Examining functional group-dependent effects on the ionization of lignin monomers using supercritical fluid chromatography/electrospray ionization mass spectrometry.

The chemical and biological conversion of biomass-derived lignin is a promising pathway for producing valuable low molecular weight aromatic chemicals, such as vanillin or guaiacol, known as lignin monomers (LMs). Various methods employing chromatography and electrospray ionization-mass spectrometry (ESI-MS) have been developed for LM analysis, but the impact of LM chemical properties on analytical performance remains unclear. This study systematically optimized ESI efficiency for 24 selected LMs, categorized by functionality. Fractional factorial designs were employed for each LM to assess ESI parameter effects on ionization efficiency using ultra-high-performance supercritical fluid chromatography/ESI-MS (UHPSFC/ESI-MS). Molecular descriptors were also investigated to explain variations in ESI parameter responses and chromatographic retention among the LMs. Structural differences among LMs led to complex optimal ESI settings. Notably, LMs with two methoxy groups benefited from higher gas and sheath gas temperatures, likely due to their lower log P and higher desolvation energy requirements. Similarly, vinyl acids and ketones showed advantages at elevated gas temperatures. The retention in UHPSFC using a diol stationary phase was correlated with the number of hydrogen bond donors. In summary, this study elucidates structural features influencing chromatographic retention and ESI efficiency in LMs. The findings can aid in developing analytical methods for specific technical lignins. However, the absence of an adequate number of LM standards limits the prediction of LM structures solely based on ESI performance data.

Development and validation of a GC-MS/MS method for the determination of iodoacetic acid in biological samples.

Iodoacetic acid (IAA) is a halogenated disinfection by-product of growing concern due to its high cytotoxicity, genotoxicity, endocrine disruptor effects, and potential carcinogenicity. However, the data on distribution and excretion of IAA after ingestion by mammals are still scarce. Here, we developed a reliable and validated method for detecting IAA in biological specimens (plasma, urine, feces, liver, kidney, and tissues) based on modified QuEChERS sample preparation combined with gas chromatography-tandem triple quadrupole mass spectrometry (GC-MS/MS). The detection method for IAA exhibited satisfactory recovery rates (62.6-108.0%) with low relative standard deviations (RSD < 12.3%) and a low detection limit for all biological matrices ranging from 0.007 to 0.032 ng/g. The study showed that the proposed method was reliable and reproducible for analyzing IAA in biological specimens. It was successfully used to detect IAA levels in biological samples from rats given gavage administration. The results indicated that IAA was found in various tissues and organs, including plasma, thyroid, the liver, the kidney, the spleen, gastrointestinal tract, and others, 6 h after exposure. This study provides the first data on the in vivo distribution in and excretion of IAA by mammals following oral exposure.

Chemical profiling of Simiao pill and quantification of main effective constituents in it by ultra-high-performance liquid chromatography coupled with Q Exactive Orbitrap and triple quadrupole mass spectrometry.

Simiao pill is one of the most commonly used prescriptions in traditional Chinese medicine for the treatment of hyperuricemia and gout. However, methods based on more accurate and comprehensive qualitative and quantitative analyses of the active ingredients are not yet perfect due to limited methodology. This not only hinders the elucidation of the pharmacological mechanism of Simiao pill, but also its comprehensive clinical development and utilization. In this study, we employed ultra-high-performance liquid chromatography-Q Exactive Orbitrap-mass spectrometry technology to perform rapid analysis and identification of the chemical constituents in Simiao pill. A total of 101 chemical components were identified, including 26 alkaloids, 15 terpenoids, 11 flavonoids, eight steroids, six fatty acids, five limonoids, four saponins, five phenylpropanoids, and 21 other compounds. In addition, we established a new method by high-throughput ultra-high-performance liquid chromatography-Q Exactive Orbitrap-mass spectrometry combined with ultra-high-performance liquid chromatography-triple quadrupole-tandem mass spectrometry technology for quantification of 14 main active ingredients, such as adenosine (1), phellodendrine (2), mangnoflorine (3), ß-ecdysterone (4), 25R-inokosterone (5), 25S-inokosterone (6), jatrorrhizine (7), palmatine (8), chikusetsu saponin IVa (9), limonin (10), atractylenolide III (11), atractylenolide I (12), obacunone (13), and atractylenolide II (14) in Simiao pill. This work laid a foundation for further analysis and quality control of effective components in Simiao pill.

Analysis of Antioxidant Properties and Compounds in Different Rosa Taxa Fruits Using UV-Vis and UPLC-TQ-MS Techniques.

