Complete Mass Spectra Research Articles

A field-deployable, chemical ionization time-of-flight mass spectrometer

Abstract. We constructed a new chemical ionization time-of-flight mass spectrometer (CI-TOFMS) that measures atmospheric trace gases in real time with high sensitivity. We apply the technique to the measurement of formic acid via negative-ion proton transfer, using acetate as the reagent ion. A novel high pressure interface, incorporating two RF-only quadrupoles is used to efficiently focus ions through four stages of differential pumping before analysis with a compact TOFMS. The high ion-duty cycle (>20 %) of the TOFMS combined with the efficient production and transmission of ions in the high pressure interface results in a highly sensitive (>300 ions s−1 pptv−1 formic acid) instrument capable of measuring and saving complete mass spectra at rates faster than 10 Hz. We demonstrate the efficient transfer and detection of both bare ions and ion-molecule clusters, and characterize the instrument during field measurements aboard the R/V Atlantis as part of the CalNex campaign during the spring of 2010. The in-field short-term precision is better than 5 % at 1 pptv (pL/L), for 1-s averages. The detection limit (3 σ, 1-s averages) of the current version of the CI-TOFMS, as applied to the in situ detection of formic acid, is limited by the magnitude and variability in the background determination and was determined to be 4 pptv. Application of the CI-TOFMS to the detection of other inorganic and organic acids, as well as the use of different reagent ion molecules (e.g. I−, CF3O−, CO3−) is promising, as we have demonstrated efficient transmission and detection of both bare ions and their associated ion-molecule clusters.

AEROSOL SIZE DISTRIBUTION AND COMPOSITION NEAR BUCHAREST DURING MAY 2010

The chemical composition, complete mass spectra and size distribution of ambient aerosols was analyzed for several weeks during spring 2010 near Bucharest, Romania. Preliminary results of the first measurements using an Aerosol Mass Spectrometer (AMS) are presented in this study. A significant accumulation mode with a peak around 350-600 nm was usually observed principally composed of sulfate, organics, ammonium and some nitrate. Particle-size distribution measurements over the full range of the fine fraction of the atmospheric aerosol have been done using two instruments based on time of flight and in a side-by-side configuration, an AMS and an aerosol particle sizer (APS). The particle size distributions characterizing different chemical components showed similar peaks and shapes suggesting that nitrate, sulfate, and organic species are probably internally mixed in the same particles.

On-line breath analysis with PTR-TOF

We report on on-line breath gas analysis with a new type of analytical instrument, which represents the next generation of proton-transfer-reaction mass spectrometers. This time-of-flight mass spectrometer in combination with the soft proton-transfer-reaction ionization (PTR-TOF) offers numerous advantages for the sensitive detection of volatile organic compounds and overcomes several limitations. First, a time-of-flight instrument allows for a measurement of a complete mass spectrum within a fraction of a second. Second, a high mass resolving power enables the separation of isobaric molecules and the identification of their chemical composition. We present the first on-line breath measurements with a PTR-TOF and demonstrate the advantages for on-line breath analysis. In combination with buffered end-tidal (BET) sampling, we obtain a complete mass spectrum up to 320 Th within one exhalation with a signal-to-noise ratio sufficient to measure down to pptv levels. We exploit the high mass resolving power to identify the main components in the breath composition of several healthy volunteers.

Data processing technique in gas chromatography/time-of-flight mass spectrometry

A complete mass spectrum was measured at an acquisition rate of 1 kHz using a femtosecond-multiphoton-ionization time-of-flight mass spectrometer for analyte eluting from a gas chromatograph. A contour-map display, i.e. a two-dimensional plot, of the data was first constructed for a simultaneous overview of the mass spectra and the mass chromatograms. The noise component in the signal was then reduced by digital filtering and reduced further by smoothing the data. The detection limit (S/N = 3) was improved from 240 to 76 fg for 2,3,4,6,7-pentachlorodibenzofuran, with no appreciable loss of resolution in the chromatogram. The achieved value was lower than the value (<100 fg) required by Japanese Industrial Standards for dioxin analysis. A new parameter, referred to as a 'reliability factor', was defined in this study to calculate the similarity between the intensity distribution of the isotope peaks observed in the mass spectrum and that calculated from the natural abundance ratio of the isotopes. This parameter was useful for evaluation of the purity of the chromatographic peak.

