Ion trap MS using high trapping gas pressure enables unequivocal structural analysis of three isobaric compounds in a mixture by using energy-resolved mass spectrometry and the survival yield technique

Differentiation of Isomeric TAT1-CARNOSINE Peptides by Energy-Resolved Mass Spectrometry and Principal Component Analysis

L-carnosine (Car) is an endogenous dipeptide with significant potential in drug discovery for neurodegenerative diseases, while TAT1, a small arginine-rich peptide derived from the HIV-1 trans-activator protein (TAT), is known to stimulate proteasome activity. In this study, three isomeric peptides were synthesised by incorporating the Car moiety at the N-terminus, C-terminus, or central position of the TAT1 sequence. To differentiate these isomers, high-resolution and energy-resolved CID MS/MS experiments were conducted. The resulting MS/MS spectra showed a high degree of similarity among the peptides, predominantly characterised by fragment ion peaks arising from arginine-specific neutral losses. Energetic analysis was similarly inconclusive in resolving the isomers. However, Principal Component Analysis (PCA) enabled clear differentiation of the three peptides by considering the entire MS/MS spectra rather than focusing solely on precursor ion intensities or major fragment peaks. PCA loadings revealed distinct fragment ions for each peptide, albeit with lower intensities, providing insights into consecutive fragmentation patterns. Some of these specific peaks could also be attributed to scrambling during fragmentation. These results demonstrate the potential of PCA as a simple chemometric tool for semi-automated peak identification in complex MS/MS spectra.

Energy-Resolved Mass Spectrometry and Mid-Infrared Spectroscopy for Purity Assessment of a Synthetic Peptide Cyclised by Intramolecular Huisgen Click Chemistry

Cyclic peptides have higher stability and better properties as therapeutic agents than their linear peptide analogues. Consequently, intramolecular click chemistry is becoming an increasingly popular method for the synthesis of cyclic peptides from their isomeric linear peptides. However, assessing the purity of these cyclic peptides by mass spectrometry is a significant challenge, as the linear and cyclic peptides have identical masses. In this paper, we have evaluated the analytical capabilities of energy-resolved mass spectrometry (ER MS) and mid-infrared microscopy (IR) to address this challenge. On the one hand, mixtures of both peptides were subjected to collision-induced dissociation tandem mass spectrometry (CID MS/MS) experiments in an ion trap mass spectrometer at several excitation energies. Two different calibration models were used: a univariate model (at a single excitation voltage) and a multivariate model (using multiple excitation voltages). The multivariate model demonstrated slightly enhanced analytical performance, which can be attributed to more effective signal averaging when multiple excitation voltages are considered. On the other hand, IR microscopy was used for the quantification of the relative amount of linear peptide. This was achieved through univariate calibration, based on the absorbance of an alkyne band specific to the linear peptide, and through Partial Least Squares (PLS) multivariate calibration. The PLS calibration model demonstrated superior performance in comparison to univariate calibration, indicating that consideration of the full IR spectrum is preferable to focusing on the specific peak of the linear peptide. The advantage of IR microscopy is that it is linear across the entire working interval, from linear peptide molar ratios of 0 (equivalent to pure cyclic peptide) up to 1 (pure linear peptide). In contrast, the ER MS calibration models exhibited linearity only up to 0.3 linear peptide molar ratio. However, ER MS showed better performances in terms of the limit of detection, intermediate precision and the root-mean-square-error of calibration. Therefore, ER MS is the optimal choice for the detection and quantification of the lowest relative amounts of linear peptides.

Removal of isobaric interference using pseudo-multiple reaction monitoring and energy-resolved mass spectrometry for the isotope dilution quantification of a tryptic peptide

Energy-resolved mass spectrometry (ERMS) and an isotopically labelled internal standard were successfully combined to accurately quantify a tryptic peptide despite the presence of an isobaric interference. For this purpose, electrospray ionisation tandem mass spectrometry (ESI-MS/MS) experiments were conducted into an ion trap instrument using an unconventional 8 m/z broadband isolation window, which encompassed both the tryptic peptide and its internal standard. Interference removal was assessed by determining an excitation voltage that was high enough to maintain a constant value for the analyte/internal standard peaks intensity ratio, thus ensuring accurate quantification even in the presence of isobaric contamination. Pseudo-multiple reaction monitoring (MRM) was employed above this excitation voltage to quantify the trypic peptide. The internal standard calibration model showed no lack of fit and exhibited a linear dynamic range from 0.5 μM up to 2.5 μM. The detection limit was 0.08 μM. The accuracy of the method was evaluated by quantifying the tryptic peptide of three reference samples intentionally contaminated with the isobaric interference. All the reference samples were accurately quantified with ∼1% deviation despite the isobaric contamination. Furthermore, we have demonstrated that this methodology can also be applied to quantify the isobaric peptide by standard additions down to 0.2 μM. Finally, liquid chromatography ERMS (LC ERMS) experiments yielded similar results, suggesting the potential of the proposed methodology for analysing complex samples.

