Intensity-based statistical scorer for tandem mass spectrometry

We describe a new statistical scorer for tandem mass spectrometry. The scorer is based on the probability that fragments with given chemical properties create measured intensity levels in the experimental spectrum. The scorer's parameters are computed using a fully automated procedure. Benchmarking the new scorer on a large set of experimental spectra, we show that it performs significantly better than the widely used cross-correlation scoring algorithm of Eng et al. (Eng, J. K; McKormack, A. L.; Yates, J. R. J. Am. Soc. Mass Spectrom. 1994, 5, 976-989.).     

Use of mass spectrometry methods as a strategy for detection and determination of residual solvents in pharmaceutical products

In the present work a strategy for the qualitative and quantitative analysis of residual solvents in pharmaceutical products is reported. First, a low-resolution chromatogram is generated for the identification of the solvents present in the samples by means of headspace generation-fast gas chromatography-mass spectrometry (HS-fast GC/MS). From the plotting of this information by means of contour plots with time and mass/charge axes, it is decided whether quantification of such compounds can be accomplished without chromatographic separation or whether it should be done by fast gas chromatography. The nonseparative method is based on direct coupling of a headspace sampler with a mass spectrometer (HS-MS) and requires a signal recording time of only 3 min, while with fast gas chromatography the time required to obtain a chromatogram is 7.16 min. The use of headspace generation for introducing the sample and standard addition as a quantification technique provided satisfactory results and minimized the matrix effect. An important advantage of the methodologies used here is related to the fact that no prior treatment of the sample is required, thus minimizing the creation of analytical artifacts and the errors associated with this step of the analytical process. The methods were applied to the determination of residual solvents in 27 different pharmaceutical products. Detection and quantitation limits were sufficiently low to enable the estimation of organic volatile impurities according to the International Conference on Harmonization (ICH) of Technical Requirements for the Registration of Pharmaceuticals for Human Use.     

Identification of major histocompatibility complex-regulated body odorants by statistical analysis of a comparative gas chromatography/mass spectrometry experiment

This paper examines the application of gas chromatography/mass spectrometry (GC/MS) in a comparative experiment to identify volatile compounds from urine that differ in concentration between two groups of inbred mice. A complex mixture might comprise several hundred or even thousands of volatile compounds. Because their number and location in a chromatogram are generally unknown, and because components overlap in populous chromatograms, the statistical problems offer significant challenges beyond traditional two-group screening procedures. We describe a statistical procedure to compare two-dimensional GC/MS profiles between groups, which entails (1) signal processing, baseline correction, and peak detection in single ion chromatograms; (2) aligning chromatograms in time; (3) normalizing differences in overall signal intensities; and (4) detecting chromatographic regions that differ between groups. In an application to chemosignaling, we detect differences in GC/MS chromatograms of ether-extracted urine collected from two inbred groups of mice that differ only in genes of the major histocompatibility complex (MHC). Several dozen MHC-regulated compounds are found, including two known mouse pheromones, 2,5-dimethylpyrazine and 2-sec-butyl-4,5-dihydrothiazole.     

Comparison of isotope dilution mass spectrometry methods for the determination of total homocysteine in plasma and serum

Two independent methods have been critically evaluated and applied to the measurement of total homocysteine in serum and plasma: solid-phase anion extraction (SPAE) gas chromatography/mass spectrometry (GC/MS) and protein precipitation liquid chromatography/tandem mass spectrometry (LC/MS/MS). In addition, analysis of samples prepared by SPAE was accomplished by liquid chromatography/mass spectrometry (LC/MS) and LC/MS/MS. These methods have been used to determine total homocysteine levels in several existing serum-based Standard Reference Materials (SRMs) from the National Institute of Standards and Technology and in patient plasma samples provided by the Centers for Disease Control and Prevention. The precision of the homocysteine measurements in serum and plasma was critically evaluated, and method comparisons were carried out using Bland-Altman plots and bias analysis. On the basis of the excellent precision and close agreement of the mass spectrometric (MS) methods, the MS-based methods will be used for certification of a serum-based SRM for homocysteine and folates.     

