Using differential mobility spectrometry to improve the specificity of targeted measurements of 2,3-dinor 11β-Prostaglandin F2α

INTRODUCTION

2,3-dinor 11β-Prostaglandin F2α (BPG) is an arachidonic acid derivative and the most abundant metabolic byproduct of prostaglandin D2, which is released during mast cell activation. Therefore, measurements of BPG in urine using liquid chromatography-tandem mass spectrometry (LC-MS/MS) provide a noninvasive method for evaluation and management of mast cell disorders. Measurements obtained by LC-MS/MS exhibit a high prevalence of chromatographic interferences resulting in challenges with optimal determination of BGP. In this investigation, differential mobility spectrometry (DMS) is utilized to overcome the limitations of current testing.

METHODS

Urine samples were extracted using an automated solid-phase extraction method. Samples were then analyzed with and without DMS devices installed on two commercially available mass spectrometry platforms to assess the benefits of DMS. Following promising results from a preliminary analytical evaluation, LC-DMS-MS/MS measurements of BPG in urine were fully validated to assess the analytical implications of using this technology.

RESULTS AND DISCUSSION

The addition of DMS devices to the LC-MS/MS systems evaluated in this investigation significantly reduced interferences observed in the chromatograms. Concomitantly, DMS reduced the number of discordant quantifier/qualifier fragment ion results that significantly exceeded the ± 20 % limits, suggesting greater analytical specificity. The validation studies yielded low interday imprecision, with %CVs less than 6.5 % across 20 replicate measurements. Validation studies assessing other aspects of analytical performance also met acceptance criteria.

CONCLUSIONS

Incorporating DMS devices greatly improved the specificity of BPG measurements by LC-MS/MS, as evidenced by the comparison of chromatograms and fragment ion results. Validation studies showed exceptional performance for established analytical metrics, indicating that this technology can be used to minimize the impact of interferences without adversely impacting other aspects of analytical or clinical performance.

Infliximab Therapeutic monitoring by tryptic peptide LC-MS/MS method improvements lead to improved accuracy with decreased imprecision and turnaround time

Introduction

Therapeutic drug monitoring of infliximab has become the standard of care for inflammatory bowel disease in the setting of loss of response to therapy, and occasionally in proactive therapy personalization. Measurement of infliximab by tryptic peptide HPLC-MS/MS has been available since 2015, mostly in reference laboratories.

Objectives

Here, we present method improvements to our original published method leading to a more efficient, robust, and high throughput tryptic peptide HPLC-MS/MS assay for infliximab quantitation.

Methods

Deidentified residual serum samples submitted for clinical testing were used for method comparison and infliximab was spiked into normal human serum for performance studies. Improvements included the addition of a stable isotope labeled full length infliximab internal standard (IS) replacing a surrogate IS, and immunoenrichment using Melon Gel for immunoglobulins replacing the saturated ammonium sulfate precipitation. Digestion and chromatography were optimized, and automation was added. The method improvements were validated to include precision, accuracy, reportable range, linearity, and analytical sensitivity.

Results

The digestion time was reduced from overnight to 1 h. The assay analytical measuring range (AMR) remained the same throughout improvements, 1-100 µg/mL, with linearity of 0.98x + 0.50, R2 = 1.00. Intra- and inter-assay imprecision were less than 5 % CV at four different concentrations. Accuracy was assessed with 106 patients within the AMR; Passing-Bablok Regression yielded a slope of 1.00 and a y-intercept of 0.25. Turnaround time was reduced by 1 day, and imprecision of three levels of quality control trended down after new method implementation.

Conclusions

Method improvements including automation have allowed for assay completion in half a day, improving robustness and turnaround time.

Improving LC-MS/MS measurements of steroids with differential mobility spectrometry

Introduction

Steroid measurements are important for diagnosis and monitoring of many conditions and treatment regiments; however, due to structural and chemical similarities amongst steroids, these analyses are challenging, even for highly specific techniques such as liquid chromatography-tandem mass spectrometry (LC-MS/MS). Differential mobility spectrometry (DMS) has the potential to improve these analyses by providing an orthogonal and complementary separation technique.

