Tandem mass spectrometry in the clinical laboratory: A tutorial overview

Comprehensive Overview of Bottom-Up Proteomics Using Mass Spectrometry

Proteomics is the large scale study of protein structure and function from biological systems through protein identification and quantification. "Shotgun proteomics" or "bottom-up proteomics" is the prevailing strategy, in which proteins are hydrolyzed into peptides that are analyzed by mass spectrometry. Proteomics studies can be applied to diverse studies ranging from simple protein identification to studies of proteoforms, protein-protein interactions, protein structural alterations, absolute and relative protein quantification, post-translational modifications, and protein stability. To enable this range of different experiments, there are diverse strategies for proteome analysis. The nuances of how proteomic workflows differ may be challenging to understand for new practitioners. Here, we provide a comprehensive overview of different proteomics methods. We cover from biochemistry basics and protein extraction to biological interpretation and orthogonal validation. We expect this Review will serve as a handbook for researchers who are new to the field of bottom-up proteomics.

Analytical methods and biomonitoring results in hair for the assessment of exposure to endocrine-disrupting chemicals: A literature review

Endocrine-disrupting chemicals (EDC) are compounds that alter functions of the endocrine system due to their ability to mimic or antagonize endogenous hormones, or that alter their synthesis and metabolism, causing adverse health effects. Human biomonitoring (HBM) is a reliable method to assess human exposure to chemicals through measurement in human body fluids and tissues. It identifies new sources of exposure and determines their distribution, thereby enabling detection of the most exposed populations. Blood and urine are commonly used for HBM of EDC, but their interest is limited for compounds presenting short half-lives. Hair appears as an interesting alternative insofar as it provides a large exposure window. For the present study, we evaluated the relevance of hair in determining EDC exposure. With this in mind, we undertook a literature review focusing on the bioanalytical aspects and performances of methods developed to determine EDC in hair. The literature review was performed through methodical bibliographical research. Relevant articles were identified using two scientific databases: PubMed and Web of Science, with search equations built from a combination of keywords, MeSH terms and Boolean operators. The search strategy identified 2949 articles. After duplicates were removed, and following title, abstract, and full-text screenings, only 31 were included for qualitative synthesis. Hair collection was mainly performed in the back of the head and preparation involved two processes: cutting into small pieces or grounding to powder. The off-line LC-MS/MS method remains the main technique used to assess EDC through hair. Differences regarding the validation of analytical methods and interpretation of HBM results were highlighted, suggesting a need for international harmonisation to obtain reliable and comparable results. External contamination of hair was identified as a main limitation in the interpretation of results, highlighting the need to better understand EDC transfers through hair and to develop relevant hair decontamination processes.

Polyphenol exposure of mothers and infants assessed by LC-MS/MS based biomonitoring in breast milk

Exposure to polyphenols is relevant throughout critical windows of infant development, including the breastfeeding phase. However, the quantitative assessment of polyphenols in human breast milk has received limited attention so far, though polyphenols may positively influence infant health. Therefore, a targeted LC-MS/MS assay was developed to investigate 86 analytes representing different polyphenol classes in human breast milk. The sample preparation consisted of liquid extraction, salting out, freeze-out, and a dilution step. Overall, nearly 70% of the chemically diverse polyphenols fulfilled all strict validation criteria for full quantitative assessment. The remaining analytes did not fulfill all criteria at every concentration level, but can still provide useful semi-quantitative insights into nutritional and biomedical research questions. The limits of detection for all analyzed polyphenols were in the range of 0.0041-87 ng*mL-1, with a median of 0.17 ng*mL-1. Moreover, the mean recovery was determined to be 82% and the mean signal suppression and enhancement effect was 117%. The developed assay was applied in a proof-of-principle study to investigate polyphenols in breast milk samples provided by twelve Nigerian mothers at three distinct time points post-delivery. In total, 50 polyphenol analytes were detected with almost half being phenolic acids. Phase II metabolites, including genistein-7-β-D-glucuronide, genistein-7-sulfate, and daidzein-7-β-D-glucuronide, were also detected in several samples. In conclusion, the developed method was demonstrated to be fit-for-purpose to simultaneously (semi-) quantify a wide variety of polyphenols in breast milk. It also demonstrated that various polyphenols including their biotransformation products were present in breast milk and therefore likely transferred to infants where they might impact microbiome development and infant health.