This comprehensive analysis of the fruits of Rosa spp. (FR) evaluates their chemical components and antioxidant activity. The study quantified total flavonoids and polyphenols using aluminum trichloride colorimetric assay and Folin-Ciocalteu methods, with the fruit of Rosa. laxa Rtez. var. mollis Yü et Ku. sample exhibiting the highest concentrations of 59.21 mg/g and 81.13 mg/g, respectively. Ultra-High-Performance Liquid Chromatography-Triple Quadrupole Mass Spectrometry (UPLC-TQ-MS) assessed seven primary components, with notable levels of euscaphic acid, ursolic acid, and gallic acid. Antioxidant activities were tested using DPPH and ABTS methods, showing strong activities in samples the fruits of Rosa. persica Mickx ex Juss. and Rosa. laxa Rtez. var. kaschgarica (Rupr.) Y. L. Han. Chemometric analyses, including similarity, cluster, principal component, and grey relational analyses, were used to explore relationships between FR varieties and their antioxidant properties. The study provides a vital basis for future FR quality assessments.

Selenium Discrepancies in Fetal Bovine Serum: Impact on Cellular Selenoprotein Expression.

Selenium is an essential trace element in our diet, crucial for the composition of human selenoproteins, which include 25 genes such as glutathione peroxidases and thioredoxin reductases. The regulation of the selenoproteome primarily hinges on the bioavailability of selenium, either from dietary sources or cell culture media. This selenium-dependent control follows a specific hierarchy, with "housekeeping" selenoproteins maintaining constant expression while "stress-regulated" counterparts respond to selenium level fluctuations. This study investigates the variability in fetal bovine serum (FBS) selenium concentrations among commercial batches and its effects on the expression of specific stress-related cellular selenoproteins. Despite the limitations of our study, which exclusively used HEK293 cells and focused on a subset of selenoproteins, our findings highlight the substantial impact of serum selenium levels on selenoprotein expression, particularly for GPX1 and GPX4. The luciferase reporter assay emerged as a sensitive and precise method for evaluating selenium levels in cell culture environments. While not exhaustive, this analysis provides valuable insights into selenium-mediated selenoprotein regulation, emphasizing the importance of serum composition in cellular responses and offering guidance for researchers in the selenoprotein field.

[Simultaneous determination of six benzodiazepine sedatives residue in aquatic products by high performance liquid chromatography-triple quadrupole mass spectrometry].

OBJECTIVE: To establish a method for the simultaneous determination of 6 benzodiazepine sedatives residue in aquatic products by high performance liquid chromatography-triple quadrupole mass spectrometry. METHODS: The samples were extracted with acetonitrile and purified by C_(18 )solid phase extraction column. The sample solution was separated by Waters ACQUITY UPLC BEH C_(18 )column(2.1 mm×50 mm, 1.7 µm) using 0.1% formic acid and methanol as mobile phase for gradient elution, determined in multiple reaction monitoring mode and quantified by internal standard method. RESULTS: Six benzodiazepine sedatives had a good linear relationship in the range of 1.0-50.0 µg/L with r>0.9990, the limits of detection and limits of quantification were 0.3 and 1.0 µg/kg. Average recoveries for the analytes at 3 spiked levels ranged from 74.2%-108.0% with relative standard deviations of 1.1%-6.7%(n=6). CONCLUSION: The method is simple, rapid, sensitive and accurate, which is suitable for simultaneous determination of 6 benzodiazepine sedatives residue in aquatic products.

[Establishment of collection methods and laboratory testing methods for active pharmaceutical ingredient in the workplace air].

Objective: To establish collection methods and laboratory testing methods for qualitative and quantitative analysis of 9 typical active pharmaceutical ingredient in the workplace air. Methods: In December 2021, a mixed solution of nine analytes was prepared and then dispersed in aerosol state to simulate sampling. Glass fiber filter membrane was selected as air collector and collected active pharmaceutical ingredient in the air at a rate of 2.0 L/min for 15 minutes. Then, the obtained filter membrane samples were eluted with 25%ACN/75%MeOH. Finally, the eluent was qualitatively and quantitatively analyzed with liquid chromatography-triple quadrupole mass spectrometer. Results: This method could effectively collect active pharmaceutical ingredient in the air, with an average sampling efficiency of more than 98.5%. The linear correlation coefficient r was greater than 0.9990. The lower limit of quantification for each analyte ranged from 0.6~500.0 ng/ml, and the average recovery rate ranged from 97.6%~102.5%. Conclusion: This method could simultaneously collect 9 active pharmaceutical ingredient in the workplace air, and could provide accurate qualitative and quantitative analysis in subsequent laboratory tests.

