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 x GC) coupled to time-of-flight mass spectrometry (TOFMS) [GC x 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 x 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 x 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 x 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 x GC-TOFMS followed by TLD/PARAFAC is demonstrated for a plant metabolite sample. A region of GC x 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.     

Pressure‐Tunable Dual‐Column Ensembles for High‐Speed GC and GC/MS

A series‐coupled ensemble of two capillary GC columns of different selectivity with an adjustable pressure at the column junction point is used to obtain tunable selectivity for high‐speed GC and GC/TOFMS. An electronic pressure controller with a 0.1‐psi step size is used to obtain numerous computer‐selected unique selectivities. System configurations for conventional, atmospheric‐pressure outlet operation with flame ionization detection and for vacuum‐outlet operation with photoionization detection are described for GC‐only experiments. Polydimethylsiloxane is used as the non‐polar column and polyethylene glycol (atmospheric outlet) or triflouropropylpolysiloxane (vacuum outlet) is used as the polar column. For GC/TOFMS experiments, 5% phenyl polydimethylsiloxane was used as the non‐polar column, and polyethylene glycol was used as the polar column. The time‐of‐flight mass spectrometer can acquire up to 500 complete mass spectra per second. Since spectral continuity is achieved across the entire chromatographic peak profile, severely overlapping peaks can be spectrally deconvoluted for high‐speed characterization of completely unknown mixtures. For mixture components with significantly different fragmentation patterns, spectral deconvolution can be achieved for chromatographic peak separations of as little as 6.0 ms. This can result is very large peak capacity for time compressed (not completely resolved) chromatograms. The use of columns with tunable selectivity allows for precise peak‐position control, which can result in more efficient utilization of available peak capacity and thus further time compression of chromatograms. The limits of tunability and deconvolution are tested for near co‐elutions of different classes of hydrocarbon compounds as well as for more multi‐functional mixtures.     

Characterization of cigarette smoke condensates by comprehensive two-dimensional gas chromatography/time-of-flight mass spectrometry (GC x GC/TOFMS). Part 2: basic fraction

Cigarette smoke condensate is a complex chemical matrix. Analysis of nitrogen-containing compounds present therein is very difficult because of the limitation of the peak capacity of conventional one-dimensional chromatography. Extensive and laborious sample preparation is frequently required or selective detectors are frequently used. In this study, the basic fraction of mainstream cigarette smoke condensate has been investigated by using comprehensive two-dimensional gas chromatography/time-of-flight mass spectrometry (GC x GC/TOFMS). Auto data processing by TOFMS software combined with manual identification was used to assign the components. 377 nitrogen-containing compounds, including 155 pyridine derivatives, 104 quinoline/isoquinoine derivatives, and 56 pyrazine derivatives were tentatively identified. By selecting appropriate unique masses and in the light of the component positions in the structured chromatogram, alkyl-substituted pyridines, pyrazines, and quinolines/isoquinolines were separately shown and further validated. The peaks of eight individual positional isomers of two-carbon-substituted pyridines and thirteen positional isomers of methyl-substituted quinolines/isoquinolines were further confirmed, based on linear incremental retention behavior in combination with TOFMS and the structured chromatogram of GC x GC.     

Qualitative mass spectrometric analysis of the volatile fraction of creosote-treated railway wood sleepers by using comprehensive two-dimensional gas chromatography

The volatile composition of 20-year-old out-of-service creosote-treated railway wood sleepers was studied. The emitted volatile fraction was collected by means of dynamic purge-and-trap concentration at ambient temperature, and analyzed by comprehensive two-dimensional gas chromatography (GC x GC) hyphenated with mass spectrometric detection systems, using quadrupole (GC x GC/qMS) and time-of-flight (GC x GC/ToF-MS) mass analyzers and selective nitrogen-phosphorus detection (GC x GC-NPD). The analysis of mass spectrometry data and GC x GC retention time allowed the tentative identification of about 300 compounds based on spectrometric data and positioning of each compound in the GC x GC plot. Major important headspace components are polyaromatic hydrocarbons, phenols and benzene derivatives, hydrocarbons and heterocyclic compounds containing nitrogen, sulphur or oxygen atoms. Many of the reported compounds are listed as belonging to toxicological substance classes which have been related to harmful health effects. GC x GC provides greater speciation and evidence of composition heterogenicity of the sample than one-dimensional GC analysis, thus allowing to better demonstrate its potential toxicity. Data obtained by specific detection systems for N-heterocycles assisted mass data interpretation assignments. The enhanced separation power obtained after GC x GC compared to one-dimensional gas chromatography (1D-GC) together with spectral deconvolution and correlation with physical-chemical data, allowed the identification of complex isomer clusters, as demonstrated for alkylquinolines, and applied also to alkylphenols, alkylbenzenes and alkylnaphthalenes.     

