Investigation of transition ion ratio variation for liquid chromatography-tandem mass spectrometry: A case study approach

Novel quality control strategies for the determination of 25-hydroxyvitamin D by LC-MS/MS

Mass spectrometry analysis has been applied in many important diagnostic fields of laboratory medicine. However, there is little literature to guide quality management systems for LC-MS/MS methods. In this study, LC-MS/MS 25-hydroxyvitamin D (25(OH)D) was used as an example to establish internal quality control strategies to ensure the accuracy of clinical vitamin D results. A total of 141 batches of samples were analyzed. Sample internal standard peak area variability, ion pair ratio, and physical examination population data were monitored as quality control strategies for 25(OH)D results. The analytical performance was evaluated by calculated Sigma metrics. Applying our quality control strategies, several abnormal data were monitored in the routine analysis. The daily peak area CV of 25(OH)D fluctuated within a certain range. By selecting P99 CV as the control target, two abnormal batches were found. The ratio of 25(OH)VD3 ion pairs was relatively stable. Among them, batch20230120 had a high CV value, which may be due to the bias caused by the limited number. According to the physical examination data, batch20220913 and batch20220919 exceeded the alarm limit. Sigma level of 25(OH)VD3 in the laboratory was 6.52, which achieved "excellent" performance. In conclusion, we established comprehensive quality control strategies for the determination of 25(OH)D by LC-MS/MS, which has high analytical performance and can provide more accurate reports for the clinic.

Development and validation of a liquid chromatography-tandem mass spectrometry assay to quantify plasma 24(S)-hydroxycholesterol and 27-hydroxycholesterol: A new approach integrating the concept of ion ratio

Accurate quantification of 24(S)-hydroxycholesterol and 27-hydroxycholesterol holds substantial biological significance due to their involvement in pivotal cellular processes, encompassing cholesterol homeostasis, inflammatory responses, neuronal signaling, and their potential as disease biomarkers. The plasma determination of these oxysterols is challenging considering their low concentrations and similarities in terms of empirical formulae, molecular structure, and physicochemical properties across all human endogenous plasma oxysterols. To overcome these sensitivity and specificity issues, we developed and validated a quantification method using liquid chromatography coupled to a tandem mass spectrometry instrument. Validation studies were designed inspired by Clinical and Laboratory Standards Institute (CLSI) C62-A Guidelines. The linearity ranged between 20 and 300 nM for both oxysterols with limits of quantification at 20 nM and 30 nM for 24(S)-OHC and 27-OHC, respectively. Inter-day precision coefficient variations (CV) were lower than 10% for both oxysterols. An optimal separation of 25-OHC was obtained from 24(S)-OHC and 27-OHC with a resolution (Rs) > 1.25. The determination and validation of ion ratios for 24(S)-OHC and 27-OHC enabled another quality check in identifying interferents that could impact the quantification. Our developed and validated LC-MS/MS method allows consistent and reliable quantification of human plasmatic 24(S)-OHC and 27-OHC that is warranted in fundamental and clinical research projects.

Multistage Detection of Tetrodotoxin Traces in Diodon hystrix Collected in El Salvador

This study describes a multistage methodology to detect minute amounts of tetrodotoxin in fishes, a plan that may be broadened to include other marine organisms. This methodology was applied to porcupinefish (Diodon hystrix) collected in Punta Chiquirín, El Salvador. A three-stage approach along with post-acquisition processing was employed, to wit: (a) Sample screening by selected reaction monitoring (HPLC-MS/MS-SRM) analyses to quickly identify possible toxin presence via a LC/MS/MS API 3200 system with a triple quadrupole; (b) HPLC-HRFTMS-full scan analyses using an ion trap-Orbitrap spectrometer combined with an MZmine 2-enhanced dereplication-like workflow to collect high-resolution mass spectra; and (c) HPLC-HRMS2 analyses. This is the first time tetrodotoxin has been reported in D. hystrix specimens collected in El Salvador.