Cationic exchange SPE combined with triple quadrupole UHPLC-MS/MS for detection of GHRHs in urine samples.

The use of growth hormone-releasing hormones (GHRHs) is prohibited in sports according to the regulations of the World Anti-Doping Agency (WADA). Considering the complexity of urine samples and the low concentrations at which these analytes should be detected, analyzing GHRHs is a challenging task. In most of the studies, GHRHs are analyzed using UHPLC-HRMS with an orbitrap. The present developed and validated method for some GHRHs (tesamorelin, CJC-1295, sermorelin (GRF 1-29), sermorelin (3-29)-NH2, somatorelin) is based on the triple quadrupole UHPLC/MS-MS method with solid phase extraction (SPE) with weak cation exchange and is able to detect concentrations as low as 0.2 ng/mL (LOD), a limit of quantification (LOQ) at 0.6 ng/mL, and linearity across the range of 0.1 ng/mL to 1.2 ng/mL. The present method developed by our doping control laboratory was validated according to WADA technical documents for selectivity, limit of detection (LOD), carryover, reliability of detection, stability and recovery. The results show that the method has adequate recoveries and sensitivity, hence, it can be employed for routine screening in anti-doping laboratories.

A dilute-and-inject low-pressure gas chromatography-tandem mass spectrometry method for phthalate determination in extra virgin olive oil.

The goal of this study was to develop a method for the determination of nine phthalic acid esters in extra virgin olive oils using low-pressure gas chromatography-triple-quadrupole mass spectrometry. Sample preparation was simple, environmental friendly, and rapid inasmuch that it involved only dilution (< 1 mL of hexane). The low-pressure gas chromatography analyses were performed by using a 5 m wide-bore column. The limit of quantification for the phthalates ranged from 0.06 to 1.14 mg kg-1 . Both intra- and interday precisions were measured, with coefficient of variation values ranging from 0.2% to 11.7%. The trueness of the method was measured by evaluating accuracy at the initial stage of the work and after 2 months, with values ranging between -8.7% and 12.1%. Moreover, blind accuracy was comprised between -11.6% and 14.2%. The method involves the use of simplified instrumentation and reduced analysis times (nearly two times faster) compared to a previously published comprehensive two-dimensional gas chromatography-triple-quadrupole mass spectrometry method, leading to a reduction of energy and helium consumption. The approaches were compared in analytical terms and for the environmental impact. In total, 23 olive oil samples were analyzed, with at least one phthalate detected in all but one sample.

Simultaneous determination of 10 first-generation histamine h1 receptor blockers in feeds by ultra-high-performance liquid chromatography triple quadrupole ion trap hybrid mass spectrometer.

A method for simultaneous determination of 10 first-generation histamine H1 receptor blockers in feeds by ultra-high-performance liquid chromatography triple quadrupole mass spectrometry combined with solid phase extraction. Instrument conditions, extraction solvents, and purification methods have been optimized. Under the optimum conditions, these analytes were separated effectively at 6 min. These feeds have been extracted by acid acetonitrile and purified by mixed cation exchange solid-phase extraction. The performance of this method meets the requirements of veterinary residue detection in feeds in China. It is appropriate for the confirmatory monitoring and quantitative analysis of 105 feed samples, five kinds of histamine H1 receptor blockers have been detected in 10 samples.

Metabolic regularity of bioactive compounds in Bufei Jianpi granule in rats using ultra-high-performance liquid chromatography coupled with triple quadrupole mass spectrometry analysis technology.

Bufei Jianpi granule (BJG) is clinically effective for treating chronic obstructive pulmonary disease (COPD). At present, there is no report regarding the drug metabolism of BJG in vivo. This work developed an ultra-high-performance liquid chromatography coupled with triple quadrupole mass spectrometry method with high accuracy and sensitivity to determine drug metabolism of this compound in vivo. After continuous administration of BJG, the concentrations of 10 components in rat plasma, namely betaine, peimine, peiminine, astragaloside A, sinensetin, nobiletin, naringin, calycosin, formononetin, and magnolol, were determined at different time points. Meanwhile, the pharmacokinetic parameters and metabolic rules of these 10 components were evaluated: Cmax , 8.624-574.645 ng/mL; Tmax , 0.250-8.667 h; AUC0-t , 17.640-8947.393 ng h/mL; T1/2 , 3.405-66.014 h; mean residence time (MRT), 6.893-11.223 h. All these components possessed anti-inflammatory, antioxidant, and other biological activities to varying degrees, contributing to improving lung function, mitigating pneumonia and pulmonary fibrosis, and preventing and treating chronic obstructive pulmonary disease. Exploring the pharmacokinetic parameters and the laws of chemical components in BJG forms the scientific basis for applying the compound clinically and identifying quality markers for the control of the compound.