Effects of pressure drop on absolute retention matching in comprehensive two-dimensional gas chromatography

Comprehensive two-dimensional gas chromatography (GC x GC) analysis has the capability to resolve many more components of complex mixtures than traditional single column GC analysis. There is an increasing need to provide reliable identification of these separated components; time-of-flight mass spectrometry (TOFMS) is the most appropriate technology to achieve this task. Rather than require MS for all GC x GC separations, it is desirable to assign peak identities to specific peak positions in the GC x GC separation space, and this necessitates matching peak retentions in the two experiments - GC x GC-FID and GC x GC-TOFMS. The atmospheric vs. vacuum outlet conditions confound this task. It is shown here that by employing a supplementary gas supply, provided to a T-union between the column outlet and the MS interface, it is possible to generate 2D chromatograms for GC x GC-FID and GC x GC-TOFMS that are essentially exactly matched. There is no degradation in separation performance or efficiency in the second column in the system interfaced to the T-union. Since the GC x GC-FID experiment uses hydrogen for maximum efficiency, and GC x GC-TOFMS uses helium carrier, translation of (conditions/retentions) must account for the different viscosities of the carrier gases. Translation of conditions is based on well-known principles established in single column analysis. Tabulated data illustrate that retention reproducibility was of the order of better than 4 s for the average first dimension retention difference, and about 40 ms for the average second dimension retention difference when comparing GC x GC-FID and GC x GC-TOFMS results. This should provide considerable support for identification in routine GC x GC-FID analysis of specific sample types, once the peaks in 2D separation space have been assigned identities through GC x GC-TOFMS analysis.     

Unravelling the composition of very complex samples by comprehensive gas chromatography coupled to time-of-flight mass spectrometry. Cigarette smoke

The potential and current limitations of comprehensive two-dimensional gas chromatography coupled to time-of-flight mass spectrometry (GC x GC-TOF-MS) for the analysis of very complex samples were studied with the separation of cigarette smoke as an example. Because of the large number of peaks in such a GC x GC chromatogram it was not possible to perform manual data processing. Instead, the GC-TOF-MS software was used to perform peak finding, deconvolution and library search in an automated fashion; this resulted in a peak table containing some 30000 peaks. Mass spectral match factors were used to evaluate the library search results. The additional use of retention indices and information from second-dimension retention times can substantially improve the identification. The combined separation power of the GC x GC-TOF-MS system and the deconvolution algorithm provide a system with a most impressive separation power.     

Characterization and pattern recognition of oil-sand naphthenic acids using comprehensive two-dimensional gas chromatography/time-of-flight mass spectrometry

Oil-sand naphthenic acids (NAs) are organic wastes produced during the oil-sand digestion and extraction processes and are very difficult to separate and analyze as individual components due to their complex compositions. A comprehensive two-dimensional gas chromatography/time of flight mass spectrometry (GC x GC/TOF-MS) system was applied for the characterization of two commercial mixtures of naphthenic acids (Fluka and Acros) and a naphthenic acid sample extracted from the Syncrude tailings. Contour plots of chromatographic distributions of different Z homologous series of the Fluka, Acros and Syncrude NAs were constructed using fragment ions that were characteristic of the NA's molecular structures. Well-ordered patterns were observed for NAs of Z= 0 and -2 which corresponded to acyclic acids and monocyclic acids, respectively. For NAs of Z= -4, -6, and -8, specific zones were observed which would allow the pattern recognition of these NAs obtained from different origins. As expected, gas chromatographic retention times increase with the number of the carbons and the number of rings in the molecules. Little signal was obtained for NAs with Z numbers of -10, or lower. Deconvoluted mass spectra of various NA isomers were derived from the reconstructed GC x GC chromatogram, permitting detailed structural elucidations for NAs in the future. The current study demonstrated that the combination of GC x GC and the TOF-MS is a powerful to identify origins of the NAs in an effective manner. GC x GC/TOF-MS alone, however, may not be enough to characterize each individual isomer in a complex mixture such as NAs. The use of mass deconvolution software followed by library search have thus become necessary to separate and study the mass spectrum of each individual NA component, allowing a detailed identification of the toxic components within the NAs mixture.     