LC-MS accurate quantification of a tryptic peptide co-eluted with an isobaric interference by using in-source collisional purification

Interferences from isobaric and isomeric compounds represent a common problem in liquid chromatography coupled to mass spectrometry (LC-MS). In this paper, in-source purification and chromatographic separation were combined with the aim of identifying isobaric contamination and quantifying accurately a compound despite the presence of an isobaric co-eluted interference. This is achieved by totally fragmenting in-source the precursor ions of the isobaric interference providing then LC-pseudo-MS2 capability, which allows an accurate quantification without the need for optimizing the chromatographic conditions to separate the co-eluted interference. To illustrate this concept, mixtures of tryptic and non-tryptic peptides were used. The ratio of peak areas of the tryptic peptide and its isotopically labelled internal standard was used not only for quantification with an internal standard calibration curve but also to know (1) if an isobaric interference co-eluted with the tryptic peptide; and (2) what is the minimum cone voltage necessary to ensure the complete removal of isobaric interference. This strategy was applied to quantify the tryptic peptide of two standards with known concentrations and, intentionally contaminated with the isobaric interference. The confidence intervals of the concentrations calculated with the internal standard calibration curve were 8.0 ± 0.5 μM (prepared at 8.0 μM) and 15.7 ± 0.5 μM (prepared at 16.1 μM) that confirm the tryptic peptide can be correctly quantified by in-source purification without the need for improving the chromatographic separation from its isobaric interference.

Study of Mono and Di-O-caffeoylquinic Acid Isomers in Acmella oleracea Extracts by HPLC-MS/MS and Application of Linear Equation of Deconvolution Analysis Algorithm for Their Characterization

Chlorogenic acids, the esters of caffeic and quinic acids, are the main phenolic acids detected in Acmella oleracea extracts and have gained increasing interest in recent years due to their important biological activities. Given their structural similarity and instability, the correct analysis and identification of these compounds in plants is challenging. This study aimed to propose a simple and rapid determination of the A. oleracea caffeoylquinic isomers, applying an HPLC-MS/MS method supported by a mathematical algorithm (Linear Equation of Deconvolution Analysis (LEDA)). The three mono- and the three di-caffeoylquinic acids in roots of Acmella plants were studied by an ion trap MS analyzer. A separation by a conventional chromatographic method was firstly performed and an MS/MS characterization by energetic dimension of collision-induced dissociation mechanism was carried out. The analyses were then replicated using a short HPLC column and a fast elution gradient (ten minutes). Each acquired MS/MS data were processed by LEDA algorithm which allowed to assign a relative abundance in the reference ion signal to each isomer present. Quantitative results showed no significant differences between the two chromatographic systems proposed, proving that the use of LEDA algorithm allowed the distinction of the six isomers in a quarter of the time.

Isomers Recognition in HPLC-MS/MS Analysis of Human Plasma Samples by Using an Ion Trap Supported by a Linear Equations-Based Algorithm

The tandem mass spectrometry (MS/MS) approach employing an ion trap mass analyzer (IT) was evaluated in isomers recognition. The proposed approach consists of sole, simple, and rapid liquid chromatographic separation (HPLC) without requiring resolution between the analytes. Then, the MS/MS properties were optimized to solve the signal assignment using post-processing data elaboration (LEDA). The IT-MS/MS experiment uses the same site, helium as collision gas, and different time steps to modify the applied conditions on the studied ions. Nevertheless, helium cannot ensure the quick energization of the precursor ion due to its small cross-section. Then, different combinations between excitation amplitude (ExA) and excitation time (ExT) were tested to achieve the activation of the fragmentation channels and the formation of the MS/MS spectrum. Usually, the IT-MS/MS acquisition cycle is longer for other multistage instruments, decreasing the frequency of sample data collection and influencing the chromatographic profile. To solve these problems, two time segments were set up, and the elution conditions were optimized with a compromise between peaks distinction and run time reduction. The developed HPLC-MS/MS method was checked and applied to analyze a series of human plasma samples spiked with an equimolar mixture of pair of isomers.