Validation of a multiplexed and targeted lipidomics assay for accurate quantification of lipidomes.

A major challenge of lipidomics is to determine and quantify the precise content of complex lipidomes to the exact lipid molecular species. Often, multiple methods are needed to achieve sufficient lipidomic coverage to make these determinations. Multiplexed targeted assays offer a practical alternative to enable quantitative lipidomics amenable to quality control standards within a scalable platform. Herein, we developed a multiplexed normal phase liquid chromatography-hydrophilic interaction chromatography multiple reaction monitoring method that quantifies lipid molecular species across over 20 lipid classes spanning wide polarities in a single 20-min run. Analytical challenges such as in-source fragmentation, isomer separations, and concentration dynamics were addressed to ensure confidence in selectivity, quantification, and reproducibility. Utilizing multiple MS/MS product ions per lipid species not only improved the confidence of lipid identification but also enabled the determination of relative abundances of positional isomers in samples. Lipid class-based calibration curves were applied to interpolate lipid concentrations and guide sample dilution. Analytical validation was performed following FDA Bioanalytical Method Validation Guidance for Industry. We report repeatable and robust quantitation of 900 lipid species measured in NIST-SRM-1950 plasma, with over 700 lipids achieving inter-assay variability below 25%. To demonstrate proof of concept for biomarker discovery, we analyzed plasma from mice treated with a glucosylceramide synthase inhibitor, benzoxazole 1. We observed expected reductions in glucosylceramide levels in treated animals but, more notably, identified novel lipid biomarker candidates from the plasma lipidome. These data highlight the utility of this qualified lipidomic platform for enabling biological discovery.

Analysis of six aromatic amines in the mainstream smoke of tobacco products.

Aromatic amines are a class of carcinogenic compounds in tobacco smoke that are listed on the FDA list of harmful and potentially harmful constituents (HPHCs). A method using solid-phase microextraction-coupled to gas chromatography-triple quadrupole mass spectrometry (SPME headspace GC-MS/MS) was developed and validated for the quantitative determination of six aromatic amines, including 1-aminonaphthalene (1-AN), 2-aminonaphthalene (2-AN), 3-aminobiphenyl (3-ABP), 4-aminobiphenyl (4-ABP), o-toluidine (o-TOL), and o-anisidine (o-ANI), in the mainstream smoke of cigarettes, cigars, and heated tobacco products. The method developed here combines high sensitivity with simple sample preparation and has demonstrated satisfactory linearity for all six aromatic amines with correlation coefficients greater than 0.9994. The limits of detection range and the limits of quantitation range were 12-96 pg/mL and 41-320 pg/mL, respectively. Their recoveries and coefficients of variation (CV%) were 90-112% and 2.1-6.6%, respectively. The new SPME headspace GC/MS/MS method has been successfully applied to measure the contents of the six aromatic amines in the mainstream smoke of cigarettes, cigars, and heated tobacco products.

Using a peptide-based mass spectrometry approach to quantitate proteolysis of an intact heterogeneous procollagen substrate by BMP1 for antagonistic antibody screening.

Proteases are critical proteins involved in cleaving substrates that may impact biological pathways, cellular processes, or disease progression. In the biopharmaceutical industry, modulating the levels of protease activity is an important strategy for mitigating many types of diseases. While a variety of analytical tools exist for characterizing substrate cleavages, in vitro functional screening for antibody inhibitors of protease activity using physiologically relevant intact protein substrates remains challenging. In addition, detecting such large protein substrates with high heterogeneity using high-throughput mass spectrometry screening has rarely been reported in the literature with concerns for assay robustness and sensitivity. In this study, we established a peptide-based in vitro functional screening assay for antibody inhibitors of mouse bone morphogenic protein 1 (mBMP1) metalloprotease using a heterogeneous recombinant 66-kDa mouse Procollagen I alpha 1 chain (mProcollagen) substrate. We compared several analytical tools including capillary gel electrophoresis Western blot (CE-Western blot), as well as both intact protein and peptide-based mass spectrometry (MS) to quantitate the mBMP1 proteolytic activity and its inhibition by antibodies using this heterogeneous mProcollagen substrate. We concluded that the peptide-based mass spectrometry screening assay was the most suitable approach in terms of throughput, sensitivity, and assay robustness. We then optimized our mBMP1 proteolysis reaction after characterizing the enzyme kinetics using the peptide-based MS assay. This assay resulted in Z' values ranging from 0.6 to 0.8 from the screening campaign. Among over 1200 antibodies screened, IC50 characterization was performed on the top candidate hits, which showed partial or complete inhibitory activities against mBMP1.

