Improving sensitivity for the targeted LC-MS/MS analysis of the peptide bradykinin using a design of experiments approach

Decoding the Challenges: navigating Intact Peptide Mass Spectrometry-Based Analysis for Biological Applications

Quantitative analysis of peptides in biological fluids offers a high diagnostic and prognostic tool to reflect the pathophysiological condition of the patient. Recently, methods based on liquid chromatography coupled with mass spectrometry (LC-MS) for the quantitative determination of intact peptides have been replacing traditionally used ligand-binding assays, which suffer from cross-reactivity issues. The use of "top-down" analysis of peptides is rapidly increasing since it does not undergo incomplete or non-reproducible digestion like "bottom-up" approaches. However, the low abundance of peptides and their peculiar characteristics, as well as the complexity of biological fluids, make their quantification challenging. Herein, the analytical pitfalls that may be encountered during the development of an LC-MS method for the analysis of intact peptides in biological fluids are discussed. Challenges in the pre-analytical phase, stability after sampling and sample processing, significantly impact the accuracy of peptide quantification. Emerging techniques, such as microextractions, are becoming crucial for improved sample cleanup and enrichment of target analytes. A comparison between the roles of high-resolution and low-resolution mass spectrometry in the quantification of intact peptides, as well as the introduction of supercharging reagents to enhance ionization, will be discussed.

Development of LC-MS/MS analytical method for the rapid determination of Diquat in water and beverages

This study aimed to develop simple, fast, and sensitive methods for the determination of diquat (DQ) in various matrices such as water and beverages. For water, direct injection was tested first, however, the sensitivity of the incurred samples were too low and couldn't possibly achieve the targeted limit of quantification. Hence, dilution with "weaker" injection solvents were tested, and the final conditions involved the dilution of water with acetonitrile (0.4 % ammonium hydroxide) which increased the sensitivity by more than ten times. Nevertheless, the beverages samples needed further treatment to achieve acceptable spiked recovery. The final conditions involved extraction using the aforementioned solvent, followed by heating and partitioning. Both of the methods satisfied the validation requirements, with an average recovery ranging from 85.9 to115 % and associated relative standard deviation (RSD %) within the range 3-8. Further applications on real samples were done to test the levels of contamination.

Detection of COVID-19-related biomarkers by electrochemical biosensors and potential for diagnosis, prognosis, and prediction of the course of the disease in the context of personalized medicine

As a more efficient and effective way to address disease diagnosis and intervention, cutting-edge technologies, devices, therapeutic approaches, and practices have emerged within the personalized medicine concept depending on the particular patient's biology and the molecular basis of the disease. Personalized medicine is expected to play a pivotal role in assessing disease risk or predicting response to treatment, understanding a person's health status, and, therefore, health care decision-making. This work discusses electrochemical biosensors for monitoring multiparametric biomarkers at different molecular levels and their potential to elucidate the health status of an individual in a personalized manner. In particular, and as an illustration, we discuss several aspects of the infection produced by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) as a current health care concern worldwide. This includes SARS-CoV-2 structure, mechanism of infection, biomarkers, and electrochemical biosensors most commonly explored for diagnostics, prognostics, and potentially assessing the risk of complications in patients in the context of personalized medicine. Finally, some concluding remarks and perspectives hint at the use of electrochemical biosensors in the frame of other cutting-edge converging/emerging technologies toward the inauguration of a new paradigm of personalized medicine.

Improving the LC-MS/MS analysis of neuromedin U-8 and neuromedin S by minimizing their adsorption behavior and optimizing UHPLC and MS parameters