A statistical model for identifying proteins by tandem mass spectrometry

A statistical model is presented for computing probabilities that proteins are present in a sample on the basis of peptides assigned to tandem mass (MS/MS) spectra acquired from a proteolytic digest of the sample. Peptides that correspond to more than a single protein in the sequence database are apportioned among all corresponding proteins, and a minimal protein list sufficient to account for the observed peptide assignments is derived using the expectation-maximization algorithm. Using peptide assignments to spectra generated from a sample of 18 purified proteins, as well as complex H. influenzae and Halobacterium samples, the model is shown to produce probabilities that are accurate and have high power to discriminate correct from incorrect protein identifications. This method allows filtering of large-scale proteomics data sets with predictable sensitivity and false positive identification error rates. Fast, consistent, and transparent, it provides a standard for publishing large-scale protein identification data sets in the literature and for comparing the results obtained from different experiments.     

Large scale pesticide multiresidue methods in food combining liquid chromatography--time-of-flight mass spectrometry and tandem mass spectrometry

Liquid chromatography tandem mass spectrometry (LC-MS/MS) and liquid chromatography time-of-flight mass spectrometry (LC-TOFMS) are powerful and complementary techniques that can independently cover the majority of the challenges related with pesticide residue food control. The sequential combination of both systems benefits from their complementary advantages and assists to increase the performance and to simplify routine large scale pesticide multiresidue methods. The proposed approach consists of three stages: (1) automated pesticide screening by LC-TOFMS; (2) identification by LC-TOFMS accurate mass measurements; and (3) confirmation and quantitation by LC-MS/MS. We have developed a fast comprehensive (identification/confirmation + quantitation) automated screening method for 100 target pesticides in crops. In the first stage, a set of data including m/z accurate mass windows (within 20 mDa width) and retention time is obtained (using a standard solution containing all the targeted pesticides) in order to build the automated screening procedure, which is created automatically by assigning retention time and the m/z mass window for each target pesticide. Samples are then analyzed, and the method enables the screening and preliminary identification of the species first by retention time and m/z mass window, followed by subsequent identification (only if positive results) by LC-TOFMS accurate mass measurements. After that, final confirmation of the positive findings using two MRM transitions and accurate quantitation is performed by LC-MS/MS using a hybrid triple quadrupole linear ion trap (QqLIT) mass spectrometer. In addition, the use of this QqLIT instrument also offers additional advantageous scanning modes (enhanced product ion and MS3 modes) for confirmatory purposes in compounds with poor fragmentation. Examples of applications to real samples show the potential of the proposed approach, including the detection of nonselected "a priori" compounds as a typical case of retrospective evaluation of banned or misused substances.     

Use of a microchip device coupled with mass spectrometry for ligand screening of a multi-protein target

Nanoflow electrospray mass spectrometry has been applied previously to investigate noncovalent protein-protein and protein-ligand interactions. Here we evaluate a commercial microchip device for this application. We show that the microchip can be used to obtain mass spectra of the noncovalent tetramer transthyretin. The device showed a 10-fold increase in signal stability compared with a nanoflow capillary and a high level of nozzle-to-nozzle reproducibility. Binding of the natural ligand thyroxine was clearly observed, and a range of small molecules proposed as inhibitors of transthyretin amyloidosis were shown to be effective in stabilizing the tetramer. We propose that measuring the ability of small molecules to stabilize protein complexes using this automated microchip technology will enable high-throughput screening of multi-protein complexes by mass spectrometry.     

Comparison of two methods for obtaining quantitative mass concentrations from aerosol time-of-flight mass spectrometry measurements

Aerosol time-of-flight mass spectrometry (ATOFMS) measurements provide continuous information on the aerodynamic size and chemical composition of individual particles. In this work, we compare two approaches for converting unscaled ATOFMS measurements into quantitative particle mass concentrations using (1) reference mass concentrations from a co-located micro-orifice uniform deposit impactor (MOUDI) with an accurate estimate of instrument busy time and (2) reference number concentrations from a co-located aerodynamic particle sizer (APS). Aerodynamic-diameter-dependent scaling factors are used for both methods to account for particle transmission efficiencies through the ATOFMS inlet. Scaling with APS data retains the high-resolution characteristics of the ambient aerosol because the scaling functions are specific for each hourly time period and account for a maximum in the ATOFMS transmission efficiency curve for larger-sized particles. Scaled mass concentrations obtained from both methods are compared with co-located PM(2.5) measurements for evaluation purposes. When compared against mass concentrations from a beta attenuation monitor (BAM), the MOUDI-scaled ATOFMS mass concentrations show correlations of 0.79 at Fresno, and the APS-scaled results show correlations of 0.91 at Angiola. Applying composition-dependent density corrections leads to a slope of nearly 1 with 0 intercept between the APS-scaled absolute mass concentration values and BAM mass measurements. This paper provides details on the methodologies used to convert ATOFMS data into continuous, quantitative, and size-resolved mass concentrations that will ultimately be used to provide a quantitative estimate of the number and mass concentrations of particles from different sources.     