Target profiling of flavonol glycosides in the extract of Ginkgo biloba leaf and their pharmacokinetics in rat plasma by ultra-high-performance liquid chromatography with tandem mass spectrometry.

The extract of Ginkgo biloba leaf is a popular herbal product or dietary supplement in the world to treat various diseases, and flavonol glycosides are considered as the main bioactive constituents. In this study, 37 flavonol glycosides were rapidly screened out by precursor ion scanning in positive ion mode with production ions at m/z 287.05, 303.05, and 317.06. Subsequently, a reliable and sensitive ultra-high-performance liquid chromatography coupled with triple quadrupole-linear ion trap mass spectrometry approach was established and validated to quantify the 20 prototype flavonol glycosides in rat plasma. Calibration curves showed good linearity (R2 ≥ 0.9894) over the corresponding concentration range. The precision, accuracy, extraction recovery, matrix effect, and stability were also satisfactory. The validated method was successfully applied to a pharmacokinetic study of prototype flavonol glycosides in rat after oral administration of the extract of G. biloba leaf. As a result, the Tmax of flavonol glycosides was short at 0.11-0.60 h. Quercetin-3-O-(2",6″-di-O-rhamnosyl)-glucoside, kaempferol-3-O-(2'',6''-di-O-rhamnosyl)-glucoside, quercetin-3-O-rutinoside, quercetin- 3-O-glucosyl-(1-2)-O-rhamnoside, and kaempferol-3-O-glucoside presented relatively high systemic exposure levels with AUC0-∞  > 500 µg h/L and Cmax  > 100 µg/L. This study would provide the valuable information for further scientific research and clinical application of the extract of G. biloba leaf.

Identification and Quantitation of Bioactive and Taste-Related Dipeptides in Low-Salt Dry-Cured Ham.

The reduction of salt in meat products influences the natural mechanisms of proteolysis occurring in their processing, and could affect the final characteristics of the product in terms of texture and flavor due to its effect on the activity of enzymes. In the present study, the quantitation of dipeptides PA, GA, VG, EE, ES, DA, and DG in low-salt Spanish dry-cured ham was carried out using a triple quadrupole mass spectrometry instrument. The developed methodology demonstrated the advantages of hydrophilic interaction liquid chromatography in the removal of salt as a clean-up/separation step before ionization. This resulted in a value of 44.88 µg/g dry-cured ham for GA dipeptide, and values ranging from 2 to 8 µg/g dry-cured ham for VG, EE, ES, DA, and DG dipeptides. PA showed the lowest concentration with a value of 0.18 µg/g dry-cured ham. These outcomes prove the remarkable activity of muscular dipeptidyl peptidases during dry-curing as well as confirming the presence of these dipeptides which are related to certain taste attributes (e.g., 'bitter' or 'umami'). Such dipeptides have also been confirmed as anti-inflammatory and potential cardiovascular protectors using in vitro assays, with the advantage of dipeptides small size increases their chance to resist both gastrointestinal digestion and intestinal/bloodstream transport without being degraded or modified.

Simultaneous Degradation Study of Isomers in Human Plasma by HPLC-MS/MS and Application of LEDA Algorithm for Their Characterization.

This paper proposes a tandem mass spectrometry (MS/MS) approach in isomer recognition by playing in the "energetic dimension" of the experiment. The chromatographic set up (HPLC) was tuned to minimize the run time, without requiring high efficiency or resolution between the isomers. Then, the MS/MS properties were explored to solve the signal assignment by performing a series of energy resolved experiments in order to optimize the parameters, and by applying an interesting post-processing data elaboration tool (LEDA). The reliability of the new approach was evaluated, determining the accuracy and precision of the quantitative results through analysis of the isomer mixture solutions. Next, the proposed method was applied in a chemical stability study of human plasma samples through the simultaneous addition of a pair of isomers. In the studied case, only one of the isomers suffered of enzymatic hydrolysis; therefore, the influence of the stable isomer on the degradation rate of the other was verified. In order to monitor this process correctly, it must be possible to distinguish each isomer present in the sample, quantify it, and plot its degradation profile. The reported results demonstrated the effectiveness of the LEDA algorithm in separating the isomers, without chromatographic resolution, and monitoring their behavior in human plasma samples.