Neuromedin U (NmU) and neuromedin S (NmS) are two closely related neuropeptides belonging to the neuromedin family. NmU usually occurs either as a truncated eight amino acid long peptide (NmU-8) or as an 25 amino acid long peptide, although other molecular forms exist depending on the species considered. NmS, on the other hand, is a 36 amino acid long peptide, sharing the same amidated C-terminal heptapeptide with NmU. Nowadays, liquid chromatography coupled to tandem mass spectrometry (LC-MS/MS) is the preferred analytical technique for peptide quantification, because of its excellent sensitivity and selectivity. However, reaching the required quantification limits for these compounds in biological samples remains an extremely challenging task, especially because of their nonspecific binding (NSB). This study highlights the difficulties that are faced when quantifying larger neuropeptides (23-36 amino acids) compared to smaller ones (< 15 amino acids). The first part of this work aims to solve the adsorption problem for NmU-8 and NmS, by investigating the different steps involved in the sample preparation, i.e. the different solvents applied and the pipetting protocol. The addition of 0.05% plasma as an adsorption competitor was found to be primordial to avoid peptide loss due to NSB. The second part of this work focusses on further improving the sensitivity of the LC-MS/MS method for NmU-8 and NmS, by evaluating some UHPLC-parameters, including the stationary phase, the column temperature and the trapping conditions. For both peptides of interest, the best results were achieved when combining a C₁₈ trap column with a C₁₈ iKey separation device containing a positively charged surface. Column temperatures of 35 and 45 °C for NmU-8 and NmS respectively, resulted in the highest peak areas and S/N ratios, while applying higher column temperatures substantially decreased sensitivity. Moreover, a gradient starting at 20% organic modifier instead of 5% significantly improved the peak shape of both peptides. Finally, some compound-specific MS parameters, i.e. the capillary and the cone voltages, were evaluated. The peak areas increased with a factor 2 and 7 for NmU-8 and NmS respectively and peptide detection in the low picomolar range is now feasible.

Reversed-Phase Liquid Chromatography of Peptides for Bottom-Up Proteomics: A Tutorial

The performance of the current bottom-up liquid chromatography hyphenated with mass spectrometry (LC-MS) analyses has undoubtedly been fueled by spectacular progress in mass spectrometry. It is thus not surprising that the MS instrument attracts the most attention during LC-MS method development, whereas optimizing conditions for peptide separation using reversed-phase liquid chromatography (RPLC) remains somewhat in its shadow. Consequently, the wisdom of the fundaments of chromatography is slowly vanishing from some laboratories. However, the full potential of advanced MS instruments cannot be achieved without highly efficient RPLC. This is impossible to attain without understanding fundamental processes in the chromatographic system and the properties of peptides important for their chromatographic behavior. We wrote this tutorial intending to give practitioners an overview of critical aspects of peptide separation using RPLC to facilitate setting the LC parameters so that they can leverage the full capabilities of their MS instruments. After briefly introducing the gradient separation of peptides, we discuss their properties that affect the quality of LC-MS chromatograms the most. Next, we address the in-column and extra-column broadening. The last section is devoted to key parameters of LC-MS methods. We also extracted trends in practice from recent bottom-up proteomics studies and correlated them with the current knowledge on peptide RPLC separation.

Dysregulation of the kallikrein-kinin system in bronchoalveolar lavage fluid of patients with severe COVID-19

Background

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) binds to the angiotensin-converting enzyme 2 (ACE2) receptor, a critical component of the kallikrein-kinin system. Its dysregulation may lead to increased vascular permeability and release of inflammatory chemokines. Interactions between the kallikrein-kinin and the coagulation system might further contribute to thromboembolic complications in COVID-19.

Methods

In this observational study, we measured plasma and tissue kallikrein hydrolytic activity, levels of kinin peptides, and myeloperoxidase (MPO)-DNA complexes as a biomarker for neutrophil extracellular traps (NETs), in bronchoalveolar lavage (BAL) fluid from patients with and without COVID-19.

Findings

In BAL fluid from patients with severe COVID-19 (n = 21, of which 19 were mechanically ventilated), we observed higher tissue kallikrein activity (18·2 pM [1·2-1535·0], median [range], n = 9 vs 3·8 [0·0-22·0], n = 11; p = 0·030), higher levels of the kinin peptide bradykinin-(1-5) (89·6 [0·0-2425·0], n = 21 vs 0·0 [0·0-374·0], n = 19, p = 0·001), and higher levels of MPO-DNA complexes (699·0 ng/mL [66·0-142621·0], n = 21 vs 70·5 [9·9-960·0], n = 19, p < 0·001) compared to patients without COVID-19.