A comparison of statistical methods for estimation of less than detectable ionising radiation exposures

Methods were developed to estimate the ionising radiation dose below the detection level (DL) of personal monitoring devices for a case-control study of protracted radiation exposure and lung cancer. Exposure data were grouped by dosemeter type and monitoring period. Each group contained dosimetry data that were interval-censored from limitations in measurement precision and included left-censoring of observations below detection. The grouped data were fit to a three parameter hybrid-lognormal distribution by maximum likelihood estimation. Using the fitted distribution, bootstrap samples were either simulated by Monte Carlo or constructed by sampling with replacement. The resulting bootstrap sample distributions were then used to predict the missing dose values and the associated uncertainty in the estimate. Among study subjects, 1357 workers were monitored with film dosimetry. Among the 39,263 dose observations 20,416 were recorded as zero dose, indicating 52% left-censoring. The statistical methods estimated 0.31 person-Sv below the DL or approximately 1% of the total collective dose for this study population.     

Measurement of total acid number (TAN) and TAN boiling point distribution in petroleum products by electrospray ionization mass spectrometry

We report a new method for rapid measurement of total acid number (TAN) and TAN boiling point (BP) distribution for petroleum crude and products. The technology is based on negative ion electrospray ionization mass spectrometry (ESI-MS) for selective ionization of petroleum acid and quantification of acid structures and molecular weight distributions. A chip-based nanoelectrospray system enables microscale (<200 mg) and higher throughput (20 samples/h) measurement. Naphthenic acid structures were assigned based on nominal masses of a set of predefined acid structures. Stearic acid is used as an internal standard to calibrate ESI-MS response factors for quantification purposes. With the use of structure-property correlations, boiling point distributions of TAN values can be calculated from the composition. The rapid measurement of TAN BP distributions by ESI is demonstrated for a series of high-TAN crudes and distillation cuts. TAN values determined by the technique agree well with those by the titration method. The distributed properties compare favorably with those measured by distillation and measurement of TAN of corresponding cuts.     

Identification of bacteria using tandem mass spectrometry combined with a proteome database and statistical scoring

Detection and identification of pathogenic bacteria and their protein toxins play a crucial role in a proper response to natural or terrorist-caused outbreaks of infectious diseases. The recent availability of whole genome sequences of priority bacterial pathogens opens new diagnostic possibilities for identification of bacteria by retrieving their genomic or proteomic information. We describe a method for identification of bacteria based on tandem mass spectrometric (MS/MS) analysis of peptides derived from bacterial proteins. This method involves bacterial cell protein extraction, trypsin digestion, liquid chromatography MS/MS analysis of the resulting peptides, and a statistical scoring algorithm to rank MS/MS spectral matching results for bacterial identification. To facilitate spectral data searching, a proteome database was constructed by translating genomes of bacteria of interest with fully or partially determined sequences. In this work, a prototype database was constructed by the automated analysis of 87 publicly available, fully sequenced bacterial genomes with the GLIMMER gene finding software. MS/MS peptide spectral matching for peptide sequence assignment against this proteome database was done by SEQUEST. To gauge the relative significance of the SEQUEST-generated matching parameters for correct peptide assignment, discriminant function (DF) analysis of these parameters was applied and DF scores were used to calculate probabilities of correct MS/MS spectra assignment to peptide sequences in the database. The peptides with DF scores exceeding a threshold value determined by the probability of correct peptide assignment were accepted and matched to the bacterial proteomes represented in the database. Sequence filtering or removal of degenerate peptides matched with multiple bacteria was then performed to further improve identification. It is demonstrated that using a preset criterion with known distributions of discriminant function scores and probabilities of correct peptide sequence assignments, a test bacterium within the 87 database microorganisms can be unambiguously identified.     

Liquid chromatography/mass spectrometry methods for distinguishing N-oxides from hydroxylated compounds