Methods

Initially, the potential for DMS to improve signal-to-noise ratio (S/N) and reduce interference was tested by comparing chromatograms acquired with and without DMS when performing measurements of six different steroids. Subsequently, a full clinical validation of cortisol and cortisone in urine was performed with the LC-DMS-MS/MS method.

Results and Discussion

DMS significantly reduced interferences observed in the chromatograms and boosted S/N by between 1.6 and 13.8 times. Additionally, DMS improved the agreement between quantifier/qualifier fragment ion results for cortisol and cortisone as indicated by the increase in R2 from approximately 0.81 to 0.98. All validation studies met acceptance criteria and we observed exceptional analytical performance in terms of precision, with % CVs less than 8%.

Conclusions

DMS improved the specificity of the steroid measurements by reducing interferences and improving S/N. The validation studies prove that these benefits did not come at the expense of other aspects of analytical performance. This study indicates that DMS has the potential to benefit not just clinical measurements of challenging analytes, but many clinical LC-MS/MS analyses.

Development of an LC-MS/MS assay with automated sample preparation for phosphatidylethanol (PEth)- Not your typical clinical marker

Phosphatidylethanol (PEth) is a group of phospholipids formed exclusively in the presence of ethanol on the erythrocyte membrane, making it a direct biomarker for long-term ethanol consumption for which a clinical reference interval has been established. Here, we describe an assay for quantitation for two most abundant PEth homologues, PEth 16:0/18:1 and PEth 16:0/18:2, from human whole blood, and present challenges overcome throughout the development process. Since PEth is localized within erythrocyte membranes, a reliable sample preparation technique is an important aspect of PEth analysis. Therefore, various erythrocyte lysing agents for recovery of exogenously spiked standards and controls were evaluated to identify one that performed comparably to the recovery of endogenous analytes found in authentic samples. A supported liquid extraction (SLE) technique was employed for sample cleanup and enrichment which together with liquid chromatography-tandem mass spectrometry (LC-MS/MS) analysis enabled automated sample preparation, appropriate chromatographic resolution, and minimal system carryover. This resulted in a laboratory developed test with an analytical measurement range (AMR) of 10-1000 ng/mL (slope = 0.9902-1.0138, R2 = 0.9958-0.9972), that was precise (intra-day precision: 3.4-4.1%; inter-day precision: 4.4-8.2% over the AMR), accurate when compared with an available external laboratory test (slope = 0.9943-1.0206, R2 = 0.9635-0.9678, no lower decision point interpretation changes), with effective analyte recovery (77.2-83.5%), and established stability characteristics, while chromatographically separating the analytes to ensure no additive effects due to the isotopic distribution of the opposing analyte.

Identification, Measurement, and Assessment of the Clinical Utility of Human Pancreatic Polypeptide by Liquid Chromatography-Tandem Mass Spectrometry

Human pancreatic polypeptide (HPP) is a 36 amino acid peptide hormone that plays a role in the bidirectional communication between the digestive system and the brain. HPP measurements are used to assess vagal nerve function following sham feeding and to detect gastroenteropancreatic-neuroendocrine tumors. These tests have historically been conducted by radioimmunoassays, but liquid chromatography-tandem mass spectrometry (LC-MS/MS) has several advantages such as improved specificity and elimination of radioactive molecules. Here, we present our LC-MS/MS method. Initially, samples were immunopurified and subjected to LC-high resolution accurate mass tandem mass spectrometry (HRAM-MS/MS) to identify circulating forms of the peptide in human plasma. We identified 23 forms of HPP, including several glycosylated forms. The most abundant peptides then were used for targeted LC-MS/MS measurements. LC-MS/MS performance for precision, accuracy, linearity, recovery, limit of detection, and carryover met our acceptance criteria based on CLIA regulations. Additionally, we observed the expected physiological rise in HPP in response to sham feeding. Our results indicate that HPP measurement by LC-MS/MS produces clinically equivalent results to our established immunoassay when several peptides are monitored, making it a suitable replacement. The measurement of peptide fragments, including modified species, might have additional clinical value.