Interpretation

Our observations support the hypothesis that dysregulation of the kallikrein-kinin system might occur in mechanically ventilated patients with severe pulmonary disease, which might help to explain the clinical presentation of patients with severe COVID-19 developing pulmonary oedema and thromboembolic complications. Therefore, targeting the kallikrein-kinin system should be further explored as a potential treatment option for patients with severe COVID-19.

Funding

Research Foundation-Flanders (G0G4720N, 1843418N), KU Leuven COVID research fund.

Optimized peptide extraction method for analysis of antimicrobial peptide Kn2-7/dKn2-7 stability in human serum by LC-MS

Aim:

To develop an extraction protocol and determine stability for antimicrobial peptide (AMP) Kn2-7 and its d-enantiomer dKn2-7 in human serum.

Materials & methods:

We compared use of ethanol, acetonitrile, RapiGest SF Surfactant and 1% formic acid in ethanol for AMP recovery from serum prior to liquid chromatography-mass spectrometry quantification.

Results:

Precipitation of samples with 1% formic acid in ethanol caused the least amount of AMP loss during extraction from serum. Time-course experiments revealed dKn2-7 was significantly more stable than Kn2-7 in 25% serum, with 78.5% of dKn2-7 and only 1.0% of Kn2-7 remaining after 24 h at 37°C.

Conclusion:

The optimized method significantly increased peptide recovery and allowed more accurate and consistent quantification of Kn2-7 and dKn2-7 serum stability.

Antimicrobial peptides are a new class of molecules being studied for treatment of infections. These peptides can easily be broken down by enzymes present in the body. Removal of the peptides by the enzymes might limit the effect of the drugs against an infection. Our work discusses the importance of testing the stability of these peptides in human serum, a bodily fluid that contains a large amount of enzymes. We describe a method to decrease loss of two potential peptide drugs during sample processing. Further, we report results of testing the stability of these two peptide drugs in human serum.

Peptide extraction was optimized for maximum recovery of antimicrobial peptides Kn2-7/dKn2-7 from serum for LC–MS analysis. Time course experiments revealed d-amino acid analogue antimicrobial peptides were more stable against host proteases.

Application of peptide biomarkers in life analysis based on liquid chromatography-mass spectrometry technology

Biomedicine is developing rapidly in the 21st century. Among them, the qualitative and quantitative analysis of peptide biomarkers is of considerable importance for the diagnosis and therapy of diseases and the quality evaluation of drugs and food. The identification and quantitative analysis of peptides have been going on for decades. Traditionally, immunoassays or biological assays are generally used to quantify peptides in biological matrices. However, the selectivity and sensitivity of these methods cannot meet the requirements of the application. The separation and analysis technique of liquid chromatography-mass spectrometry (LC-MS) supplies a reliable alternative. In contrast to immunoassays, LC-MS methods are capable of providing the analytical prowess necessary to satisfy the demands of peptide biomarker research in the life sciences arena. This review article provides a historical account of the in-roads made by LC-MS technology for the detection of peptide biomarkers in the past 10 years, with the focus on the qualification/quantification developments and their applications.

Two-Dimensional FAIMS-IMS Characterization of Peptide Conformers with Resolution Exceeding 1000