Flexible Implementation of the Trilinearity Constraint in Multivariate Curve Resolution Alternating Least Squares (MCR-ALS) of Chromatographic and Other Type of Data

Multivariate Curve Resolution Alternating Least Squares (MCR-ALS) can analyze three-way data under the assumption of a trilinear model using the trilinearity constraint. However, the rigid application of this constraint can produce unrealistic solutions in practice due to the inadequacy of the analyzed data to the characteristics and requirements of the trilinear model. Different methods for the relaxation of the trilinear model data requirements have been proposed, like in the PARAFAC2 and in the direct non-trilinear decomposition (DNTD) methods. In this work, the trilinearity constraint of MCR-ALS is adapted to different data scenarios where the profiles of all or some of the components of the system are shifted (not equally synchronized) or even change their shape among different slices in one of their data modes. This adaptation is especially useful in gas and liquid chromatography (GC and LC) and in Flow Injection Analysis (FIA) with multivariate spectroscopic detection. In a first data example, a synthetic LC-DAD dataset is built to investigate the possibilities of the proposed method to handle systematic changes (shifts) in the retention times of the elution profiles and the results are compared with those obtained using alternative methods like ATLD, PARAFAC, PARAFAC2 and DNTD. In a second data example, multiple wine samples were simultaneously analyzed by GC-MS where elution profiles presented large deviations (shifts) in their peak retention times, although they still preserve the same peak shape. Different modelling scenarios are tested and the results are also compared. Finally, in the third example, sample mixtures of acid compounds were analyzed by FIA under a pH gradient and monitored by UV spectroscopy and also examined by different chemometric methods using a different number of components. In this case, however, the departure of the trilinear model comes from the acid base speciation of the system depending on the pH more than from the shifting of the FIA diffusion profiles.     

Analysis of gin essential oil mixtures by multidimensional and one-dimensional gas chromatography/mass spectrometry with spectral deconvolution

The composition of essential oils and their mixtures used to formulate gin is usually too complex to separate all sample components by standard capillary gas chromatography (GC). In particular, minor constituents that possess important organoleptic properties can be masked by co-elution with major sample components. A solution is provided that combines gas chromatography/mass spectrometry (GC/MS) with "interactive" spectral deconvolution software. Sequential two-dimensional (2D) GC/MS is used to produce a target compound library, with orthogonal GC-GC providing the separation power required to obtain peak retention times and the corresponding mass spectra needed for the deconvolution database. The combination of these two techniques, mass spectral deconvolution and automated sequential 2D-GC/MS, offers a very effective synergy for both identifying key constituents that determine the perception of flavor and aroma and the quality control needed to analyze mixtures of complex essential oils.     

Search criteria and rules for comprehensive two-dimensional gas chromatography-time-of-flight mass spectrometry analysis of airborne particulate matter

Direct thermal desorption-gas chromatography-time-of-flight mass spectrometry (DTD-GC-TOFMS) and comprehensive two-dimensional (2D) gas chromatography-time-of-flight mass spectrometry (GC x GC-TOFMS) was applied for characterisation of semi-volatile organic compounds (SVOC) in fine particulate matter (PM), with a diameter of up to 2.5 microm (PM2.5), from ambient air in Augsburg, Germany. DTD-GC-TOFMS measurements on the SVOC in PM2.5 are done on a daily basis (time series over several years). The data will be used in an epidemiological study questioning the influence of SVOC in PM2.5 on ambient aerosol related health effects. The outcome of the first measurements periods is that the organic inventory in the ambient aerosol can undergo drastic fluctuations, e.g. due to meteorological influences or specific emission sources. This includes also the large fraction of chromatographically not resolved peaks (unresolved carbonaceous matter (UCM)). The UCM fraction contains about 70% of the SVOC mass in PM2.5. GC x GC-TOFMS is a suited technique to study the nature of the yet unidentified compounds forming the UCM. The considerably increased chromatographic resolution in GC x GC allows separation of many UCM compounds while the TOFMS supplies mass spectral data of all separated compounds. However, the data sets are getting enormously complex. In a typical PM2.5 sample from Augsburg more than 15,000 peaks can be detected. Thus, it is important to classify the observed GC x GC peaks by rational means. A classification procedure based on GC x GC retention times and the fragmentation patterns is suggested. With a preliminary classification procedure it is already possible to group compounds with some certainty into substance classes. After some further development, this approach can be used for classifying GC x GC data, e.g. for environmental and epidemiological studies.     