Ion Soft Landing Using a Rectilinear Ion Trap Mass Spectrometer

A new ion soft landing instrument has been built for the controlled deposition of mass selected polyatomic ions. The instrument has been operated with an electrospray ionization source; its major components are an electrodynamic ion funnel to reduce ion loss, a 90-degree bent square quadrupole that prevents deposition of fast neutral molecules onto the landing surface, and a novel rectilinear ion trap (RIT) mass analyzer. The ion trap is elongated (inner dimensions: 8 mm x 10 mm x 10 cm). Three methods of mass analysis have been implemented. (i) A conventional mass-selective instability scan with radial resonance ejection can provide a complete mass spectrum. (ii) The RIT can also be operated as a continuous rf/dc mass filter for isolation and subsequent soft landing of ions of the desired m/ z value. (iii) The 90-degree bent square quadrupole can also be used as a continuous rf/dc mass filter. The mass resolution (50% definition) of the RIT in the trapping mode (radial ion ejection) is approximately 550. Ions from various test mixtures have been mass selected and collected on fluorinated self-assembled monolayers on gold substrates, as verified by analysis of the surface rinses. Desorption electrospray ionization (DESI) has been used to confirm intact deposition of [Val (5)]-Angiotensin I on a surface. Nonmass selective currents up to 1.1 nA and mass-selected currents of up to 500 pA have been collected at the landing surface using continuous rf/dc filtering with the RIT. A quantitative analysis of rinsed surfaces showed that the overall solution-to-solution soft landing yields are between 0.2 and 0.4%. Similar experiments were performed with rf/dc isolation of both arginine and lysine from a mixture using the bent square quadrupole in the rf/dc mode. The unconventional continuous mass selection methods maximize soft landing yields, while still allowing the simple acquisition of full mass spectra.

In situ molecular imaging of proteins in tissues using mass spectrometry

In situ molecular imaging of proteins in tissues using mass spectrometry

Pulsed radiofrequency glow discharge time of flight mass spectrometer for the direct analysis of bulk and thin coated glasses

Direct solid analysis of bulk and thin coated glasses by pulsed radiofrequency (rf) glow discharge time-of-flight mass spectrometry (GD-TOFMS) is investigated. Modulated low pressure plasma created by pulsed-rf-GD has been coupled to a fast TOFMS in order to obtain complete mass spectra information from the different GD pulse domains (pre-peak, plateau and afterglow). In particular, it was observed that the analytes show the highest atomic ion signals in the afterglow region some hundred microseconds after the maximum of the Ar ion signal. However, it should be highlighted that the analyte ions exhibited their peak maxima at different delay times, depending on the element, after the end of the GD pulse. Such ion signal delays have been measured for different selected isotopes, covering a mass spectrum from light to heavy isotopes at different conditions of pressure and applied power. The results showed that ion signal delays are influenced by both the isotope mass and the pressure of the GD. Furthermore, GD operating conditions (pressure and applied power) were optimised in terms of sensitivity, using a bulk glass certified reference material (NIST 1411). The best analytical performance was observed at low pressure (150–200 Pa) and high applied power (135 W). Moreover, different pulse GD duty cycles (relationship between pulse duration and pulse period) were investigated. An optimum value of 50–65% duty-cycle was selected considering the signal stability and the signal intensity.

Improvement of the duty cycle of an orthogonal acceleration time‐of‐flight mass spectrometer using ion gates

A method to control the duty cycle of a time-of-flight mass spectrometer is described. The method relies on one or more ion gates placed in the beam path that have the function to transmit or stop the beam. These ion gates can switch from the open state to the closed state in tens of nanoseconds and effectively select portions of the mass range. The method is useful in circumstances where recording the complete mass spectrum is not an essential requirement, for example, in the analysis of known compounds where sensitivity and speed of operation are more important. It will be of benefit for applications in separation sciences with techniques involving fast chromatographic separations, where hundreds of mass spectra may be required per second. In such circumstances analytical identification may require only a limited number of masses (or mass regions) to be continuously monitored. Improvement of the duty cycle is particularly important for orthogonal-acceleration time-of-flight (oa-TOF) mass spectrometry instruments whose performance suffers from a low duty cycle. The duty cycle is not a constant for an instrument design but is a mass-dependent function and is least for smaller masses. The method described here is capable of raising the duty cycle to 100%. A theory is developed for one or more ion gate arrangements, for both linear- and reflectron-TOF systems. For a two-gate system the relationship between the positions of the first and second gates is described by a '2/3 rule'. Experimental results are shown for one-gate and two-gate operation, both in linear and in reflectron modes of operation, on an oa-TOF system built in-house.