A high-performance field asymmetric waveform ion mobility spectrometry (FAIMS)-IMS-MS platform was developed and applied to explore the conformational diversity of the singly and doubly charged bradykinin (BK + H⁺)⁺ and (BK + 2H⁺)²⁺ ions. With pure N₂ as the FAIMS carrier gas, more than ten conformers of (BK + H⁺)⁺ can be resolved using FAIMS-IMS, as compared to only four conformers resolved using either FAIMS or IMS alone. Interestingly, multiple conformers of (BK + H⁺)⁺ were found to have completely different values of FAIMS compensation voltage (CV), while their IMS drift times were essentially the same, which were also proven experimentally to not result from the structural annealing by the collisional heating in the ion funnel. The separations in the FAIMS and IMS dimensions are substantially orthogonal, and the overall resolving power of two-dimensional FAIMS-IMS separation is largely proportional to the product of the separation resolving powers of FAIMS and IMS. Using a gas mixture of N₂/He to further improve the resolving power of the FAIMS separation, the total resolving powers of the combined FAIMS and IMS separation were estimated to be about 1020 and 1400 for (BK + H⁺)⁺ and (BK + 2H⁺)²⁺ ions, respectively, which are significantly higher than the resolving power of any ion mobility-based separation techniques demonstrated so far. The combined FAIMS-IMS can thus be a much more powerful technique to explore the structural diversity of biomolecules.

A comprehensive review on LED-induced fluorescence in diagnostic pathology

Sensitivity, specificity, mobility, and affordability are important criteria to consider for developing diagnostic instruments in common use. Fluorescence spectroscopy has been demonstrating substantial potential in the clinical diagnosis of diseases and evaluating the underlying causes of pathogenesis. A higher degree of device integration with appropriate sensitivity and reasonable cost would further boost the value of the fluorescence techniques in clinical diagnosis and aid in the reduction of healthcare expenses, which is a key economic concern in emerging markets. Light-emitting diodes (LEDs), which are inexpensive and smaller are attractive alternatives to conventional excitation sources in fluorescence spectroscopy, are gaining a lot of momentum in the development of affordable, compact analytical instruments of clinical relevance. The commercial availability of a broad range of LED wavelengths (255-4600 nm) has opened up new avenues for targeting a wide range of clinically significant molecules (both endogenous and exogenous), thereby diagnosing a range of clinical illnesses. As a result, we have specifically examined the uses of LED-induced fluorescence (LED-IF) in preclinical and clinical evaluations of pathological conditions, considering the present advancements in the field.

Mass spectrometric study of variation in kinin peptide profiles in nasal fluids and plasma of adult healthy individuals

BACKGROUND

The kallikrein-kinin system is assumed to have a multifunctional role in health and disease, but its in vivo role in humans currently remains unclear owing to the divergence of plasma kinin level data published ranging from the low picomolar to high nanomolar range, even in healthy volunteers. Moreover, existing data are often restricted on reporting levels of single kinins, thus neglecting the distinct effects of active kinins on bradykinin (BK) receptors considering diverse metabolic pathways. A well-characterized and comprehensively evaluated healthy cohort is imperative for a better understanding of the biological variability of kinin profiles to enable reliable differentiation concerning disease-specific kinin profiles.

METHODS

To study biological levels and variability of kinin profiles comprehensively, 28 healthy adult volunteers were enrolled. Nasal lavage fluid and plasma were sampled in customized protease inhibitor prespiked tubes using standardized protocols, proven to limit inter-day and interindividual variability significantly. Nine kinins were quantitatively assessed using validated LC-MS/MS platforms: kallidin (KD), Hyp4-KD, KD1-9, BK, Hyp3-BK, BK1-8, BK1-7, BK1-5, and BK2-9. Kinin concentrations in nasal epithelial lining fluid were estimated by correlation using urea.

RESULTS

Circulating plasma kinin levels were confirmed in the very low picomolar range with levels below 4.2 pM for BK and even lower levels for the other kinins. Endogenous kinin levels in nasal epithelial lining fluids were substantially higher, including median levels of 80.0 pM for KD and 139.1 pM for BK. Hydroxylated BK levels were higher than mean BK concentrations (Hyp3-BK/BK = 1.6), but hydroxylated KD levels were substantially lower than KD (Hyp4-KD/KD = 0.37). No gender-specific differences on endogenous kinin levels were found.

CONCLUSIONS

This well-characterized healthy cohort enables investigation of the potential of kinins as biomarkers and would provide a valid control group to study alterations of kinin profiles in diseases, such as angioedema, sepsis, stroke, Alzheimer's disease, and COVID-19.