Online hyphenation of in-capillary aptamer-functionalized solid-phase microextraction and extraction nanoelectrospray ionization for miniature mass spectrometry analysis

Direct mass spectrometry (MS) analysis is vital to chemical and biological investigations. However, measuring complex samples is challenging due to matrix interference, resulting in compromised MS performance. In this study, an integrated experimental protocol has been developed, combining in-capillary aptamer-functionalized solid-phase microextraction (SPME), extraction nanoelectrospray ionization (nanoESI), and miniature MS analysis. The established method was applied to analyze caffeine in electronic cigarette liquid and beverage samples as proof-of-concept demonstrations. A custom SPME strip fabricated with caffeine-binding aptamers was prepared with an immobilization density of up to 0.812 nmol cm^-2. Critical parameters affecting the effects of extraction, desorption, and ionization were optimized. A novel transition ion ratio-based strategy with enhanced quantitation accuracy was developed. The analytical performance of the proposed method was evaluated under optimized conditions. Acceptable recoveries of 87.5-111.5% with relative standard deviations of 3.1-6.1% and satisfactory sensitivity with limits of detection of 1.5 and 3 ng mL^-1 and limits of quantitation of 5 and 10 ng mL^-1 were obtained, respectively. The developed approach demonstrates a promising potential for rapid on-site applications with appealing analytical performance and efficiency.

System Performance Monitoring in Clinical Liquid Chromatography-Tandem Mass Spectrometry (LC-MS/MS)

Quality assurance (QA) activities enable continuous improvement through ongoing post-implementation monitoring to identify, evaluate, and correct problems. QA for clinical liquid chromatography tandem mass spectrometry (LC-MS/MS) assays should include specific components that address the unique aspects of these methods. This chapter briefly describes approaches for clinical LC-MS/MS system performance monitoring using batch and peak review metrics, largely following CLSI-C62A guidance. Though routine checks ensure the quality of results reported for each run, there is also a need to evaluate metrics between runs over time. Post-implementation performance monitoring of LC-MS/MS methods is typically focused on calibration curves, retention times, peak intensities, and ion ratios.

Review of the Use of Liquid Chromatography-Tandem Mass Spectrometry in Clinical Laboratories: Part II-Operations

Liquid chromatography-tandem mass spectrometry (LC-MS/MS) is increasingly utilized in clinical laboratories because it has advantages in terms of specificity and sensitivity over other analytical technologies. These advantages come with additional responsibilities and challenges given that many assays and platforms are not provided to laboratories as a single kit or device. The skills, staff, and assays used in LC-MS/MS are internally developed by the laboratory, with relatively few exceptions. Hence, a laboratory that deploys LC-MS/MS assays must be conscientious of the practices and procedures adopted to overcome the challenges associated with the technology. This review discusses the post-development landscape of LC-MS/MS assays, including validation, quality assurance, operations, and troubleshooting. The content knowledge of LC-MS/MS users is quite broad and deep and spans multiple scientific fields, including biology, clinical chemistry, chromatography, engineering, and MS. However, there are no formal academic programs or specific literature to train laboratory staff on the fundamentals of LC-MS/MS beyond the reports on method development. Therefore, depending on their experience level, some readers may be familiar with aspects of the laboratory practices described herein, while others may be not. This review endeavors to assemble aspects of LC-MS/MS operations in the clinical laboratory to provide a framework for the thoughtful development and execution of LC-MS/MS applications.