Comparison of intact protein and digested peptide techniques for high throughput proteotyping of ApoE

Introduction

Apolipoprotein E (ApoE) genotyping has been shown to have diagnostic value in the evaluation of cardiovascular diseases and neurodegenerative disorders such as Alzheimer’s disease. Although genetic testing is well established for this application, liquid chromatography-mass spectrometry (LC–MS) has the potential to provide a high throughput, low-cost alternative for ApoE evaluation.

Methods

Serum samples were analyzed by peptide, intact protein, and genomic techniques. For peptide analysis, samples were digested with trypsin followed by liquid chromatography-tandem mass spectrometry analysis (LC–MS/MS) using a high-throughput multichannel LC system coupled to a Sciex 7500 mass spectrometer. For intact protein analysis, ApoE was immuno-purified using a monoclonal antibody immobilized on magnetic beads followed by high-resolution LC–MS analysis using an Exploris 480. DNA was extracted and evaluated using Sanger sequencing as a reference method.

Results and discussion

The peptide measurement method produced one discrepant result when compared to genomic sequencing (out of 38 sequenced samples), whereas the intact protein analysis followed by deconvolution resulted in two discrepant results and when the intact protein data was processed with chromatographic integration there were three discrepant results. Therefore, the intact protein method proved slightly less accurate, required longer analysis time, and is substantially more costly, while providing only a 30 min improvement in sample preparation time.

Conclusions

With current MS technology clinical laboratories appear to be better served to utilize trypsin digest sample preparation and LC–MS/MS as opposed to high-resolution LC–MS intact protein analysis techniques for evaluation of ApoE proteotype. Peptide analysis methods are capable of producing accurate results with high throughput and minimal cost.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12014-022-09379-5.

Comparison of anti-peptide and anti-protein antibody-based purification techniques for detection of SARS-CoV-2 by targeted LC-MS/MS

The COVID-19 pandemic has necessitated exploration of alternative testing methods for detection of Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) to ensure clinical laboratories can continue to provide critical testing results. Liquid chromatography-tandem mass spectrometry (LC-MS/MS) is established in many clinical laboratories due its high specificity and sensitivity, making it a logical alternative methodology. However, matching the sensitivity of quantitative reverse transcription-polymerase chain reaction (qRT-PCR) remains challenging, which forced utilization of antibody-based enrichment prior to targeted LC-MS/MS analysis. When utilizing antibody purification techniques, investigators must decide whether to enrich the target protein or peptides, but there are few studies comparing the two approaches to assist in this decision-making process. In this work, we present a comparison of intact protein and peptide antibody-based purification for LC-MS/MS based detection of SARS-CoV-2. We have found that protein purification yields more intense LC-MS/MS signals, but is also less specific, yielding higher noise and more background when compared to peptide purification techniques. Therefore, when using traditional data analysis techniques, the enrichment technique that provides superior sensitivity varies for individual peptides and no definitive overall conclusion can be made. These observations are corroborated when using a novel machine learning approach to determine positive/negative test results, which yielded superior sensitivity when using protein purification, but better specificity and area under the ROC curve when performing peptide purification.

Targeted Detection of SARS-CoV-2 Nucleocapsid Sequence Variants by Mass Spectrometric Analysis of Tryptic Peptides