Picomolar Sensitivity Analysis of Multiple Bradykinin-Related Peptides in the Blood Plasma of Patients With Hereditary Angioedema in Remission: A Pilot Study

Background

Hereditary angioedema (HAE) is a rare autosomal dominant disease; the most well understood forms concern the haplodeficiency of C1 esterase inhibitor (C1INH) and a gain of function mutation of factor XII (FXII). The acute forms of these conditions are mediated by an excessive bradykinin (BK) formation by plasma kallikrein.

Methods

A validated LC-MS/MS platform of picomolar sensitivity developed for the analysis of eleven bradykinin-related peptides was applied to the plasma of HAE-C1INH and HAE-FXII sampled during remission.

Results

In HAE-C1INH plasma, the concentrations of the relatively stable BK1−5 fragment (mean ± S.E.M.: 12.0 ± 4.2 pmol/L), of BK2−9 (0.7 ± 0.2 pmol/L) and of the sums of BK and its tested fragments (18.0 ± 6.4 pmol/L) are significantly greater than those recorded in the plasma of healthy volunteers (1.9 ± 0.6, 0.03 ± 0.03 and 4.3 ± 0.8 pmol/L, respectively), consistent with the previous evidence of permanent plasma kallikrein activity in this disease. Kinin levels in the plasma of HAE-FXII patients did not differ from controls, suggesting that triggering factors for contact system activation are not active during remission.

Conclusion

BK1−5, BK2−9 and the sum of BK and its fragments determined by the sensitive LC-MS/MS technique are proposed as potential biomarkers of HAE-C1INH in remission while this was not applicable to HAE-FXII patients.

Reliable measurement of plasma kinin peptides: Importance of preanalytical variables

BACKGROUND

The kallikrein-kinin system is involved in many (patho)physiological processes and kinin peptides are considered potential clinical biomarkers. Variance in blood specimen collection and processing, artificial ex vivo bradykinin formation, and rapid degradation of kinins have contributed to divergence in published plasma levels, therefore limiting their significance. Thus, reliable preanalytical settings are highly required.

OBJECTIVES

This study aimed to develop and evaluate a standardized preanalytical procedure for reliable kinin quantification. The procedure was based on identification of the most impactful variables on ex vivo plasma level alterations.

METHODS

Suitable protease inhibitors and blood specimen collection and handling conditions were systematically investigated. Their influence on plasma levels of seven kinins was monitored using an established in-house liquid chromatography-tandem mass spectrometry platform.

RESULTS

In nonstandardized settings, ex vivo rise of bradykinin was found to already occur 30 seconds after blood sampling with high interindividual variation. The screening of 17 protease inhibitors resulted in a customized seven-component protease inhibitor, which efficiently stabilized ex vivo kinin levels. The reliability of kinin levels was substantially jeopardized by prolonged rest time until centrifugation, phlebotomy methodology (eg, straight needles, catheters), vacuum sampling technique, or any time delays during venipuncture. The subsequently developed standardized procedure was applied to healthy volunteers and proved it significantly limited interday and interindividual kinin level variability.

CONCLUSION

The developed procedure for blood specimen collection and handling is feasible in clinical settings and allows for determination of reliable kinin levels. It may contribute to further elucidating the role of the kallikrein-kinin system in diseases like angioedema, sepsis, or coronavirus disease 2019.

Development of an antibody-free ID-LC MS method for the quantification of procalcitonin in human serum at sub-microgram per liter level using a peptide-based calibration