Therapeutic drug monitoring of glycopeptide antimicrobials: An overview of liquid chromatography-tandem mass spectrometry methods

Therapeutic drug monitoring (TDM) is a critical clinical tool used to optimize the safety and effectiveness of drugs by measuring their concentration in biological fluids. These fluids are primarily plasma or blood. TDM, together with real-time dosage adjustment, contributes highly to the successful management of glycopeptide antimicrobial therapies. Understanding pharmacokinetic/pharmacodynamic (PK/PD) properties is vital for optimizing antimicrobial therapies, as the efficacy of these therapies depends on both the exposure of the patient to the drug (PK) and pharmacodynamic (PD) parameters such as the in vitro estimated minimum drug concentration that inhibits bacterial growth (MIC). Liquid chromatography coupled to tandem mass spectrometry (LC-MS/MS) is widely recognized as the gold standard for measuring small molecules, such as antibiotics. This review provides a comprehensive overview of LC-MS/MS methods available for TDM of glycopeptide antibiotics, including vancomycin, teicoplanin, dalbavancin, oritavancin, and telavancin.

GC-MS and GC-MS/MS measurement of malondialdehyde (MDA) in clinical studies: Pre-analytical and clinical considerations

Malondialdehyde (MDA; 1,3-propanedial, OHC-CH2-CHO) is one of the most frequently measured biomarkers of oxidative stress in plasma and serum. L-Arginine (Arg) is the substrate of nitric oxide synthases (NOS), which convert L-arginine to nitric oxide (NO) and L-citrulline. The Arg/NO pathway comprises several members, including the endogenous NOS-activity inhibitor asymmetric dimethylarginine (ADMA) and its major metabolite dimethyl amine (DMA), and nitrite and nitrate, the major NO metabolites. Reliable measurement of MDA and members of the Arg/NO pathway in plasma, serum, urine and in other biological samples, such as saliva and cerebrospinal fluid, is highly challenging both for analytical and pre-analytical reasons. In our group, we use validated gas chromatography-mass spectrometry (GC-MS) and gas chromatography-tandem mass spectrometry (GC-MS/MS) methods for the quantitative determination in clinical studies of MDA as a biomarker of oxidative stress, and various Arg/NO metabolites that describe the status of this pathway. Here, the importance of pre-analytical issues, which has emerged from the use of GC-MS and GC-MS/MS in clinico-pharmacological studies, is discussed. Paradigmatically, two studies on the long-term oral administration of L-arginine dihydrochloride to patients suffering from peripheral arterial occlusive disease (PAOD) or coronary artery disease (CAD) were considered. Pre-analytical issues that were addressed include blood sampling, plasma or serum storage, study design (notably in long-term studies), and the alternative of measuring MDA in human urine.

Automated LC-MS/MS: Ready for the clinical routine Laboratory?

Background

Liquid chromatography-tandem mass spectrometry (LC-MS/MS) is a sensitive method with high specificity. However, its routine use in the clinical laboratory is hampered by its high complexity and lack of automation. Studies demonstrate excellent analytical performance using the first fully automated LC-MS/MS for 25-hydroxy vitamin D and immunosuppressant drugs (ISD) in hospital routine laboratories.

Objectives

Our objectives were (1) to verify the suitability of an automated LC-MS/MS in a commercial laboratory, which differs from the needs of hospital laboratories, and (2) examine its usability among operators with various professional backgrounds.

Methods

We assessed the analytical assay performance for vitamin D and the ISDs cyclosporine A and tacrolimus over five months. The assays were compared to an identical analyzer in a hospital laboratory, to in-house LC-MS/MS methods, and to chemiluminescent microparticle immunoassays (CMIA). Nine operators evaluated the usability of the fully automated LC-MS/MS system by means of a structured questionnaire.

Results

The automated system exhibited a high precision (CV < 8%), accuracy (bias < 7%) and good agreement with concentrations of external quality assessment (EQA) samples. Comparable results were obtained with an identical analyzer in a hospital routine laboratory. Acceptable median deviations of results versus an in-house LC-MS/MS were observed for 25-OH vitamin D3 (-10.6%), cyclosporine A (-4.3%) and tacrolimus (-6.6%). The median bias between the automated system and immunoassays was only acceptable for 25-OH vitamin D3 (6.6%). All users stated that they had had a good experience with the fully automated LC-MS/MS system.

