Understanding Gas Phase Ion Chemistry Is the Key to Reliable Selected Ion Flow Tube-Mass Spectrometry Analyses

Boosting the sensitivity of single photon ionization time-of-flight mass spectrometry using a segmented focus quadrupole-ion guide

Single photon ionization time-of-flight mass spectrometry (SPI-TOF-MS) is a powerful analytical technique for real-time detection of trace VOCs. However, efficient ion transmission within the ionization chamber has always been a challenging issue in SPI-TOF-MS. In this study, a novel ion guide termed the Segmented Focus Quadrupole Ion Guide (SFQ-IG) was introduced for SPI-TOF-MS. The SFQ-IG device consists of 12 printed circuit boards (PCB), each containing four quarter-ring electrodes with inner diameters progressively decreasing from 26 to 4 mm. The simulation results demonstrated that SFQ-IG exhibited superior ion transmission efficiency than both ion funnel (IF) field and direct current-only (DC-only) field. By integrating into a SPI-TOF-MS, this ion guide was optimized in terms of the ionization source pressure, direct current gradient, and radio frequency amplitude. Further comparative experiments demonstrated that the SPI-TOF-MS with the SFQ-IG exhibited higher sensitivity than both the IF field (1.3-7.4 times) and DC-only field (3.5-8.8 times) for the test VOCs. The improvements in limit of detection (LOD) with the SFQ-IG ranged from 1.6 to 5.3 times compared to the DC-only field for the test VOCs. Fabricated using PCB technology, the SFQ-IG is characterized by its cost-effectiveness, compact size, and high transmission efficiency, facilitating its integration into other mass spectrometers.

Robust Automated SIFT-MS Quantitation of Volatile Compounds in Air Using a Multicomponent Gas Standard

Selected ion flow tube mass spectrometry, SIFT-MS, has been widely used in industry and research since its introduction in the mid-1990s. Previously described quantitation methods have been advanced to include a gas standard for a more robust and repeatable analytical performance. The details of this approach to calculate the concentrations from ion-molecule reaction kinetics based on reaction times and instrument calibration functions determined from known concentrations in the standard mix are discussed. Important practical issues such as the overlap of product ions are outlined, and best-practice approaches are presented to enable them to be addressed during method development. This review provides a fundamental basis for a plethora of studies in broad application areas that are possible with SIFT-MS instruments.

Accurate selected ion flow tube mass spectrometry quantification of ethylene oxide contamination in the presence of acetaldehyde

In September 2020, traces of ethylene oxide (a toxic substance used as a pesticide in developing countries but banned for use on food items within the European Union) were found in foodstuffs containing ingredients derived from imported sesame seed products. Vast numbers of foodstuffs were recalled across Europe due to this contamination, leading to expensive market losses and extensive trace exposure of ethylene oxide to consumers. Therefore, a rapid analysis method is needed to ensure food safety by high-throughput screening for ethylene oxide contamination. Selected ion flow tube mass spectrometry (SIFT-MS) is a suitable method for rapid quantification of trace amounts of vapours in the headspace of food samples. It turns out, however, that the presence of acetaldehyde complicates SIFT-MS analyses of its isomer ethylene oxide. It was proposed that a combination of the H3O+ and NO+ reagent ions can be used to analyse ethylene oxide in the presence of acetaldehyde. This method is, however, not robust because of the product ion overlaps and potential interferences from other matrix species. Thus, we studied the kinetics of the reactions of the H3O+, NO+, OH- and O-˙ ions with these two compounds and obtained their rate coefficients and product ion branching ratios. Interpretation of these experimental data revealed that the OH- anions are the most suitable SIFT-MS reagents because the product ions of their reactions with acetaldehyde (CH2CHO- at m/z 43) and ethylene oxide (C2H3O2- at m/z 59) do not overlap.