Tandem mass spectrometry approaches for recognition of isomeric compounds mixtures

The present review aims to collect the published literature pertaining the recognition of isobaric compounds (isomers or stereoisomers) using the features of tandem mass spectrometry (MS) experiments without any chromatographic separation or chemical modification (derivatization or isotopic enrichment) of the analytes. MS/MS methods possess high selectivity, wide dynamic range and high throughput capabilities. Generally, tandem MS has limited capability for distinguishing isomers that fragment similarly. However, some MS/MS methods have been developed and positively applied to isomers discrimination. Among the literature on this topic, the applications that fit on the review subject can be summarized as follow: (1) chiral discrimination by the kinetic method, (2) the use energy-resolved tandem mass spectra and the survival yield (SY) representation, (3) the kinetics evaluation of the ion-molecule interaction and (4) the postprocessing mathematical algorithm to resolve the isomers in MS/MS signal.

Deciphering and investigating fragment mechanism of quinolones using multi-collision energy mass spectrometry and computational chemistry strategy

RATIONALE

Quinolones show characteristic fragments in mass spectrometry (MS) analysis due to their common core structures, and energy-dependent differences among these fragments are generated through the same fragmentation pathway of different molecules. Computational chemistry, which provides quantitative results of molecule parameters, is helpful for investigating the mechanisms of chemistry.

METHODS

MS/MS spectra of five quinolones, namely norfloxacin (NOR), enoxacin (ENO), enrofloxacin (ENR), gatifloxacin (GAT), and lomefloxacin (LOM), were acquired for deciphering fragmentation pathways under multi-collision energy (CE). Computational methods were used for excluding little possibility pathways from the point of view of energy and stable conformations, whereas optimized collision energy (OCE) and maximum relative intensity (MRI) of major competitive fragments were investigated and confirmed using computational results.

RESULTS

Fragmentation results of NOR, ENO, ENR, and GAT were deciphered using experimental and computational data, of which fragmentation regularities were summarized. Fragmentation pathways of LOM were deciphered under the guidance of foregoing regularities. Meanwhile, the whole process was validated by comparing OCE and MRI and computational energy results, which showed good agreement.

CONCLUSIONS

A strategy for explaining quinolone fragmentation results of multi-CE values and deciphering fragment mechanism using computational methods was developed. Relevant data and strategy may provide ideas for how to design and decipher new drug molecules with similar structures.

Application of LEDA algorithm for the recognition of P-glycoprotein and Carbonic Anhydrase hybrid inhibitors and evaluation of their plasma stability by HPLC-MS/MS analysis

Design and synthesis of new candidate drugs produces a large number of compounds that must be qualified and tested to evaluate their characteristics and potential applications. Therefore, many studies will be scheduled and, consequently, it will be necessary to arrange specific, reliable, fast and relatively cheap analytic methods to support this research. The manuscript proposes a new approach in the HPLC-MS/MS analysis by using a sole chromatographic set up, tuned to minimize the run time, without requiring high efficiency or resolution between the analytes. The chromatographic column was used only to avoid or limit the interference of sample matrix towards the analyte ionization process (matrix-effects). Then, the MS/MS properties were explored to solve the signal assignment, by performing a series of energy resolved experiments to optimize the parameters and applying an interesting post-processing data elaboration tool (LEDA). The reliability of the new approach was evaluated in a chemical stability study in PBS and human plasma samples of a series of isomeric compounds P-glycoprotein/Carbonic Anhydrase (P-gp/CA) hybrid inhibitors. The obtained results demonstrated the effectiveness (reliability 97%-100%) of the LEDA algorithm to recognize and to separate the possible isomers present in the samples. The obtained matrix-effects values (ME 96%-106%) established that the chromatographic set up (short column and fast elution gradient) was proper to avoid the matrix interferences, while recovery values (RE 88%-108%) indicate a suitable sample preparation, despite only a protein precipitation was carried out. The quantitative performances of proposed HPLC-MS/MS methods showed an accuracy ranging between 92% and 108% and a precision lower than 13% that allows to be confident on the determination of new P-gp/CA hybrid inhibitors in the degradation study. Therefore, the general procedure proposed was found adequate to study a series of isomeric compounds without their chromatographic separation but only by applying and developing the MS/MS features.