A rapid and reliable liquid chromatography/mass spectrometry method for SARS-CoV-2 analysis from gargle solutions and saliva.

We describe a rapid liquid chromatography/tandem mass spectrometry (LC-MS/MS) method for the direct detection and quantitation of SARS-CoV-2 nucleoprotein in gargle solutions and saliva. The method is based on a multiple-reaction monitoring (MRM) mass spectrometry approach with a total cycle time of 5 min per analysis and allows the detection and accurate quantitation of SARS-CoV-2 nucleoprotein as low as 500 amol/µL. We improved the sample preparation protocol of our recent piloting SARS-CoV-2 LC-MS study regarding sensitivity, reproducibility, and compatibility with a complementary reverse transcriptase quantitative polymerase chain reaction (RT-qPCR) analysis of the same sample. The aim of this work is to promote diagnostic tools that allow identifying and monitoring SARS-CoV-2 infections by LC-MS/MS methods in a routine clinical environment.

Targeted and untargeted quantification of quorum sensing signalling molecules in bacterial cultures and biological samples via HPLC-TQ MS techniques.

Quorum sensing (QS) is the ability of some bacteria to detect and to respond to population density through signalling molecules. QS molecules are involved in motility and cell aggregation mechanisms in diseases such as sepsis. Few biomarkers are currently available to diagnose sepsis, especially in high-risk conditions. The aim of this study was the development of new analytical methods based on liquid chromatography-mass spectrometry for the detection and quantification of QS signalling molecules, including N-acyl homoserine lactones (AHL) and hydroxyquinolones (HQ), in biofluids. Biological samples used in the study were Pseudomonas aeruginosa bacterial cultures and plasma from patients with sepsis. We developed two MS analytical methods, based on neutral loss (NL) and product ion (PI) experiments, to identify and characterize unknown AHL and HQ molecules. We then established a multiple-reaction-monitoring (MRM) method to quantify specific QS compounds. We validated the HPLC-MS-based approaches (MRM-NL-PI), and data were in accord with the validation guidelines. With the NL and PI MS-based methods, we identified and characterized 3 and 13 unknown AHL and HQ compounds, respectively, in biological samples. One of the newly found AHL molecules was C12-AHL, first quantified in Pseudomonas aeruginosa bacterial cultures. The MRM quantitation of analytes in plasma from patients with sepsis confirmed the analytical ability of MRM for the quantification of virulence factors during sepsis. Graphical abstract.

Exploiting targeted and untargeted approaches for the analysis of bacterial metabolites under altered growth conditions.

In the host, pathogenic microorganisms have developed stress responses to cope with constantly changing environments. Stress responses are directly related to changes in several metabolomic pathways, which could hamper microorganisms' unequivocal identification. We evaluated the effect of various in vitro stress conditions (acidic, basic, oxidative, ethanolic, and saline conditions) on the metabolism of Staphylococcus aureus, Bacillus cereus, and Pseudomonas aeruginosa, which are common lung pathogens. The metabolite profiles of the bacteria were analyzed using liquid chromatography coupled to triple quadrupole and quadrupole time-of-flight mass spectrometry. The advantages of targeted and untargeted analysis combined with univariate and multivariate statistical analysis (principal component analysis, hierarchical cluster analysis, partial least square discriminant analysis, random forest) were combined to unequivocally identify bacterial species. In normal in vitro conditions, the targeted methodology, based on the analysis of primary metabolites, enabled the rapid and efficient discrimination of the three bacteria. In changing in vitro conditions and specifically in presence of the various stressors, the untargeted methodology proved to be more valuable for the global and accurate differentiation of the three bacteria, also considering the type of stress environment within each species. In addition, species-specific metabolites (i.e., fatty acids, polysaccharides, peptides, and nucleotide bases derivatives) were putatively identified. Good intra-day repeatability and inter-day repeatability (< 10% RSD and < 15% RSD, respectively) were obtained for the targeted and the untargeted methods. This untargeted approach highlights its importance in unusual (and less known) bacterial growth environments, being a powerful tool for infectious disease diagnosis, where the accurate classification of microorganisms is sought.