This study describes the application of liquid chromatography/mass spectrometry (LC/MS) methods for distinguishing between aliphatic and aromatic hydroxylations and between hydroxylations and N-oxidations. Hydroxylations and N-oxidations are common biotransformation reactions of drugs. Electrospray (ESI) and atmospheric pressure chemical ionization (APCI) were used to generate ions from liquid chromatographic effluents. ESI-MS, ESI-MS/MS, APCI-MS, and APCI-MS/MS experiments were performed on several metabolites and derivatives of loratadine (a long-acting and nonsedating tricyclic antihistamine) using an ion trap mass spectrometer (LCQ) and a triple-quadrupole mass spectrometer (TSQ). The observations are as follows: (1) LC/ESI-MS produced predominantly [M + H]+ ions with minor fragmentation. (2) LC/ESI-MS/MS data, however, showed a predominant loss of water from metabolites with aliphatic hydroxylation while the loss of water was not favored when hydroxylation was phenolic. N-Oxides (aromatic and aliphatic) showed only a small amount of water loss in the MS/MS spectra. (3) Under LC/APCI-MS conditions, aliphatic hydroxylation could be readily distinguished from aromatic hydroxylation based on the extent of water loss. In addition, N-oxides produced distinct [M + H - O]+ ions. These [M + H - O]+ ions were not produced in the APCI-MS spectra of hydroxylated metabolites. (4) Similar to the ESI-MS/MS spectra, the APCI-MS/MS spectra from the (M + H)+ ions of N-oxides yielded a small amount of water loss but no [M + H - O]+ ions. These results indicate that LC/APCI-MS can be used to distinguish between hydroxylated metabolites and N-oxides.     

Sensitivity effects in Uk'37 paleotemperature estimation by chemical ionization mass spectrometry

Analysis of C37 alkenone mixtures by gas chromatography (GC) with flame ionization detection (FID) and GC coupled to mass spectrometry (GC/MS) in the chemical ionization mode (CI) shows that the later is useful for paleotemperature estimation when ammonia is used as reagent gas. Conversely, the use of isobutane gives rise to Uk'37 readings that are dependent on the amount of C37 alkenones introduced in the system, being unreliable for paleoclimatic studies. However, ammonia CI GC/MS may produce Uk'37 measurements that deviate from those obtained by GC-FID, the method calibrated for temperature estimation from algal cultures and marine sedimentary data. The differences result from changes in relative sensitivity between the di- and triunsaturated alkenones and depend on the instrument used and operational conditions. This problem is solved in the present study by determination of the response factor linear equations for each alkenone and their average relative sensitivity (R) using mixtures of known composition. These parameters allow the transformation of the GC/MS readings into the GC-FID equivalents using the following equation: UG = R x UM/(1 - UM(1 - R)). Examples of the suitability of this approach are given.     

Use of the inductively coupled plasma mass spectrometry for element analysis of environmental objects

Capabilities and limits of the inductively coupled plasma mass spectrometry (ICP-MS) are discussed by the examples of element analysis of natural and drinking water, soils, ground, bottom sediments, phytogenous samples, and aerosols. It is shown that this method in combination with simpler atomic-emission technique allows for widening the range of detected elements, simplify the mass-spectrometry analysis, and improve its reliability. Examples and metrological characteristics of techniques for studying various environmental objects are discussed.     

Development and evaluation of a candidate reference method for the determination of total cortisol in human serum using isotope dilution liquid chromatography/mass spectrometry and liquid chromatography/tandem mass spectrometry

Cortisol is an important diagnostic marker for the production of steroid hormones, and accurate measurements of serum cortisol are necessary for proper diagnosis of adrenal function. A candidate reference method involving isotope dilution coupled with liquid chromatography/mass spectrometry (LC/MS) and liquid chromatography/tandem mass spectrometry (LC/MS/MS) has been developed and critically evaluated. An isotopically labeled internal standard, cortisol-d(3), was added to serum, followed by equilibration and solid-phase and ethyl acetate extractions to prepare samples for liquid chromatography/mass spectrometry electrospray ionization (LC/MS-ESI) and liquid chromatography/tandem mass spectrometry electrospray ionization (LC/MS/MS-ESI) analyses. (M + H)(+) ions at m/z 363 and 366 for cortisol and its labeled internal standard were monitored for LC/MS. The transitions of (M + H)(+) --> [(M + H)(+) - 2H(2)O] at m/z 363 --> 327 and 366 --> 330 were monitored for LC/MS/MS. The accuracy of the measurement was evaluated by a comparison of results of this candidate reference method on lyophilized human serum reference materials for cortisol [Certified Reference Materials 192 and 193] with the certified values determined by gas chromatography/mass spectrometry reference methods and by a recovery study for the added cortisol. The results of this method for total cortisol agreed with the certified values within 1.1%. The recovery of the added cortisol ranged from 99.8% to 101.0%. This method was applied to the determination of cortisol in samples of frozen serum pools. Excellent precision was obtained with within-set CVs of 0.3%-1.5% and between-set CVs of 0.04%-0.4% for both LC/MS and LC/MS/MS analyses. The correlation coefficients of all linear regression lines ranged from 0.998 to 1.000. The detection limits (at a signal-to-noise ratio of approximately 3-5) were 10 and 15 pg for LC/MS and LC/MS/MS, respectively. This method, which demonstrates good accuracy and precision, and is free from interferences from structural analogues, qualifies as a candidate reference method and can be used as an alternative reference method to provide an accuracy base to which the routine methods can be compared.     