Targeted Metabolomics Using LC-MS in Neurospora crassa

The filamentous fungus Neurospora crassa has historically been a model for understanding the relationship between genes and metabolism-auxotrophic mutants of N. crassa were used by Beadle and Tatum to develop the one-gene-one-enzyme hypothesis for which they earned the Nobel Prize in 1958. In the ensuing decades, several techniques have been developed for the systematic analysis of metabolites in N. crassa and other fungi. Untargeted and targeted approaches have been used, with a focus on secondary metabolites over primary metabolism. Here, we describe a pipeline for sample preparation, metabolite extraction, Liquid Chromatography-Mass Spectrometry (LC-MS), and data analysis that can be used for targeted metabolomics of primary metabolites in N. crassa. Liquid cultures are grown with shaking in a defined minimal medium and then collected using filtration. Samples are lyophilized for 2 days at -80°C, pulverized, and mixed with a solution to extract polar metabolites. The metabolites are separated and identified using LC-MS, with downstream analysis using Skyline interpretive software. Relative levels of hundreds of metabolites can be detected and compared across strains. © 2022 Wiley Periodicals LLC. Basic Protocol: Metabolite extraction and detection from Neurospora crassa cell cultures using Liquid Chromatography-Mass Spectrometry.

Review of the Use of Liquid Chromatography-Tandem Mass Spectrometry in Clinical Laboratories: Part I-Development

The process of method development for a diagnostic assay based on liquid chromatography-tandem mass spectrometry (LC-MS/MS) involves several disparate technologies and specialties. Additionally, method development details are typically not disclosed in journal publications. Method developers may need to search widely for pertinent information on their assay(s). This review summarizes the current practices and procedures in method development. Additionally, it probes aspects of method development that are generally not discussed, such as how exactly to calibrate an assay or where to place quality controls, using examples from the literature. This review intends to provide a comprehensive resource and induce critical thinking around the experiments for and execution of developing a clinically meaningful LC-MS/MS assay.

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.

Potential 2-Aminoindane Fatality Invalidated By Careful Mass Spectrometric Analysis

We describe herewith the case of a patient presenting to the emergency department for worsening ear-nose-throat symptoms. As chemsex was evocated by the family, patient's serum was submitted to a new psychoactive substances screening. After a simple liquid liquid extraction, serum was injected on a high-resolution mass spectrometer using quite usual conditions (C18 column, gradient mode with acidic buffer, methanol and acetonitrile). An almost perfect match with 2-aminoindane (2-AI) was observed considering that the precursor ion was present in the sample but absent in the commercial library. Literature concerning 2-AI is sparse, and further investigations were undertaken. After injection of the reference standard, a small retention time shift has been observed (0.3 min) between the standard and the sample. The case was only closed while spiking the sample with the standard, giving rise to two distinct peaks. As a result, 2-AI was then considered as absent from the sample and death was attributed only to infection. Moreover, a rapid liquid chromatography tandem mass spectrometry method dedicated to 2-AI was developed. It generated the same false positive result highlighted by significant differences observed in ion ratios (2.37 for the sample versus 6.62 for the neat standard).

Quality Control and Outlier Detection of Targeted Mass Spectrometry Data from Multiplex Protein Panels

Increased throughput as well as increased multiplexing of liquid chromatography coupled to selected reaction monitoring mass spectrometry (LC-SRM-MS) assays for protein quantification challenges routine data analysis. Despite the measurement of multiple transitions from multiple peptides, for clinical applications a single (quantifier) transition from one (quantifier) signature peptide is used to represent the protein quantity with most data used solely to validate the quantifier result. To support the generation of reliable protein results from multiplexed LC-SRM-MS assays with large sample numbers, we developed a data analysis process for quality control and outlier detection using data from an 11-protein multiplex LC-SRM-MS method for dried blood samples (195 492 chromatographic peaks from 1481 samples * 11 proteins * 2 peptides * 3 transitions * 2 isotopologues). The 2-tiered data analysis process detects outliers for ion transition ratio, peptide ratio, and % difference between duplicates, applying less stringent criteria to samples with a small % difference between duplicates (Tier 1) and more stringent criteria to samples with unassessed or a large % difference between duplicates (Tier 2). After manual peak review, 1127 samples (76%) were selected based on the sample quality. The data analysis process thereafter automatically selected quantifier transitions/peptides, removed quality control failures and outliers (8%), averaged duplicates, and generated a comprehensive report listing 6085 quality controlled protein-level results. The proposed data analysis process serves as a starting point toward standardized data analysis of multiplexed LC-SRM-MS protein assays.