The Resonant Excitation Process in Commercial Quadrupole Ion Traps Revisited

The collision-induced resonant excitation process in real quadrupole ion traps is revisited theoretically and experimentally by explicitly including in the discussion the influence of higher order potential impurities. This includes mainly the dependence of the secular oscillation frequency f_ion on the ion's oscillation amplitude z_max. Due to frequency calibration, commercial ion traps use excitation frequencies f_exc that are higher than the theoretical secular oscillation frequency f_ion. This may lead to switching in frequency order between f_exc and f_ion that can allow ions to stay longer in on-resonance. It is also found that there is a most efficient but also a harshest excitation frequency, which are not identical. These phenomena are explained and described with a simple harmonic oscillator model and precise numerical calculations, using the trajectory simulation program ITSIM 5.0. Experimental MS² have been performed with the thermometer ion leucine-enkephalin, which are then in line with expectations from the trajectory calculations. The important difference to the existing literature is that, here, overexcitation is characterized by the observed a₄/b₄ fragment-ion ratio, while the fragmentation efficiency was kept constant. By slightly increasing the excitation frequency one can obtain drastically different effective collisional temperatures. This knowledge gives even commercial ion traps, without instrument adjustments, the possibility of producing energetically versatile fragment ion spectra. It is also shown that the damped driven harmonic oscillator cannot be used as a simplified model of the motion during the resonant excitation process in real ion traps.

Structural analysis of a compound despite the presence of an isobaric interference by using in-source Collision Induced Dissociation and tandem mass spectrometry

The presence of an isobaric contaminant can drastically affect MS and MS/MS patterns leading to erroneous structural and quantitative analysis, which is a real challenge in mass spectrometry. Herein, we demonstrate that MS and MS/MS structural analysis of a compound can be successfully performed despite the presence of an isobaric interference with as low as few millidaltons mass difference by using pseudo-MS³ . To this end, in-source collisional excitation (in-source CID) and the Survival Yield (SY) technique (energy-resolved collision induced dissociation MS/MS) were performed on two different source geometries: a Z-spray and an orthogonal spray (with a transfer capillary) ionization sources on two different mass spectrometers. By using soft ionization conditions, the SY curve for the mixture is a linear combination of the SY curves from the pure compounds demonstrating the presence of two components in the mixture. In the case of harsher ionization conditions, the SY curve of the mixture perfectly overlaps the SY curve from the pure analyte. This observation demonstrates the isobaric interference has been completely removed by in-source CID fragmentation, independently of the source design, leaving then the analyte precursor ions only. Therefore, by measuring the MS spectrum in harsh ionization conditions and according to SY criterium, the compound of interest can be made free from isobaric interference paving the way for, for example, unequivocal HPLC-MS as well as HPLC-MS/MS structural and quantitative analysis despite the presence of a co-eluting isobaric interference.

Determination of coeluted isomers in wine samples by application of MS/MS deconvolution analysis

Two organic acids isomers, 3-isopropylmalic acid (3-IPMA) and 2-isopropylmalic acid (2-IPMA), were identified and quantified in wine samples by using an LC-MS/MS method without any chromatographic separation, but processing the MS/MS data with a recently developed deconvolution algorithm (LEDA: linear equations deconvolution analysis), thus decreasing the time necessary for the process. In particular, the LEDA tool processes the MS/MS signals and assigns the relative concentrations (abundances) of the isomers in the sample, at the mg L^-1 level. The efficiency of MS/MS signal assignment was improved by introducing five linear equations to define the LEDA matrix. Then, as a novel approach, an overdetermined system of linear equations was applied for the deconvolution of isomers. The use of LEDA to identify and quantify the isomers in wine samples, together with the choice of a short LC column and a fast elution gradient, simplifies the process and shortens the time needed. Furthermore, it was evaluated the quantitative determination of the IPMA isomers by using the calibration curve provided by the precursor ion MRM transition data. The calculated values of accuracy (recovery between 82.6% and 99.8%) and precision (RSD between 0.4% and 4.0%) confirm the validity of this quantitative approach and the ability of LEDA to establish the correct percentage of the MS/MS signal for each isomer. Finally, to compare the conventional LC-MS/MS method and our proposed method of LC-MS/MS coupled with LEDA post-processing elaboration, a series of real wine samples were analysed by both methods, and the results were compared.