Conclusions

A fully automated LC-MS/MS can be easily integrated for routine diagnostics in a commercial laboratory.

Mass spectrometry-based proteomics as an emerging tool in clinical laboratories

Mass spectrometry (MS)-based proteomics have been increasingly implemented in various disciplines of laboratory medicine to identify and quantify biomolecules in a variety of biological specimens. MS-based proteomics is continuously expanding and widely applied in biomarker discovery for early detection, prognosis and markers for treatment response prediction and monitoring. Furthermore, making these advanced tests more accessible and affordable will have the greatest healthcare benefit.This review article highlights the new paradigms MS-based clinical proteomics has created in microbiology laboratories, cancer research and diagnosis of metabolic disorders. The technique is preferred over conventional methods in disease detection and therapy monitoring for its combined advantages in multiplexing capacity, remarkable analytical specificity and sensitivity and low turnaround time.Despite the achievements in the development and adoption of a number of MS-based clinical proteomics practices, more are expected to undergo transition from bench to bedside in the near future. The review provides insights from early trials and recent progresses (mainly covering literature from the NCBI database) in the application of proteomics in clinical laboratories.

Innovative thermally assisted on-line solid phase extraction-reversed phase liquid chromatography applied to targeted nutrimetabolomics in human biofluids

In this study, the use of thermal desorption in on-line solid phase extraction coupled with reversed phase liquid chromatography (on-line SPE-LC) was for the first time proposed and demonstrated for the desorption of analytes strongly retained by multiple interaction polymeric sorbents. In detail, this analytical strategy was applied to the on-line SPE-LC targeted analysis of a model set of 34 human gut metabolites characterized by heterogeneous physicochemical properties (i.e., octanol-water partition coefficient in the range -0.3 - 3.4). The novel thermally assisted on-line SPE approach was investigated in comparison to conventional room temperature desorption strategies based on the use of (i) an optimized elution gradient or (ii) organic desorption followed by post-cartridge dilution. The thermally assisted desorption strategy has been shown to be better performing and suitable for the development of a reliable and sensitive method for the analysis of the model group of analytes in urine and serum. In more detail, under the optimized experimental conditions, the proposed method provided negligible matrix effects in both biofluids for almost all target analytes. Moreover, method quantification limits were in the ranges 0.026-7.2 μg L^-1 and 0.033-23 μg L^-1 for urine and serum, respectively, i.e., comparable to or lower than those reported in methods previously published.

MS-based proteomics of body fluids: The end of the beginning

Accurate biomarkers are a crucial and necessary precondition for precision medicine, yet existing ones are often unspecific and new ones have been very slow to enter the clinic. Mass spectrometry (MS)-based proteomics excels by its untargeted nature, specificity of identification and quantification making it an ideal technology for biomarker discovery and routine measurement. It has unique attributes compared to affinity binder technologies, such as OLINK Proximity Extension Assay and SOMAscan. In a previous review we described technological and conceptual limitations that had held back success (Geyer et al., 2017). We proposed a 'rectangular strategy' to better separate true biomarkers by minimizing cohort-specific effects. Today, this has converged with advances in MS-based proteomics technology, such as increased sample throughput, depth of identification and quantification. As a result, biomarker discovery studies have become more successful, producing biomarker candidates that withstand independent verification and, in some cases, already outperform state-of-the-art clinical assays. We summarize developments over the last years, including the benefits of large and independent cohorts, which are necessary for clinical acceptance. They are also required for machine learning or deep learning. Shorter gradients, new scan modes and multiplexing are about to drastically increase throughput, cross-study integration, and quantification, including proxies for absolute levels. We have found that multi-protein panels are inherently more robust than current single analyte tests and better capture the complexity of human phenotypes. Routine MS measurement in the clinic is fast becoming a viable option. The full set of proteins in a body fluid (global proteome) is the most important reference and the best process control. Additionally, it increasingly has all the information that could be obtained from targeted analysis although the latter may be the most straightforward way to enter into regular use. Many challenges remain, not least of a regulatory and ethical nature, but the outlook for MS-based clinical applications has never been brighter.