Qualitative analysis of phenols and alcohols in complex samples after derivatization to esters of ferrocene carboxylic acid by gas chromatography with mass spectrometric detection

Phenols and alcohols in complex petrochemical samples are derivatized to esters of ferrocene carboxylic acid in a rapid and simple reaction. These esters show several characteristic ions of high intensity in gas chromatography coupled with electron impact ionization mass spectrometry (GC–EI–MS) which can be used for the identification of the analyte. A differentiation between alcohols and phenols is possible due to the McLafferty rearrangement shown only by the alcohol esters. Selective ion monitoring of m/ z 213 yields a phenol-selective chromatogram and m/ z 230 an alcohol-selective chromatogram. For all iron containing fragments, the isotopic pattern of iron can be observed which enhances the reliability of the peak identification. The ferrocene esters of 11 alcohols, 20 alkylphenols (including octyl- and nonylphenol), phenylphenol, naphthol and hydroxyphenanthrene, several chloro- and all mononitrophenols were synthesized as well as the esters of pentadeutero- and two fluorinated phenols. Their fragmentation pattern under EI ionization is studied and a GC-ion trap-MS system was optimized for simultaneous use of the full scan mode and an MS/MS experiment in the same run. This provides for a very high selectivity in the detection of the esters and makes available the complete mass spectra without any additional measurements. The benefits of the simple and rapid derivatization procedure in combination with this powerful detection method are demonstrated for selected petrochemical samples. Several alkylphenols could be successfully identified in such samples and molecular information about unknown phenolic components could be easily obtained.

Classification of high-speed gas chromatography–mass spectrometry data by principal component analysis coupled with piecewise alignment and feature selection

A useful methodology is introduced for the analysis of data obtained via gas chromatography with mass spectrometry (GC–MS) utilizing a complete mass spectrum at each retention time interval in which a mass spectrum was collected. Principal component analysis (PCA) with preprocessing by both piecewise retention time alignment and analysis of variance (ANOVA) feature selection is applied to all mass channels collected. The methodology involves concatenating all concurrently measured individual m/ z chromatograms from m/ z 20 to 120 for each GC–MS separation into a row vector. All of the sample row vectors are incorporated into a matrix where each row is a sample vector. This matrix is piecewise aligned and reduced by ANOVA feature selection. Application of the preprocessing steps (retention time alignment and feature selection) to all mass channels collected during the chromatographic separation allows considerably more selective chemical information to be incorporated in the PCA classification, and is the primary novelty of the report. This methodology is objective and requires no knowledge of the specific analytes of interest, as in selective ion monitoring (SIM), and does not restrict the mass spectral data used, as in both SIM and total ion current (TIC) methods. Significantly, the methodology allows for the classification of data with low resolution in the chromatographic dimension because of the added selectivity from the complete mass spectral dimension. This allows for the successful classification of data over significantly decreased chromatographic separation times, since high-speed separations can be employed. The methodology is demonstrated through the analysis of a set of four differing gasoline samples that serve as model complex samples. For comparison, the gasoline samples are analyzed by GC–MS over both 10-min and 10-s separation times. The successfully classified 10-min GC–MS TIC data served as the benchmark analysis to compare to the 10-s data. When only alignment and feature selection was applied to the 10-s gasoline separations using GC–MS TIC data, PCA failed. PCA was successful for 10-s gasoline separations when the methodology was applied with all the m/ z information. With ANOVA feature selection, chromatographic regions with Fisher ratios greater than 1500 were retained in a new matrix and subjected to PCA yielding successful classification for the 10-s separations.

Chemical composition of essential oil from seeds of Anethum graveolens cultivated in China