Increasing the Robustness of SIFT-MS Volatilome Fingerprinting by Introducing Notional Analyte Concentrations

Selected ion flow tube-mass spectrometry (SIFT-MS) is an analytical technique for volatile detection and quantification. SIFT-MS can be applied in a "white box" approach, measuring concentrations of target compounds, or as a "black box" fingerprinting technique, scanning all product ions during a full scan. Combining SIFT-MS full scan data acquired from multibatches or large-scale experiments remains problematic due to signal fluctuation over time. The standard approach of normalizing full scan data to the total signal intensity was insufficient. This study proposes a new approach to correct SIFT-MS fingerprinting data. In this concept, all of the product ions from a full scan are considered individual compounds for which notional concentrations can be calculated. Converting ion count rates into notional analyte concentrations accounts for any changes in the instrument parameters. The benefits of the proposed approach are demonstrated on three years of data from both multibatches and long-term experiments showing a significant reduction of system-induced fluctuations providing a better focus on the changes of interest.

How to Use Ion-Molecule Reaction Data Previously Obtained in Helium at 300 K in the New Generation of Selected Ion Flow Tube Mass Spectrometry Instruments Operating in Nitrogen at 393 K

Selected ion flow tube mass spectrometry (SIFT-MS) instruments have significantly developed since this technique was introduced more than 20 years ago. Most studies of the ion-molecule reaction kinetics that are essential for accurate analyses of trace gases and vapors in air and breath were conducted in He carrier gas at 300 K, while the new SIFT-MS instruments (optimized to quantify concentrations down to parts per trillion by volume) operate with N₂ carrier gas at 393 K. Thus, we pose the question of how to reuse the data from the extensive body of previous literature using He at room temperature in the new instruments operating with N₂ carrier gas at elevated temperatures. Experimentally, we found the product ions to be qualitatively similar, although there were differences in the branching ratios, and some reaction rate coefficients were lower in the heated N₂ carrier gas. The differences in the reaction kinetics may be attributed to temperature, an electric field in the current flow tubes, and the change from He to N₂ carrier gas. These results highlight the importance of adopting an updated reaction kinetics library that accounts for the new instruments' specific conditions. In conclusion, almost all previous rate coefficients may be used after adjustment for higher temperatures, while some product ion branching ratios need to be updated.

Recent developments and applications of selected ion flow tube mass spectrometry (SIFT-MS)

Selected ion flow tube mass spectrometry (SIFT-MS) is now recognized as the most versatile analytical technique for the identification and quantification of trace gases down to the parts-per-trillion by volume, pptv, range. This statement is supported by the wide reach of its applications, from real-time analysis, obviating sample collection of very humid exhaled breath, to its adoption in industrial scenarios for air quality monitoring. This review touches on the recent extensions to the underpinning ion chemistry kinetics library and the alternative challenge of using nitrogen carrier gas instead of helium. The addition of reagent anions in the Voice200 series of SIFT-MS instruments has enhanced the analytical capability, thus allowing analyses of volatile trace compounds in humid air that cannot be analyzed using reagent cations alone, as clarified by outlining the anion chemistry involved. Case studies are reviewed of breath analysis and bacterial culture volatile organic compound (VOC), emissions, environmental applications such as air, water, and soil analysis, workplace safety such as transport container fumigants, airborne contamination in semiconductor fabrication, food flavor and spoilage, drugs contamination and VOC emissions from packaging to demonstrate the stated qualities and uniqueness of the new generation SIFT-MS instrumentation. Finally, some advancements that can be made to improve the analytical capability and reach of SIFT-MS are mentioned.

Kinetics of reactions of NH4 + with some biogenic organic molecules and monoterpenes in helium and nitrogen carrier gases: A potential reagent ion for selected ion flow tube mass spectrometry

RATIONALE

To assess the suitability of NH₄ ⁺ as a reagent ion for trace gas analysis by selected ion flow tube mass spectrometry, SIFT-MS, its ion chemistry must be understood. Thus, rate coefficients and product ions for its reactions with typical biogenic molecules and monoterpenes need to be experimentally determined in both helium, He, and nitrogen, N₂ , carrier gases.