Application of comprehensive multidimensional gas chromatography combined with time-of-flight mass spectrometry (GC x GC-TOFMS) for high resolution analysis of hop essential oil

The selection and quality of hops is a major determinant in beer flavour. Brewers acknowledge that distinctive characteristics of different hop varieties can be traced to the composition of their essential oils. The difficulty in characterising complex mixtures such as hop oil using 1-D chromatography is that many compounds co-elute. With the introduction of comprehensive multidimensional capillary gas chromatography (GC x GC), there is a tremendous improvement in the separation power or peak capacity. Recent work using GC x GC with flame ionisation detection has suggested that there may be over 1,000 compounds in hop oil. This work describes the use of GC x GC combined with TOFMS detection (Leco Pegasus 4D instrument) to analyse Target hop oil. The TOFMS spectral acquisition rate of 60 Hz provided sufficient spectra per peak (2-D peak base width of 0.1-0.2 s) for identification (119 components were identified with 45 previously unreported compounds). When analysing results, an advantage of GC x GC coupled to TOFMS is that 2-D chromatograms can be viewed for individual masses that are characteristic of particular functional groups. This allows the analyst to view the various homologous series of compounds although in certain cases coelution may still be present as shown by the esters with mass 75.     

Comprehensive two-dimensional gas chromatography/mass spectrometric analysis of pepper volatiles

The headspace compositions of 13 pepper and peppercorn samples of different species, colloquially also referred to as pepper, were analyzed, and more than 300 compounds were tentatively characterized by means of comprehensive two-dimensional gas chromatography in tandem with flame ionization detection, quadrupole mass spectrometric detection and time-of-flight mass spectrometric detection (GC x GC-FID, GC x GC/qMS and GC x GC/TOFMS, respectively). The analysis of volatile organic compounds (VOCs) was performed after solid-phase microextraction (SPME) using a 75-microm PDMS/DVB fibre. Fingerprint comparison between the three techniques permitted peaks to be assigned in the GC x GC-FID experiment based on the analogous MS analysis, taking into account retention shifts arising from method variations. When using GC x GC/TOFMS, about five times more peaks were identified than in GC x GC/qMS. Retention indices for all peaks were calculated in the bi-dimensional column set comprising of a 5% phenyl polysilphenylene-siloxane primary column and a polyethylene glycol second column. The spectra obtained by both mass detection techniques (qMS and TOFMS) give very similar results when spectral library searching was performed. The majority of the identified compounds eluted as pure components as a result of high-resolution GC x GC separations, which significantly reduces co-elution, and therefore increases the likelihood that pure spectra can be obtained. The differences between TOFMS and qMS (in fast scanning mode) spectra were generally small. Whilst spectral quality and relative ion ratios across a narrow peak (e.g. w(b) approximately 100-150 ms) do vary more for the fast peaks obtained in GC x GC/qMS operation, than with TOFMS, in general adequate spectral matching with the library can be achieved.     

Application of parallel factor analysis to total synchronous fluorescence spectrum of dilute multifluorophoric solutions: Addressing the issue of lack of trilinearity in total synchronous fluorescence data set

In recent years, total synchronous fluorescence (TSF) spectroscopy has become popular for the analysis of multifluorophoric systems. Application of PARAFAC, a popular deconvolution tool, requires trilinear structure in the three-way data array. The present work shows that TSF based three-way array data set of dimension sample × wavelength × Δλ does not have trilinear structure and hence it should not be subjected to PARAFAC analysis. This work also proposes that a TSF data set can be converted to an excitation–emission matrix fluorescence (EEMF) like data set which has trilinear structure, so that PARAFAC analysis can be performed on it. This also enables the retrieval of PARAFAC-separated component TSF spectra.     