Dill, Anethum graveolens L. (Apiaceae), is an annual plant with a strong spicy odor [1]. Dill has been known since antiquity as an agent for increasing the stomach tonus and has been used for aches in the stomach and intestines, dispepsia, bladder inflammation, liver diseases, headaches, cramps, and insomnia [2]. The essential oil (EO) of dill seeds contains biologically active compounds [3, 4]. We used EO from dill seeds collected in the Xinjiang—Uigur Autonomous Region of China. EO was extracted from dill seeds (50 g) by steam distillation for 4 h and extracted from the aqueous phase by diethylether. The ether extract was dried with Na2SO4. Solvent was removed overnight. The yield of EO was 3.8% of the seed mass. EO of dill was an oily light yellow liquid with a unique odor and a density of 0.925 g/cm3. The chemical composition of the EO was studied by GC—MS on a Perkin—Elmer Turbo Mass Aid System XL gas chromatograph with a quadrupole mass spectrometer as the detector. We used a 30-m PE-5MS capillary quartz column (copolymer 5% phenylmethylsilicone) with internal diameter 0.25 mm and stationary-phase film thickness 25 μm, flow rate 35 mL/min, He carrier gas with temperature programming. The column was held for 2 min at 75°C, heated to 100°C at 2°C/min, to 160°C at 4°C/min, to 220°C at 2°C/min, and held for 2 min at that temperature. The final isothermal duration was 20 min at 230°C. Samples (0.2 μL) were injected. The evaporator temperature was 180°C; detector, 220°C; ionization potential, 70 eV, m/z, 30-550. The contents of oil components were calculated using the areas of the GC peaks without correction coefficients. Quantitative analysis was based on comparison of retention times and complete mass spectra with those of standard oil components, pure compounds, and mass spectrometric libraries of NBS, NIST, and Wiley.

Bile Acid Synthesis in Humans Has a Rapid Diurnal Variation That Is Asynchronous With Cholesterol Synthesis

The conversion of cholesterol to bile acids by the liver is an important regulator of body cholesterol homeostasis. In rodents, both cholesterol and bile acid synthesis have marked diurnal rhythms that peak synchronously at midnight. The aim of this study was to establish whether such diurnal rhythms are also present in healthy humans. Serum levels of the markers 7alpha-hydroxy-4-cholesten-3-one (C4) monitoring bile acid biosynthesis and lathosterol reflecting cholesterol synthesis were determined at 90-minute intervals in 8 human volunteers during standardized dietary conditions. Serum C4 showed 2 distinct peaks (2- to 4-fold above baseline) during a 24-hour period, the first at 1:00 pm and the second at 9:00 pm. During the night, C4 levels declined, and they returned to baseline levels the next morning. In contrast, serum lathosterol levels peaked at night, between midnight and 4:00 am. The diurnal changes of C4 were not synchronous with serum lipid changes or with the postprandial increase in serum bile acids and were maintained in cholecystectomized subjects. Bile acid synthesis in humans has a diurnal rhythm, with 2 peaks during the daytime, that is opposite from the circadian rhythm of cholesterol synthesis. This is completely different from the pattern in rodents and indicates the presence of an important species variation in the regulation of cholesterol homeostasis.

Analysis of Glass Fragments by Laser Ablation-Inductively Coupled Plasma-Mass Spectrometry and Principal Component Analysis

Laser ablation-inductively coupled plasma-mass spectrometry (LA-ICP-MS) is used to differentiate glass samples with similar optical and physical properties based on trace elemental composition. Laser ablation increases the number of elements that can be used for differentiation by eliminating problems commonly associated with dissolution and contamination. In this study, standard residential window and tempered glass samples that could not be differentiated by refractive index or density were successfully differentiated by LA-ICP-MS. The primary analysis approach used is Principal Component Analysis (PCA) of the complete mass spectrum. PCA, a multivariate analysis technique, provides rapid analysis of samples without time-consuming pair-wise comparison of calibrated analyses or prior knowledge of the elements present in the samples. Probabilities for positive association of the individual samples are derived from PCA. Utilization of the Q-statistic with PCA allowed us to distinguish all samples within the set to a certainty greater than the 99% confidence interval.

A Novel Polymorphic Cytochrome P450 Formed by Splicing of CYP3A7 and the Pseudogene CYP3AP1

The cytochrome P450 3A7 (CYP3A7) is the most abundant CYP in human liver during fetal development and first months of postnatal age, playing an important role in the metabolism of endogenous hormones, drugs, differentiation factors, and potentially toxic and teratogenic substrates. Here we describe and characterize a novel enzyme, CYP3A7.1L, encompassing the CYP3A7.1 protein with the last four carboxyl-terminal amino acids replaced by a unique sequence of 36 amino acids, generated by splicing of CYP3A7 with CYP3AP1 RNA. The corresponding CYP3A7-3AP1 mRNA had a significant expression in liver, kidney, and gastrointestinal tract, and its presence was found to be tissue-specific and dependent on the developmental stage. Heterologous expression in yeast revealed that CYP3A7.1L was a functional enzyme with a specific activity similar to that of CYP3A7.1 and, in some conditions, a different hydroxylation specificity than CYP3A7.1 using dehydroepiandrosterone as a substrate. CYP3A7.1L was found to be polymorphic due to a mutation at position -6 of the first splicing site of CYP3AP1 (CYP3A7_39256T-->A), which abrogates the pseudogene splicing. This polymorphism had pronounced interethnic differences and was in linkage disequilibrium with other functional polymorphisms described in the CYP3A locus: CYP3A7*2 and CYP3A5*1. Therefore, the resulting CYP3A haplotypes express different sets of enzymes within the population. In conclusion, a novel mechanism, consisting of the splicing of the pseudogene CYP3AP1 to CYP3A7, causes the formation of the novel CYP3A7.1L having a different tissue distribution and functional properties than the parent CYP3A7 enzyme, with possible developmental, physiological, and toxicological consequences.