METHODS

NH₄ ⁺ and H₃ O⁺ were generated in a microwave gas discharge through an NH₃ and H₂ O vapour mixture and, after m/z selection, injected into He and N₂ carrier gas. Using the conventional SIFT method, NH₄ ⁺ reactions were then studied with M, the biogenic molecules acetone, 1-propanol, 2-butenal, trans-2-heptenal, heptanal, 2-heptanone, 2,3-heptanedione and 15 monoterpene isomers to obtain rate coefficients, k, and product ion branching ratios. Polarisabilities and dipole moments of the reactant molecules and the enthalpy changes in proton transfer reactions were calculated using density functional theory.

RESULTS

The k values for the reactions of the biogenic molecules were invariably faster in N₂ than in He but similar in both bath gases for the monoterpenes. Adducts NH₄ ⁺ M were the dominant product ions in He and N₂ for the biogenic molecules, whereas both MH⁺ and NH₄ ⁺ M product ions were observed in the monoterpene reactions; the monoterpene ratio correlating (R²  = 0.7) with the proton affinity, PA, of the monoterpene molecule as calculated. The data indicate that this adduct ion formation is the result of bimolecular rather than termolecular association.

CONCLUSIONS

NH₄ ⁺ can be a useful reagent ion for SIFT-MS analyses of molecules with PA(M) < PA(NH₃ ) when the dominant single product ion is the adduct NH₄ ⁺ M. For molecules with PA(M) > PA(NH₃ ), such as monoterpenes, both MH⁺ and NH₄ ⁺ M ions are likely products, which must be determined along with k by experiment.

Study of the Chemical Ionization of Organophosphate Esters in Air Using Selected Ion Flow Tube-Mass Spectrometry for Direct Analysis

Organophosphate esters are an emerging environmental concern since they spread persistently across all environmental compartments (air, soil, water, etc.). Measurements of semivolatile organic compounds are important but not without challenges due to their physicochemical properties. Selected ion flow tube-mass spectrometry (SIFT-MS) can be relevant for their analysis in air because it is a direct analytical method without separation that requires little preparation and no external calibration. SIFT-MS is based on the chemical reactivity of analytes with reactant ions. For volatile and semivolatile organic compound analysis in the gas phase, knowledge of ion-molecule reactions and kinetic parameters is essential for the utilization of this technology. In the present work, we focused on organophosphate esters, semivolatile compounds that are now ubiquitous in the environment. The ion-molecule reactions of eight precursor ions that are available in SIFT-MS (H₃O⁺, NO⁺, O₂^•+, OH^-, O^•-, O₂^•-, NO₂^-, and NO₃^-) with six organophosphate esters were investigated. The modeling of ion-molecule reaction pathways by calculations supported and complemented the experimental work. Organophosphate esters reacted with six of the eight precursor ions with characteristic reaction mechanisms, such as protonation with hydronium precursor ions and association with NO⁺ ions, while nucleophilic substitution occurred with OH^-, O^•-, and O₂^•-. No reaction was observed with NO₂^- and NO₃^- ions. This work shows that the direct analysis of semivolatile organic compounds is feasible using SIFT-MS with both positive and negative ionization modes.

Ternary association reactions of H3 O+ , NO+ and O2 +• with N2 , O2 , CO2 and H2 O; implications for selected ion flow tube mass spectrometry analyses of air and breath

RATIONALE

The reactions of the reagent ions used for trace gas analysis in selected ion flow tube mass spectrometry (SIFT-MS), R⁺ , viz. H₃ O⁺ , NO⁺ and O₂ ⁺ , with the major gases in air and breath samples, M, viz. N₂ , O₂ , CO₂ and H₂ O, are investigated. These reactions are seen to form weakly-bound adduct ions, R⁺ M, by ternary association reactions that must not be mistaken for genuine volatile organic compound (VOC) analyte ions.