Steroid Profiling for the Diagnosis of Congenital Adrenal Hyperplasia by Microbore Ultra-performance Liquid Chromatography-Tandem Mass Spectrometry

BACKGROUND

A rapid and accurate measurement approach for 17α-hydroxyprogesterone (17-OHP) and related steroids in amount/volume-limited clinic samples is of importance for precise newborn diagnosis of congenital adrenal hyperplasia (CAH) and its subtypes in clinic.

METHODS

Sixteen steroids (17-OHP, androstenedione, cortisol, tetrahydro-11-deoxycortisol, pregnenolone, progesterone, 11-deoxycorticosterone, corticosterone, 21-deoxycortisol, 11-deoxycortisol, dehydroepiandrosterone, testosterone, aldosterone, 17α-hydroxypregnenolone, dihydrotestosterone and 18-hydroxycorticosterone) were included in the panel of high-throughput microbore ultra-performance liquid chromatography-tandem mass spectrometry. Samples were collected from 126 normal subjects and 65 patients including different subtypes of CAH.

RESULTS

The method was validated with satisfactory analytical performance in linearity, repeatability, recovery and limit of detection. Reference intervals for 16 steroids were established by quantifying the level of steroids detected in normal infants. The applicability of the method was tested by differentiating steroid metabolic characteristics between normal infants and infants with CAH, as well as between infants with different CAH subtypes. The relevance of 17-OHP, 21-deoxycortisol, and 17-OHP/11-deoxycortisol for 21-hydroxylase deficiency screening was demonstrated. The level of 11-deoxycorticosterone, 11-deoxycortisol, progesterone and androstenedione can be used for the diagnosis of different rare subtypes of CAH.

CONCLUSION

This study provides a strategy for highly efficient steroid analysis of amount/volume-limited clinic samples and holds great potential for clinical diagnosis of CAH.

Methods and Advances in the Design, Testing and Development of In Vitro Diagnostic Instruments

With the continuous improvement of medical testing and instrumentation engineering technologies, the design, testing and development methods of in vitro diagnostic instruments are developing rapidly. In vitro diagnostic instruments are also gradually developing into a class of typical high-end medical equipment. The design of in vitro diagnostic instruments involves a variety of medical diagnostic methods and biochemical, physical and other related technologies, and its development process involves complex system engineering. This paper systematically organizes and summarizes the design, testing and development methods of in vitro diagnostic instruments and their development in recent years, focusing on summarizing the related technologies and core aspects of the R&D process, and analyzes the development trend of the in vitro diagnostic instrument market.

A multiplex protein panel assay for severity prediction and outcome prognosis in patients with COVID-19: An observational multi-cohort study

Background

Global healthcare systems continue to be challenged by the COVID-19 pandemic, and there is a need for clinical assays that can help optimise resource allocation, support treatment decisions, and accelerate the development and evaluation of new therapies.

Methods

We developed a multiplexed proteomics assay for determining disease severity and prognosis in COVID-19. The assay quantifies up to 50 peptides, derived from 30 known and newly introduced COVID-19-related protein markers, in a single measurement using routine-lab compatible analytical flow rate liquid chromatography and multiple reaction monitoring (LC-MRM). We conducted two observational studies in patients with COVID-19 hospitalised at Charité - Universitätsmedizin Berlin, Germany before (from March 1 to 26, 2020, n=30) and after (from April 4 to November 19, 2020, n=164) dexamethasone became standard of care. The study is registered in the German and the WHO International Clinical Trials Registry (DRKS00021688).

Findings

The assay produces reproducible (median inter-batch CV of 10.9%) absolute quantification of 47 peptides with high sensitivity (median LLOQ of 143 ng/ml) and accuracy (median 96.8%). In both studies, the assay reproducibly captured hallmarks of COVID-19 infection and severity, as it distinguished healthy individuals, mild, moderate, and severe COVID-19. In the post-dexamethasone cohort, the assay predicted survival with an accuracy of 0.83 (108/130), and death with an accuracy of 0.76 (26/34) in the median 2.5 weeks before the outcome, thereby outperforming compound clinical risk assessments such as SOFA, APACHE II, and ABCS scores.