Qualitative evaluation of thermal desorption-programmable temperature vaporization-comprehensive two-dimensional gas chromatography-time-of-flight mass spectrometry for the analysis of selected halogenated contaminants

The separation of 38 toxic and predominant polychlorinated biphenyl (PCB) congeners, 11 persistent halogenated pesticides, 1 brominated biphenyl (BB), and 8 polybrominated diphenyl ethers (PBDEs) has been optimized using comprehensive two-dimensional gas chromatography coupled to time-of-flight mass spectrometry (GC x GC-TOFMS). A thermal desorption-programmable temperature vaporization (TD-PTV) step was used for the injection. Different column sets were investigated, and a 100% dimethylpolysiloxane (15 m x 0.25 mm i.d. x 0.25 microm film thickness) narrowbore capillary column coupled to a high temperature (8% phenyl)-polycarborane-siloxane (2 m x 0.10 mm i.d. x 0.10 microm film thickness) microbore column set was selected. Of the 58 compounds investigated, only one pair of PCBs was not resolved. All other analytes were either baseline separated into the chromatographic plane or were virtually separated using the deconvolution capability of the TOFMS.     

Approaching the direct exponential curve resolution algorithm from a maximum likelihood perspective

The implementation of maximum likelihood parallel factor analysis (MLPARAFAC) in conjunction with the direct exponential curve resolution algorithm (DECRA) is described. DECRA takes advantage of the intrinsic exponential structure of some bilinear data sets to produce trilinear data by a simple shifting scheme, but this manipulation generates an error structure that is not optimally handled by traditional three-way chemometrics methods such as TLD and PARAFAC. In this work, the effects of these violations are studied using simulated and experimental data used in conjunction with the well-established TLD and PARAFAC. The results obtained by both methods are compared with the results obtained by MLPARAFAC, which is a method designed to optimally accomodate a variety of measurement error structures. The impact on the estimates of different parameters linked to the data sets and the DECRA method is investigated using simulated data. The results indicate that PARAFAC produces estimates of much poorer quality than TLD and MLPARAFAC. Also, it was found that the quality TLD estimates was comparable or only marginally poorer than the MLPARAFAC estimates. A number of commonly used algorithms were also compared to MLPARAFAC using two sets of published experimental data from kinetic studies. The MLPARAFAC estimates of rate constants were more precise than the other methods examined.     

Direct determination of free amino acids and sugars in green tea by anion-exchange chromatography with integrated pulsed amperometric detection

Solutes analysed with LC-MS are characterised by their retention times and mass spectra, and quantified by the intensities measured. This highly selective information can be extracted by multiway modelling. However, for full use and interpretability it is necessary that the assumptions made for the model are valid. For PARAFAC modelling, the assumption is a trilinear data structure. With LC-MS, several factors, e.g. non-linear detector response and ionisation suppression may introduce deviations from trilinearity. The single largest problem, however, is the retention time shifts not related to the true sample variations. In this paper, a time warping algorithm for alignment of LC-MS data in the chromatographic direction has been examined. Several refinements have been implemented and the features are demonstrated for both simulated and real data. With moderate time shifts present in the data, pre-processing with this algorithm yields approximately trilinear data for which reasonable models can be made.     

Detection of verapamil drug by fluorescence and trilinear decomposition techniques

A three-way analytical methodology experimentally based on fluorescence excitation emission matrix (EEM) and in PARAFAC and TLD chemometric analysis was assessed for the quantification of verapamil drug in a tablet formulation. A standard addition procedure generates experimental information compatible with the chemometric data analysis model allowing the estimation of verapamil with a detection limit of about 0.04 mg/l using methanol as solvent. The structure of the verapamil EEM follows a trilinear model, but background signals (first- and second-order scatter bands) did not—a trilinear three-factor model is necessary to describe experimental datasets. The comparison of a three-factor PARAFAC model with a United States Pharmacopoeia (USP) standard chromatographic method showed similar results.     