Use of thermal desorption mass spectrometry for the detection of free acid impurities in pharmaceutical products

A method utilizing thermal desorption mass spectrometry (TDMS) for the detection and quantitation of free acid forms in pharmaceutical drug products formulated as salts is presented. Selective detection of neutral drug forms is possible because the volatility of a drug present in its free acid form is typically much higher than that of its corresponding salt forms, which have negligible volatility even at high temperatures. Tandem mass spectrometric detection allows selective quantitation of the desired free acid drug forms without significant interferences from formulation excipients. The application of the TDMS approach is demonstrated for a sodium salt of a representative, carboxylated drug molecule. Excellent sensitivity, specificity, and adequate linearity of detector signal as a function of micrograms of free acid added were demonstrated in the presence of the sodium salt of the drug and formulation excipients. The sensitivity of the method was demonstrated at free acid levels of 0.6% w/w (6 microg absolute mass). Tablet samples were analyzed by thermal desorption EI-MS/MS with reference to external standards using a commercially available quadrupole ion trap mass spectrometer. The relative drug form stabilities in three different tablet formulations were differentiated using this method; the salt-to-free acid form conversion ranged between less than the limit of detection to near complete conversion during the stability study.     

Compound-specific chlorine isotope analysis: a comparison of gas chromatography/isotope ratio mass spectrometry and gas chromatography/quadrupole mass spectrometry methods in an interlaboratory study

Chlorine isotope analysis of chlorinated hydrocarbons like trichloroethylene (TCE) is of emerging demand because these species are important environmental pollutants. Continuous flow analysis of noncombusted TCE molecules, either by gas chromatography/isotope ratio mass spectrometry (GC/IRMS) or by GC/quadrupole mass spectrometry (GC/qMS), was recently brought forward as innovative analytical solution. Despite early implementations, a benchmark for routine applications has been missing. This study systematically compared the performance of GC/qMS versus GC/IRMS in six laboratories involving eight different instruments (GC/IRMS, Isoprime and Thermo MAT-253; GC/qMS, Agilent 5973N, two Agilent 5975C, two Thermo DSQII, and one Thermo DSQI). Calibrations of (37)Cl/(35)Cl instrument data against the international SMOC scale (Standard Mean Ocean Chloride) deviated between instruments and over time. Therefore, at least two calibration standards are required to obtain true differences between samples. Amount dependency of δ(37)Cl was pronounced for some instruments, but could be eliminated by corrections, or by adjusting amplitudes of standards and samples. Precision decreased in the order GC/IRMS (1σ ≈ 0.1‰), to GC/qMS (1σ ≈ 0.2-0.5‰ for Agilent GC/qMS and 1σ ≈ 0.2-0.9‰ for Thermo GC/qMS). Nonetheless, δ(37)Cl values between laboratories showed good agreement when the same external standards were used. These results lend confidence to the methods and may serve as a benchmark for future applications.     

Use of nitrocellulose membranes for protein characterization by matrix-assisted laser desorption/ionization mass spectrometry

We present an improved method for MALDI-MS analysis of proteins that have been electroblotted onto a nitrocellulose (NC) membrane. With this approach, electroblotted proteins can be analyzed directly for intact molecular weight determination or after on-membrane digestion by dissolution of the nitrocellulose in MALDI matrix solution containing 70% acetonitrile and 30% methanol. This solution helps maintain solubility of proteins and peptides while dissolving the NC membrane, which is dissolved by 100% acetone in other protocols. On-membrane tryptic digestion using this method requires half the time of in-gel digestion and results in fewer missed cleavages and better protein coverage. For the membrane proteins studied, bovine uroplakins II and III, the protein coverage was almost twice that provided by conventional in-gel digestion, and the transmembrane domains of both uroplakins were detected only after on-membrane digestion. We also demonstrated the compatibility with MALDI-MS of a new dye, MemCode, which is specifically designed for staining NC membrane-immobilized proteins and is faster and more sensitive than Ponceau-S. Our improved on-membrane digestion protocol greatly improves the study of soluble and, particularly strikingly, integral membrane proteins by mass spectrometry.