METHODS

The ternary association rate coefficients mediated by helium (He) carrier gas atoms, k_3a , have been determined for all combinations of R⁺ and M, which form R⁺ M adduct ions ranging in m/z from 47 (H₃ O⁺ N₂ ) to 76 (O₂ ^+• CO₂ ). This was achieved by adding variable amounts of M (up to 0.5 mbar pressure) into the He carrier gas (pressure of 1.33 mbar) in a SIFT-MS flow tube at 300 K. Parabolic curvature was observed on some of the semi-logarithmic decay curves that allowed the rate coefficients mediated by M molecules, k_3b , to be estimated.

RESULTS

Values of k_3a were found to range from 1 × 10^-31  cm⁶  s^-1 to 5 × 10^-29  cm⁶  s^-1 , which form mass spectral R⁺ M "ghost peaks" of significant strength when analysing VOCs at parts-per-billion concentrations. It was seen that the R⁺ M adduct ions (except when M is H₂ O) react with H₂ O molecules by ligand switching forming the readily recognised monohydrates of the initial reagent cations R⁺ H₂ O. Whilst this ligand switching diminishes the R⁺ M adduct ghost peaks, it does not eliminate them entirely.

CONCLUSIONS

The significance of these adduct ions for trace gas analysis by SIFT-MS in the low m/z region is alluded to, and some examples are given of m/z spectral overlaps of the R⁺ M and R⁺ H₂ O adduct cations with analyte cations of VOCs formed by analysis of complex media like exhaled breath, warning that ghost peaks will be enhanced using nitrogen carrier gas in SIFT-MS.

Evaluation and optimization of the influence of silver cluster ions on the MALDI-TOF-MS analysis of polystyrene nanoplastic polymers

In the analysis of polystyrene nanoplastics (PSNs), a nonpolar polymer (NP), using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS), silver salts were used as cationization reagents and simultaneously brought the potential problems of silver clusters that interfered with the PSN signal of MS. To detect PSNs, silver trifluoroacetate (AgTFA) and silver nitrate (AgNO₃) were mixed with five polar matrices, namely 2-(4-hydroxyphenylazo) benzoic acid (HABA), dithranol (DI), sinapic acid (SA), trans-3-indoleacrylic acid (IAA), and 2,5-dihydroxybenzoic acid (DHB), and three nonpolar matrices, namely pyrene (PRN), anthracene (ATH) and acenaphthene (ACTH). The results showed that silver salt cluster ions were detected in the range of m/z 1000-4000. Five polar matrices with silver salts produced silver clusters, which interfered with the signals in the mass spectrum of PSNs, but the combination of these matrices with copper II chloride (CuCl₂) salt did not produce copper-related clusters. However, the use of nonpolar matrices such as PRN, ATH or ACTH significantly decreased the signals of silver salt cluster ions, and this alteration of matrix types is considered a promising optimization approach for silver cluster ions. The nonpolar matrix conditions were optimized without producing silver cluster ions and the optimal detection conditions were found to be under nonpolar matrices (e.g., pyrene) with silver salts (e.g., AgTFA). The results suggest that when polar matrices, such as HABA, DI, SA, IAA, and DHB, are combined with silver salts in MALDI-TOF-MS analysis, silver-related clusters are detected in the range of m/z 1000-4000. Inhibition of the production of silver cluster ions can be achieved by the use of a nonpolar matrix (e.g., PRN) or polar matrix (e.g., DHB) with copper salts.

Untargeted selected ion flow tube mass spectrometry headspace analysis: High-throughput differentiation of virgin and recycled polyethylene pellets

RATIONALE

Recycled plastics are increasingly used for packaging of fast-moving consumer goods (FMCG). Compared with packaging made from virgin polymers, there is greater risk of taints entering products due to prior use of the polymers and incomplete cleaning. Increased quality assurance testing of polymer feedstock is required for recycled packaging. Selected ion flow tube mass spectrometry (SIFT-MS) analysis coupled with multivariate statistical data processing can provide high-throughput untargeted screening of recycled polymers at low cost per sample.