The novel use of gas chromatography-ion mobility-time of flight mass spectrometry with secondary electrospray ionization for complex mixture analysis

Increasing the dimensionality of an analysis enables more detailed and comprehensive investigations of complex mixtures. One dimensional separation techniques like gas chromatography (GC) and ion mobility spectrometry (IMS) provide limited chemical information about complex mixtures. The combination of GC, ion mobility spectrometry, and time-of-flight mass spectrometry (GC-IM-TOFMS) provides three-dimensional separation of complex mixtures. In this work, a hybrid GC-IM-TOFMS with a secondary electrospray ionization (SESI) source provided four types of analytical information: GC retention time, ion mobility drift time, mass-to-charge ratios, and ion intensity. The use of secondary electrospray ionization enables efficient and soft ionization of gaseous sample vapors at atmospheric pressure. Several complex mixtures, including lavender and peppermint essential oils, were analyzed by GC-SESI-IM-TOFMS. The resulting 3D data from these mixtures, each containing greater than 50 components, were plotted as 3D projections. In particular, post-processed data plotted in three dimensions showed that many mass selected GC peaks were resolved into different ion mobility peaks. This technique shows clear promise for further in-depth analyses of complex chemical and biological mixtures.     

Analysis of methoxypyrazines in wine using headspace solid phase microextraction with isotope dilution and comprehensive two-dimensional gas chromatography

This study reports an optimized headspace-solid phase microextraction (HS-SPME) method for the determination of methoxypyrazines in wine. Analysis was performed by using comprehensive two-dimensional gas chromatography with novel detection capabilities, including nitrogen phosphorus detection (GC x GC-NPD) and time-of-flight mass spectrometry (GC x GC-TOFMS). In the latter, stable isotope dilution was performed for the quantitation of 2-methoxy-3-(2-methylpropyl) pyrazine (IBMP), using labelled 2-(2H3)methoxy-3-(2-methylpropyl)pyrazine (d3-IBMP) as the internal standard, and resolution of the two analogues was facilitated using the deconvolution capabilities of the TOFMS. This research represents the first report of HS-SPME with isotope dilution and GC x GC-TOFMS (GC x GC-IDTOFMS). Analysis by GC x GC-NPD enabled detection limits of 0.5 ng/L for the quantitation of IBMP, which was superior to that obtained using GC x GC-IDTOFMS (1.95 ng/L). Nevertheless, both methods were adequately sensitive for real wine analysis, yielding highly comparable IBMP concentrations of 26.1 and 27.8 ng/L, respectively, from a Sauvignon blanc wine. The complexity of the real wine headspace was simplified as a result of selective detection using GC x GC-NPD and, in the case of GC x GC-IDTOFMS, the use of extracted ion chromatograms (EICs).     

Quantification of naphthalenes in jet fuel with GC x GC/Tri-PLS and windowed rank minimization retention time alignment

Comprehensive, two-dimensional gas chromatography (GC x GC) is used in conjunction with trilinear partial least squares (Tri-PLS) to quantify the percent weight of naphthalenes (two-ring aromatic compounds) in jet fuel samples. The increased peak capacity and selectivity of GC x GC makes the technique attractive for the rapid, and possibly less tedious analysis of jet fuel. The analysis of complex mixtures by GC x GC is further enhanced through the use of chemometric techniques, including those designed for use on 2-D data such as Tri-PLS. Unfortunately, retention time variation, unless corrected, can be an impediment to chemometric analysis. Previous work has demonstrated that the effects of retention time variation can be mitigated in sub-regions of GC x GC chromatograms through the application of an objective retention time alignment algorithm based on rank minimization. Building upon this previous work, it is demonstrated here that the effects of retention time variation can be mitigated throughout an entire GC x GC chromatogram with an objective retention time alignment algorithm based on windowed rank minimization alignment. A significant decrease in calibration error is observed when the algorithm is applied to chromatograms prior to construction of Tri-PLS models. Fourteen jet fuel samples with known weight percentages of naphthalenes (ASTM D1840) were obtained. Each sample was subjected to five replicate five-minute GC x GC separations over a period of two days. A subset of nine samples spanning the range of weight percentages of naphthalenes was chosen as a calibration set and Tri-PLS calibration models were subsequently developed in order to predict the naphthalene content of the samples from the GC x GC chromatograms of the remaining five samples. Calibration models constructed from GC x GC chromatograms that were retention time corrected are shown to exhibit a root mean square error of prediction of roughly half that of calibration models constructed from uncorrected chromatograms. The error of prediction is lowered further to a value that nearly matches the uncertainty in the standard percent weight values (ca. 1% of the median percent volume value) when the aligned chromatograms are truncated to include only regions of the chromatogram populated by naphthalenes and compounds of similar polarity and boiling point.