Maximum likelihood principal component analysis of time-of-flight secondary ion mass spectrometry spectral images

Many modern surface analytical instruments are able to acquire huge amounts of data in the form of spectral images. Time-of-flight secondary ion mass spectrometry (TOF-SIMS), for instance, can easily generate a complete mass spectrum at each point in a two-dimensional or three-dimensional spatial array. The challenge for the data analyst, then, is to garner the analytically useful information from the overwhelming quantity of raw spectral data. Factor analysis techniques such as principal component analysis (PCA) have proven quite useful in this endeavor. Standard PCA, however, assumes that noise in the data is uniform, that is, that it does not depend on the magnitude of signal. This is clearly not correct for methods that rely on particle counting where the noise is governed by Poisson statistics. In this case, properly accounting for heteroscedasticity is essential to extracting the chemical information into a minimum number of factors while optimally excluding noise. Maximum likelihood PCA (MLPCA) is one approach to addressing this issue. MLPCA can, in principle, incorporate a separate uncertainty estimate for each individual observation in a data set. This article will present a MLPCA analysis of a simple and intuitive TOF-SIMS spectral image. The results show that there is a trade-off between the number of uncertainty parameters included in the model and the quality of each and, in fact, using poor estimates may be worse than ignoring the noise characteristics altogether. The best results were obtained by using a low-rank approximation to the noise rather than individual estimates. MLPCA will also be compared with an optimal scaling approach. For the particular example given, the added benefits of MLPCA do not outweigh the greatly increased computational demands of the technique.

Single Particle Laser Ablation Time-of-Flight Mass Spectrometer: An Introduction to SPLAT

We present our single particle mass spectrometer we call SPLAT. SPLAT was designed to make possible the detection and characterization of particles down to 100 nm, generate reproducible single particle mass spectra, and collect data at a high rate. The final instrument presented here is capable of characterizing individual particles down to 50 nm at the rate of 20 particles per second. In SPLAT mass spectra are generated by a two-step process, thet uses a pulsed infrared laser to heat the particle and a time delayed pulsed UV laser to create ions. We describe a mode of operation that makes it possible to take advantage of the gas phase ionization of the semivolatile components of the particle, while also generating mass spectral signatures of the nonvolatile fraction, thereby proividing complete particle mass spectra. We present some sample results from two field deployments of SPLAT.

Concentration of N and P in SiC Investigated by Time-Of-Flight Secondary Ion Mass Spectrometry (TOF-SIMS)

The concentration of nitrogen and phosphorous in SiC bulk material and epitaxial layers was investigated using time-of-flight secondary ion mass spectrometry (TOF-SIMS). The advantage of TOF-SIMS of acquiring a complete mass spectrum in a single run was used to identify the most sensitive atomic ion or ionic cluster for the selected element to be monitored. For the investigation of N with its intrinsic low ionization yield the use of a Cs containing cluster ion is necessary. Selection of a CNCs2 + cluster allows to reach a detection limit of about cN,min » 5×1016 cm-3. In the case of P the elemental ion was used. However, the adjacent mass of 30SiH influences the P peak as well as its background and has to be suppressed. This can be achieved by limiting the residual gas re-adsorption during the measurement resulting in a detection limit of about cP,min » 5×1015 cm-3. These measurement parameters were used to investigate a single crystal SiC bulk sample grown by the modified Lely method with intentional P doping and an N doped epitaxial SiC layer sample.