COVID-19 vaccines are becoming more widely available, but accurate and rapid testing remains a crucial tool for slowing the spread of the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) virus. Although the quantitative reverse transcription-polymerase chain reaction (qRT-PCR) remains the most prevalent testing methodology, numerous tests have been developed that are predicated on detection of the SARS-CoV-2 nucleocapsid protein, including liquid chromatography-tandem mass spectrometry (LC-MS/MS) and immunoassay-based approaches. The continuing emergence of SARS-CoV-2 variants has complicated these approaches, as both qRT-PCR and antigen detection methods can be prone to missing viral variants. In this study, we describe several COVID-19 cases where we were unable to detect the expected peptide targets from clinical nasopharyngeal swabs. Whole genome sequencing revealed that single nucleotide polymorphisms in the gene encoding the viral nucleocapsid protein led to sequence variants that were not monitored in the targeted assay. Minor modifications to the LC-MS/MS method ensured detection of the variants of the target peptide. Additional nucleocapsid variants could be detected by performing the bottom-up proteomic analysis of whole viral genome-sequenced samples. This study demonstrates the importance of considering variants of SARS-CoV-2 in the assay design and highlights the flexibility of mass spectrometry-based approaches to detect variants as they evolve.

Analytical sensitivity and specificity of four point of care rapid antigen diagnostic tests for SARS-CoV-2 using real-time quantitative PCR, quantitative droplet digital PCR, and a mass spectrometric antigen assay as comparator methods

BACKGROUND

We evaluated the analytical sensitivity and specificity of four rapid antigen diagnostic tests (Ag RDTs) for SARS-CoV-2, using reverse transcription quantitative PCR (RT-qPCR) as the reference method; and further characterizing samples using droplet digital quantitative PCR (ddPCR) and a mass spectrometric antigen test.

METHODS

350 (150 negative and 200 RT-qPCR positive) residual phosphate buffered saline (PBS) samples were tested for antigen using the BD Veritor lateral flow (LF), ACON LF, ACON fluorescence immunoassay (FIA), and LumiraDx FIA. ddPCR was performed on RT-qPCR positive samples to quantitate the viral load in copies/mL applied to each Ag RDT. Mass spectrometric antigen testing was performed on PBS samples to obtain a set of RT-qPCR positive, antigen positive samples for further analysis.

RESULTS

All Ag RDTs had nearly 100% specificity compared to RT-qPCR. Overall analytical sensitivity varied from 66.5% to 88.3%. All methods detected antigen in samples with viral load >1,500,000 copies/mL RNA, and detected ≥75% of samples with viral load of 500,000 to 1,500,000 copies/mL. The BD Veritor LF detected only 25% of samples with viral load between 50,000-500,000 copies/mL, compared to 75% for the ACON LF device and >80% for LumiraDx and ACON FIA. The ACON FIA detected significantly more samples with viral load <50,000 copies/mL compared to the BD Veritor. Among samples with detectable antigen and viral load <50,000 copies/mL, sensitivity of the Ag RDT varied between 13.0% (BD Veritor) and 78.3% (ACON FIA).

CONCLUSIONS

Ag RDTs differ significantly in analytical sensitivity, particularly at viral load <500,000 copies/mL.

Dysfunctional crosstalk of cardiomyocytes and cardiac fibroblasts in a pluripotent stem cell model of dilated cardiomyopathy

Background/Purpose

Dilated cardiomyopathy (DCM) is characterized by left ventricular dilation and contractile dysfunction. Fibrosis is one major phenotypic result in DCM, pointing to the contribution of both, cardiomyocytes (CM) and cardiac fibroblasts (cFB) to DCM. The molecular basis of most DCM cases remains unknown. Nevertheless, it is known that up to 35% of all cases have a family history, linked to mutations in more than 30 gene loci. The aim of this study is to analyse the crosstalk of iPSC-CM and cFB and the underlying genetic and molecular causes in a patient-specific induced pluripotent stem cell (iPSC) model of DCM.

