Ar ICP are presented. The application of the instrument to the analysis of solid samples by laser ablation is discussed.