Interpretation

Disease severity and clinical outcomes of patients with COVID-19 can be stratified and predicted by the routine-applicable panel assay that combines known and novel COVID-19 biomarkers. The prognostic value of this assay should be prospectively assessed in larger patient cohorts for future support of clinical decisions, including evaluation of sample flow in routine setting. The possibility to objectively classify COVID-19 severity can be helpful for monitoring of novel therapies, especially in early clinical trials.

Funding

This research was funded in part by the European Research Council (ERC) under grant agreement ERC-SyG-2020 951475 (to M.R) and by the Wellcome Trust (IA 200829/Z/16/Z to M.R.). The work was further supported by the Ministry of Education and Research (BMBF) as part of the National Research Node 'Mass Spectrometry in Systems Medicine (MSCoresys)', under grant agreements 031L0220 and 161L0221. J.H. was supported by a Swiss National Science Foundation (SNSF) Postdoc Mobility fellowship (project number 191052). This study was further supported by the BMBF grant NaFoUniMedCOVID-19 - NUM-NAPKON, FKZ: 01KX2021. The study was co-funded by the UK's innovation agency, Innovate UK, under project numbers 75594 and 56328.

Detection of Dengue Fever Nonstructural Protein 1 Antigen by Proteolytic Peptide Imprinting Technology and UHPLC-MS/MS

Dengue fever is caused by mosquito-transmitted dengue virus infection and continues to increase worldwide, threatening public health in tropical and subtropical regions. The primary difficulties in preventing a reduction of the medical burden of dengue fever lies in the lack of effective mosquito control, preventive dengue vaccines, and clinically effective antiviral drugs to treat dengue infections. Rapid and accurate diagnosis is crucial for proper patient care and effective control of epidemics. The present work proposes an alternative strategy for detecting the dengue virus nonstructural protein 1 (NS1) antigen in clinical serum samples by using ultrahigh-performance liquid chromatography tandem mass spectrometry (UHPLC-MS/MS) in combination with the molecularly imprinted polymers. Rather than the whole protein, the NS1 signature peptide is selected as a template for molecular imprinting and quantified as a stoichiometric readout of NS1. Three functional monomers with hydrophobic, positively charged, and negatively charged groups were synthesized by click reactions in terms of the signature peptide. These three functional monomers provide abundant recognition sites for the peptide, allowing the peptide template to be effectively imprinted during polymerization. The imprinting conditions were optimized, and the molecularly imprinted polymers were characterized and used for enriching the signature peptide from digested serum samples by solid-phase extraction and then detected by UHPLC-MS/MS. The proposed method is used to detect the dengue virus NS1 in clinical samples and holds significant promise for early confirmation of dengue virus infection.

Comparison of analyte identification criteria and other aspects in triple quadrupole tandem mass spectrometry: Case study using UHPLC-MS/MS for regulatory analysis of veterinary drug residues in liquid and powdered eggs

Ultrahigh-performance liquid chromatography (UHPLC) coupled with triple quadrupole tandem mass spectrometry (MS/MS) is one of the most powerful tools for the multiclass, multiresidue analysis of veterinary drugs, pesticides, mycotoxins, and other chemical contaminants in foods and other sample types. Until approximately 2010, commercial MS/MS instruments using multiple reaction monitoring (MRM) were generally limited to minimum dwell (and inter-dwell) times of 10 ms per ion transition. To achieve the needed accuracy and detection limits for hundreds of targeted analytes, older UHPLC-MS/MS methods typically acquired only two ion transitions per analyte (yielding only one ion ratio for qualitative identification purposes), which is still the norm despite technological advancements. Newer instruments permit as little as 1 ms (inter-)dwell times to afford monitoring of more MRMs/analyte with minimal sacrifices in accuracy and sensitivity. In this study, quantification and identification were assessed in the validation of 169 veterinary drugs in liquid and powdered eggs. Quantitatively, an "extract-and-inject" sample preparation method yielded acceptable 70-120% recoveries and < 25% RSD for 139-141 (82-83%) of the 169 diverse drug analytes spiked into powdered and liquid eggs, respectively, at three levels of regulatory interest. Qualitatively, rates of false positives and negatives were compared when applying three different regulatory identification criteria in which two or three MRMs/drug were used in each case. Independent of the identification criteria, rates of false positives remained <10% for 95-99% of the drugs whether 2 or 3 ions were monitored, but the percent of drugs with >10% false negatives decreased from 25-45 to 10-12% when using 2 vs. 3 MRMs/analyte, respectively. Use of a concentration threshold at 10% of the regulatory level as an identification criterion was also very useful to reduce rates of false positives independent of ion ratios. Based on these results, monitoring >2 ion transitions per analyte is advised when using MS/MS for analysis, independent of SANTE/12682/2019, FDA/USDA, or 2002/657/EC identification criteria. (Quant)identification results using all three criteria were similar, but the SANTE criteria were advantageous in their greater simplicity and practical ease of use.