METHODS

SIFT-MS is a direct-injection MS technique that provides high-throughput automated headspace analysis of polymer samples when coupled with a syringe-injection autosampler (12 incubated samples per hour). Full-scan SIFT-MS data were processed using multivariate statistical analysis (specifically, the soft independent modeling by class analogy (SIMCA) algorithm).

RESULTS

SIFT-MS full-scan data were acquired for ten replicates each of ten recycled and four virgin high-density polyethylene (HDPE) pellet products from multiple manufacturers. The samples varied approximately 20-fold in terms of total volatile residue, while showing very high repeatability across replicates. SIFT-MS scan data were dominated by aliphatic and monoterpene hydrocarbon residues, and - to a lesser extent - alcohols. Application of the SIMCA algorithm to the data resulted in successful classification by both individual samples and manufacturers.

CONCLUSIONS

Automated, untargeted SIFT-MS analysis coupled with multivariate statistical data analysis has the potential to provide rapid, effective screening of recycled polymer products, which would provide increased quality assurance of recycled polymers used for FMCG.

Lipases as Effective Green Biocatalysts for Phytosterol Esters’ Production: A Review

Lipases are versatile enzymes widely used in the pharmaceutical, cosmetic, and food industries. They are green biocatalysts with a high potential for industrial use compared to traditional chemical methods. In recent years, lipases have been used to synthesize a wide variety of molecules of industrial interest, and extraordinary results have been reported. In this sense, this review describes the important role of lipases in the synthesis of phytosterol esters, which have attracted the scientific community’s attention due to their beneficial effects on health. A systematic search for articles and patents published in the last 20 years with the terms “phytosterol AND esters AND lipase” was carried out using the Scopus, Web of Science, Scielo, and Google Scholar databases, and the results showed that Candida rugosa lipases are the most relevant biocatalysts for the production of phytosterol esters, being used in more than 50% of the studies. The optimal temperature and time for the enzymatic synthesis of phytosterol esters mainly ranged from 30 to 101 °C and from 1 to 72 h. The esterification yield was greater than 90% for most analyzed studies. Therefore, this manuscript presents the new technological approaches and the gaps that need to be filled by future studies so that the enzymatic synthesis of phytosterol esters is widely developed.

Selected ion flow tube mass spectrometry for targeted analysis of volatile organic compounds in human breath

The analysis of volatile organic compounds (VOCs) within breath for noninvasive disease detection and monitoring is an emergent research field that has the potential to reshape current clinical practice. However, adoption of breath testing has been limited by a lack of standardization. This protocol provides a comprehensive workflow for online and offline breath analysis using selected ion flow tube mass spectrometry (SIFT-MS). Following the suggested protocol, 50 human breath samples can be analyzed and interpreted in <3 h. Key advantages of SIFT-MS are exploited, including the acquisition of real-time results and direct compound quantification without need for calibration curves. The protocol includes details of methods developed for targeted analysis of disease-specific VOCs, specifically short-chain fatty acids, aldehydes, phenols, alcohols and alkanes. A procedure to make custom breath collection bags is also described. This standardized protocol for VOC analysis using SIFT-MS is intended to provide a basis for wider application and the use of breath analysis in clinical studies.

Standard Validation Protocol for Selected Ion Flow Tube Mass Spectrometry Methods Applied to Direct Headspace Analysis of Aqueous Volatile Organic Compounds