The quantification of low abundant proteins in complex matrices by liquid chromatography coupled to tandem mass spectrometry (LC-MS/MS) remains challenging. A measurement procedure based on optimized antibody-free sample preparation and isotope dilution coupled to LC-MS/MS was developed to quantify procalcitonin (PCT) in human serum at sub-microgram per liter level. A combination of sodium deoxycholate-assisted protein precipitation with acetonitrile, solid-phase extraction, and trypsin digestion assisted with Tween-20 enhanced the method sensitivity. Linearity was established through peptide-based calibration curves in the serum matrix (0.092-5.222 μg/L of PCT) with a good linear fit (R2 ≥ 0.999). Quality control materials spiked with known amounts of protein-based standards were used to evaluate the method's accuracy. The bias ranged from -2.6 to +4.3%, and the intra-day and inter-day coefficients of variations (CVs) were below 2.2% for peptide-based quality controls. A well-characterized correction factor was determined and applied to compensate for digestion incompleteness and material loss before the internal standards spike. Results with metrological traceability to the SI units were established using standard peptide of well-characterized purity determined by peptide impurity corrected amino acid analysis. The validated method enables accurate quantification of PCT in human serum at a limit of quantification down to 0.245 μg/L (bias -1.9%, precision 9.1%). The method was successfully applied to serum samples obtained from patients with sepsis. Interestingly, the PCT concentration reported implementing the isotope dilution LC-MS/MS method was twofold lower than the concentration provided by an immunoassay.

Targeted LC-MS/MS platform for the comprehensive determination of peptides in the kallikrein-kinin system

The kallikrein-kinin system (KKS) is involved in many physiological and pathophysiological processes and is assumed to be connected to the development of clinical symptoms of angioedema or COVID-19, among other diseases. However, despite its diverse role in the regulation of physiological and pathophysiological functions, knowledge about the KKS in vivo remains limited. The short half-lives of kinins, their low abundance and structural similarities and the artificial generation of the kinin bradykinin greatly hinder reliable and accurate determination of kinin levels in plasma. To address these issues, a sensitive LC-MS/MS platform for the comprehensive and simultaneous determination of the four active kinins bradykinin, kallidin, des-Arg(9)-bradykinin and des-Arg(10)-kallidin and their major metabolites bradykinin 2-9, bradykinin 1-7 and bradykinin 1-5 was developed. This platform was validated according to the bioanalytical guideline of the US Food and Drug Administration regarding linearity, accuracy, precision, sensitivity, carry-over, recovery, parallelism, matrix effects and stability in plasma of healthy volunteers. The validated platform encompassed a broad calibration curve range from 2.0-15.3 pg/mL (depending on the kinin) up to 1000 pg/mL, covering the expected concentrations in disease states. No source-dependent matrix effects were identified, and suitable stability of the analytes in plasma was observed. The applicability of the developed platform was proven by the determination of endogenous levels in healthy volunteers, whose plasma kinin levels were successfully detected in the low pg/mL range. The established platform facilitates the investigation of kinin-mediated diseases (e.g. angioedema, COVID-19) and enables the assessment of the impact of altered enzyme activities on the formation or degradation of kinins.

Sensitive mass spectrometric determination of kinin-kallikrein system peptides in light of COVID-19

The outbreak of COVID-19 has raised interest in the kinin-kallikrein system. Viral blockade of the angiotensin-converting enzyme 2 impedes degradation of the active kinin des-Arg(9)-bradykinin, which thus increasingly activates bradykinin receptors known to promote inflammation, cough, and edema-symptoms that are commonly observed in COVID-19. However, lean and reliable investigation of the postulated alterations is currently hindered by non-specific peptide adsorption, lacking sensitivity, and cross-reactivity of applicable assays. Here, an LC-MS/MS method was established to determine the following kinins in respiratory lavage fluids: kallidin, bradykinin, des-Arg(10)-kallidin, des-Arg(9)-bradykinin, bradykinin 1-7, bradykinin 2-9 and bradykinin 1-5. This method was fully validated according to regulatory bioanalytical guidelines of the European Medicine Agency and the US Food and Drug Administration and has a broad calibration curve range (up to a factor of 10³), encompassing low quantification limits of 4.4-22.8 pg/mL (depending on the individual kinin). The application of the developed LC-MS/MS method to nasal lavage fluid allowed for the rapid (~ 2 h), comprehensive and low-volume (100 µL) determination of kinins. Hence, this novel assay may support current efforts to investigate the pathophysiology of COVID-19, but can also be extended to other diseases.