HPLC with spectrophotometric or mass spectrometric detection for quantifying very-long chain fatty acids in human plasma and its association with cardiac risk factors

BACKGROUND

We developed and compared two liquid chromatography methods, one with UV/Visible spectrophotometric detection (HPLC) and the other with mass spectrometric detection (LC-MS), for quantifying very-long chain fatty acids (VLCFA) in human plasma. Association of VLCFA with various cardiovascular risk factors were evaluated.

METHOD

Fasting blood samples were collected from 541 human volunteers (242 men and 299 women; mean age ±SD, 58.9 ± 12.4 years), including 429 and 112 individuals with and without hypertriglyceridemia, respectively. Esterified VLCFA were saponified and derivatized with 2-nitrophenylhydrazine. Separation of VLCFA species was achieved with C4 Mightysil column (HPLC) and Ascentis Express Phenyl-Hexyl column (LC-MS) followed by spectrophotometric and selected-reaction monitoring mode of mass spectrometric detection, respectively.

RESULTS

The HPLC assay of VLCFA was precise with intra-assay imprecision of 2.5% to 6.9% and inter-assay imprecision of 3.2% to 9.5%. Moreover, there was an excellent correlation (r > 0.96) between HPLC and LC-MS methods. The 95 percentile reference intervals (RI; upper limit) of VLCFA were determined to be 41.3 µmol/L in healthy volunteers. Plasma VLCFA were significantly correlated with triglycerides (Spearman's ρ = 0.306, P < 0.001) and total cholesterol (Spearman's ρ = 0.251, P < 0.001). All species of VLCFA were significantly elevated in hypertriglyceridaemic individuals compared with control.

CONCLUSION

We established LC-based assays of VLCFA with either spectrophotometry or mass spectrometry as a detection system. Hypertriglyceridaemia is significantly associated with elevated concentration of each species of VLCFA.

Design of experiments for development and optimization of a liquid chromatography coupled to tandem mass spectrometry bioanalytical assay

Design of experiments (DoE) is a valuable tool for the optimization of quantitative bioanalytical methods utilizing liquid chromatography coupled to tandem mass spectrometry (LC-MS/MS). Liquid chromatography mass spectrometry (LC-MS) is composed of several processes, including, liquid introduction and analyte ionization. The goal is to transfer analytes from atmospheric pressure to vacuum and maintain conditions that are compatible for both LC and MS. These processes involve many experimental factors which need to be simultaneously optimized to obtain maximum sensitivity and resolution at minimum retention time. In this tutorial, the basic concepts of DoE will be explained with focus on practical use of DoE. Three case studies optimized with DoE for liquid chromatography tandem mass spectrometry (LC-MS/MS) quantitative assays will then be presented.

After another decade: LC-MS/MS became routine in clinical diagnostics

Tandem mass spectrometry - especially in combination with liquid chromatography (LC-MS/MS) - is applied in a multitude of important diagnostic niches of laboratory medicine. It is unquestioned in its routine use and is often unreplaceable by alternative technologies. This overview illustrates the development in the past decade (2009-2019) and intends to provide insight into the current standing and future directions of the field. The instrumentation matured significantly, the applications are well understood, and the in vitro diagnostics (IVD) industry is shaping the market by providing assay kits, certified instruments, and the first laboratory automated LC-MS/MS instruments as an analytical core. In many settings the application of LC-MS/MS is still burdensome with locally lab developed test (LDT) designs relying on highly specialized staff. The current routine applications cover a wide range of analytes in therapeutic drug monitoring, endocrinology including newborn screening, and toxicology. The tasks that remain to be mastered are, for example, the quantification of proteins by means of LC-MS/MS and the transition from targeted to untargeted omics approaches relying on pattern recognition/pattern discrimination as a key technology for the establishment of diagnostic decisions.