Analysis of volatile organic compounds (VOCs) in water is conventionally conducted using gas chromatography (GC)-based methods, for which sample preparation demands are relatively high and throughput is relatively low due to the time taken to achieve chromatographic separation. Direct mass spectrometry (DMS) techniques such as selected ion flow tube mass spectrometry (SIFT-MS) have potential to analyze water headspace (HS) at high sensitivity with minimal sample preparation, eliminating preconcentration/purging and/or water management steps. However, the dearth of guidance for validation of DMS methods is an impediment to their adoption in routine analysis. This study applies and adapts an internationally recognized pharmaceutical industry guidance document for method validation to a prototypical SIFT-MS headspace analysis method for 17 toxic VOCs in water. The approach to validation is, however, applicable to any routine analysis conducted using SIFT-MS, and very likely to any methods developed using other DMS techniques. For the method developed and validated here, linearities (as measured by the linear regression coefficient, R²) were better than 0.990 for all compounds. Repeatability (measured using relative standard deviation, RSD) was less than 10% for all compounds. Similar method performance was observed for accuracy and recovery. The performance criteria achieved by this HS-SIFT-MS method suggest it has potential application in environmental and pharmaceutical routine analyses, perhaps as a rapid screening tool.

Secondary Ion Chemistry Mediated by Ozone and Acidic Organic Molecules in Iodide-Adduct Chemical Ionization Mass Spectrometry

Iodide-adduct chemical ionization mass spectrometry (I-CIMS) is a widely used technique in the atmospheric chemistry community to detect oxygenated volatile organic compounds (OVOCs) in real time. In this work, we report the occurrence of secondary ion chemistry from interactions between a strong oxygen donor (such as O₃ and peracids) and acidic OVOCs (such as carboxylic acids and organic hydroperoxides) in the ion-molecule reaction (IMR) region of I-CIMS. Such interactions can lead to acidic organic molecules (HA or HB) clustering with [IO]^- (e.g., [HA + IO]^-) and dimer adducts ([A + B + I]^-), in addition to the well-known iodide clusters ([HA + I]^-). This ion chemistry was probed using common chemical standards as well as the gas-phase oxidation products of α-pinene and isoprene in a flowtube reactor. The results show that secondary ion chemistry can lead to misinterpretations of molecular compositions and distributions of the gas-phase products and an overestimation of the elemental O/C ratio overall. Nevertheless, the varying degrees of signal change in response to the secondary ion chemistry might be a clue to inform OVOCs' functionalities. Specifically, in the α-pinene ozonolysis system, the extents of ion signal reduction in the presence of additional acids in the IMR suggest that C₉H₁₄O₄ produced in the gas phase is a peracid, rather than the often-assumed pinic acid. Thus, we suggest that the potential application of the secondary ion chemistry to inform organic functionalities is promising, which could help better understand the molecular compositions of gas-phase OVOCs and the reaction mechanisms therein.

Plastic breeze: Volatile organic compounds (VOCs) emitted by degrading macro- and microplastics analyzed by selected ion flow-tube mass spectrometry

Pollution from microplastics (MPs) has become one of the most relevant topics in environmental chemistry. The risks related to MPs include their capability to adsorb toxic and harmful molecular species, and to release additives and degradation products into ecosystems. Their role as a primary source of a broad range of harmful volatile organic compounds (VOCs) has also been recently reported. In this work, we applied a non-destructive approach based on selected-ion flow tube mass spectrometry (SIFT-MS) for the characterization of VOCs released from a set of plastic debris collected from a sandy beach in northern Tuscany. The interpretation of the individual SIFT-MS spectra, aided by principal component data analysis, allowed us to relate the aged polymeric materials that make up the plastic debris (polyethylene, polypropylene, and polyethylene terephthalate) to their VOC emission profile, degradation level, and sampling site. The study proves the potential of SIFT-MS application in the field, as a major advance to obtain fast and reliable information on the VOCs emitted from microplastics. The possibility to obtain qualitative and quantitative data on plastic debris in less than 2 min also makes SIFT-MS a useful and innovative tool for future monitoring campaigns involving statistically significant sets of environmental samples.

Reagent and analyte ion hydrates in secondary electrospray ionization mass spectrometry (SESI-MS), their equilibrium distributions and dehydration in an ion transfer capillary: Modelling and experiments

RATIONALE

Secondary electrospray ionization (SESI) in a water spray environment at atmospheric pressure involves the reactions of hydrated hydronium reagent ions, H₃ O⁺ (H₂ O)_n , with trace analyte compounds in air samples. Understanding the formation and dehydration of reagent and analyte ions is the foundation for meaningful quantification of trace compounds by SESI-mass spectrometry (MS).