Algorithm for locating analytes of interest based on mass spectral similarity in GC × GC–TOF-MS data: analysis of metabolites in human infant urine

The developed algorithm reported herein, referred to as “DotMap,” addresses the need to rapidly identify analyte peak locations in gas chromatography × gas chromatography–time of flight mass spectrometry (GC × GC–TOF-MS) data. The third-order structure of GC × GC–TOF-MS data is such that at each point in the GC × GC chromatogram, a complete mass spectrum is measured. DotMap utilizes this third-order structure to search for the location of a given spectrum of interest in a complete data set, or in a user selected portion of the complete data set. The algorithm returns a contour plot indicating the location of signal(s) with the most similar mass spectra to the analyte of interest. A spectrum from the region indicated is then subjected to an automated mass spectral search to give immediate feedback on the accuracy of the analysis. This algorithm was investigated with a trimethylsilyl (TMS) derivatized human infant urine sample that contained organic acid metabolites. One hundred percent of 12 selected TMS derivatized organic acid metabolites in human infant urine were located with the DotMap algorithm. A typical automated DotMap analysis takes 30 s on a 1.6 GHz PC with 1024 MB of RAM. Vanillic acid (TMS) was located by DotMap, but also exhibited overlap with other organic acids. The presence of vanillic acid (TMS) was confirmed by subjecting the appropriate GC × GC region to chemometric signal deconvolution by PARAFAC to yield pure component information suitable for subsequent quantification.

Multivariate selectivity as a metric for evaluating comprehensive two-dimensional gas chromatography–time-of-flight mass spectrometry subjected to chemometric peak deconvolution☆

Two-dimensional gas chromatography (GC × GC) coupled to time-of-flight mass spectrometry (TOFMS) [GC × GC–TOFMS)] is a highly selective technique well suited to analyzing complex mixtures. The data generated is information-rich, making it applicable to multivariate quantitative analysis and pattern recognition. One separation on a GC × GC–TOFMS provides retention times on two chromatographic columns and a complete mass spectrum for each component within the mixture. In this report, we demonstrate how GC × GC–TOFMS combined with trilinear chemometric techniques, specifically parallel factor analysis (PARAFAC) initiated by trilinear decomposition (TLD), results in a powerful analytical methodology for multivariate deconvolution. Using PARAFAC, partially resolved components in complex mixtures can be deconvoluted and identified without requiring a standard data set, signal shape assumptions or any fully selective mass signals. A set of four isomers (iso-butyl, sec-butyl, tert-butyl, and n-butyl benzenes) is used to investigate the practical limitations of PARAFAC for the deconvolution of isomers at varying degrees of chromatographic resolution and mass spectral selectivity. In this report, multivariate selectivity was tested as a metric for evaluating GC × GC–TOFMS data that is subjected to PARAFAC peak deconvolution. It was found that deconvolution results were best with multivariate selectivities over 0.18. Furthermore, the application of GC × GC–TOFMS followed by TLD/PARAFAC is demonstrated for a plant metabolite sample. A region of GC × GC–TOFMS data from a complex natural sample of a derivatized metabolic plant extract from Huilmo (Sisyrinchium striatum) was analyzed using TLD/PARAFAC, demonstrating the utility of this analytical technique on a natural sample containing overlapped analytes without selective ions or peak shape assumptions.

Algorithm for locating analytes of interest based on mass spectral similarity in GC × GC–TOF-MS data: analysis of metabolites in human infant urine

The developed algorithm reported herein, referred to as “DotMap,” addresses the need to rapidly identify analyte peak locations in gas chromatography × gas chromatography–time of flight mass spectrometry (GC × GC–TOF-MS) data. The third-order structure of GC × GC–TOF-MS data is such that at each point in the GC × GC chromatogram, a complete mass spectrum is measured. DotMap utilizes this third-order structure to search for the location of a given spectrum of interest in a complete data set, or in a user selected portion of the complete data set. The algorithm returns a contour plot indicating the location of signal(s) with the most similar mass spectra to the analyte of interest. A spectrum from the region indicated is then subjected to an automated mass spectral search to give immediate feedback on the accuracy of the analysis. This algorithm was investigated with a trimethylsilyl (TMS) derivatized human infant urine sample that contained organic acid metabolites. One hundred percent of 12 selected TMS derivatized organic acid metabolites in human infant urine were located with the DotMap algorithm. A typical automated DotMap analysis takes 30 s on a 1.6 GHz PC with 1024 MB of RAM. Vanillic acid (TMS) was located by DotMap, but also exhibited overlap with other organic acids. The presence of vanillic acid (TMS) was confirmed by subjecting the appropriate GC × GC region to chemometric signal deconvolution by PARAFAC to yield pure component information suitable for subsequent quantification.