METHODS

A numerical model based on gas-phase ion thermochemistry is developed that describes equilibria in H₃ O⁺ (H₂ O)_n reagent cluster ion distributions and ligand switching reactions with polar NH₃ molecules leading to equilibrated hydrated ammonium ions NH₄ ⁺ (H₂ O)_m . The model predictions are compared with experimental results obtained using a cylindrical SESI source coupled to an ion-trap mass spectrometer via a heated ion transfer capillary. Non-polar isoprene, C₅ H₈ , was used to further probe the nature of the reagent ions.

RESULTS

Equilibrium distributions of H₃ O⁺ (H₂ O)_n ions and their reactions with NH₃ molecules have been characterized by the model in the near-atmospheric pressure SESI source. NH₃ analyte molecules displace H₂ O ligands from the H₃ O⁺ (H₂ O)_n ions at the collisional rate forming NH₄ ⁺ (H₂ O)_m ions, which travel through the heated ion transfer capillary losing H₂ O molecules. The data for variable NH₃ concentrations match the model predictions and the C₅ H₈ test substantiates the notion of dehydration in the heated capillary.

CONCLUSIONS

Large cluster ions formed in the SESI region are dehydrated to H₃ O⁺ (H₂ O)_1,2,3 and NH₄ ⁺ (H₂ O)_1,2 while passing through the heated capillary, and considerable diffusion losses also occur. This phenomenon is also predicted for other polar analyte molecules, A, that can undergo similar switching reactions, thus forming AH⁺ and AH⁺ (H₂ O)_m analyte ions.

Feasibility study on exhaled-breath analysis by untargeted Selected-Ion Flow-Tube Mass Spectrometry in children with cystic fibrosis, asthma, and healthy controls: Comparison of data pretreatment and classification techniques

Selected-Ion Flow-Tube Mass Spectrometry (SIFT-MS) has been applied in a clinical context as diagnostic tool for breath samples using target biomarkers. Exhaled breath sampling is non-invasive and therefore much more patient friendly compared to bronchoscopy, which is the golden standard for evaluating airway inflammation. In the actual pilot study, 55 exhaled breath samples of children with asthma, cystic-fibrosis and healthy individuals were included. Rather than focusing on the analysis of target biomarkers or on the identification of biomarkers, different data analysis strategies, including a variety of pretreatment, classification and discrimination techniques, are evaluated regarding their capacity to distinguish the three classes based on subtle differences in their full scan SIFT-MS spectra. Proper data-analysis strategies are required because these full scan spectra contain much external, i.e. unwanted, variation. Each SIFT-MS analysis generates three spectra resulting from ion-molecule reactions of analyte molecules with H₃O⁺, NO⁺ and O₂⁺. Models were built with Linear Discriminant Analysis, Quadratic Discriminant Analysis, Soft Independent Modelling by Class Analogy, Partial Least Squares - Discriminant Analysis, K-Nearest Neighbours, and Classification and Regression Trees. Perfect models, concerning overall sensitivity and specificity (100% for both) were found using Direct Orthogonal Signal Correction (DOSC) pretreatment. Given the uncertainty related to the classification models associated with DOSC pretreatments (i.e. good classification found also for random classes), other models are built applying other preprocessing approaches. A Partial Least Squares - Discriminant Analysis model with a combined pre-processing method considering single value imputation results in 100% sensitivity and specificity for calibration, but was less good predictive. Pareto scaling prior to Quadratic Discriminant Analysis resulted in 41/55 correctly classified samples for calibration and 34/55 for cross-validation. In future, the uncertainty with DOSC and the applicability of the promising preprocessing methods and models must be further studied applying a larger representative data set with a more extensive number of samples for each class. Nevertheless, this pilot study showed already some potential for the untargeted SIFT-MS application as a rapid pattern-recognition technique, useful in the diagnosis of clinical breath samples.