Methods and results

For this purpose a 4-member family was recruited containing 2 patients (father and daughter) with severe DCM and heart transplantation. iPSCs of all family members were generated and differentiated into iPSC-CMs. All iPSC-CMs express general cardiac markers, e.g. βMHC, α-actinin. Interestingly, αMHC expression was decreased in diseased iPSC-CMs in comparison to control cells. Additionally, the sarcomeric regularity was decreased in diseased iPSC-CMs. As we found significantly increased fibrosis (22%) in explanted myocardium of the diseased father compared to healthy myocardium (8%), both cFB and CM seem to play an important role. From the same myocardium primary cFBs were isolated and shown to express typical cFB markers clearly distinguishing these cells from non-fibroblasts as well as from fibroblasts with different origin. To analyse the contribution of cFBs and CMs to DCM on a functional level, 3D engineered heart muscles (EHMs) were generated in different diseased/healthy cell combinations. EHMs composed of both or either one affected DCM-iPSC-CMs and/or DCM-cFBs in comparison to healthy control EHMs did not produce any measurable force, indicating that the DCM-EHM phenotype is clearly diseased. Evaluation of tissues' viscoelasticity showed that DCM-cFB, DCM-iPSC-CMs and DCM-EHMs were stiffer than healthy control EHMs. Thus these data suggest that apart from the obvious dysfunction of DCM CMs, DCM cFBs clearly contribute to the contractile pathophysiology in DCM EHMs. Furthermore, whole exome sequencing of iPSCs was conducted to identify disease-causing variants. This analyses point towards a new genetic variant in the FLNc gene coding for a protein important in development, stabilization and maintenance of myofibrils. Rescue of this variant by CRISPR Cas9 genome editing will shed more light onto the role of this variant during DCM development in the future.

Conclusion

Using a ps-iPSC-CM model of a 4-member family with two severe DCM patients, we could demonstrate a clear contribution of both cell types, iPSC-CMs and cFB, to the contractile pathophysiology of DCM. We identified a potentially disease-causing new variant in the FLNc gene, which may contribute to the impaired functionality within the diseased iPSC-CMs and EHM. This makes FLNc a new therapeutic target for DCM.

Funding Acknowledgement

Type of funding source: Public grant(s) – National budget only. Main funding source(s): IRTG1816

Detection and identification of a protein biomarker in antibiotic-resistant Escherichia coli using intact protein LC offline MALDI-MS and MS/MS

AIMS

The identification and differentiation of antibiotic-resistant bacteria by matrix-assisted laser desorption/ionization-time of flight-mass spectrometry (MALDI-TOF-MS) profiling remains a challenge due to the difficulty in detecting unique protein biomarkers associated with this trait. To expand the detectable proteome in antibiotic-resistant bacteria, we describe a method implementing offline LC protein separation/fractionation prior to MALDI-ToF-MS and top-down MALDI-ToF/ToF-MS (tandem MS or MS/MS) for the analysis of several antibiotic-resistant Escherichia coli isolates.

METHODS AND RESULTS

Coupling offline LC with MALDI-ToF-MS increased the number of detected protein signals in the typically analyzed mass regions (m/z 3000-20 000) by a factor of 13. Using the developed LC-MALDI-ToF-MS protocol in conjunction with supervised principal components analysis, we detected a protein biomarker at m/z 9355 which correlated to β-lactam resistance among the E. coli bacteria tested. Implementing a top-down MALDI-ToF/ToF-MS approach, the prefractionated protein biomarker was inferred as a DNA-binding HU protein, likely translated from the bla_CMY-2 gene (encoding AmpC-type β-lactamase) in the incompatibility plasmid complex A/C (IncA/C).

CONCLUSIONS

Our results demonstrate the utility of LC-MALDI-MS and MS/MS to extend the number of proteins detected and perform MALDI-accessible protein biomarker discovery in microorganisms.

SIGNIFICANCE AND IMPACT OF THE STUDY

This outcome is significant since it expands the detectable bacterial proteome via MALDI-ToF-MS.

Enhanced protein identification using graphite-modified MALDI plates for offline LC-MALDI-MS/MS bottom-up proteomics

The use of offline liquid chromatography-matrix assisted laser desorption/ionization (LC-MALDI) tandem mass spectrometry (MS/MS) for bottom-up proteomics offers advantages in terms of cost, ease of use, and the time-decoupled nature of the separation step and the mass analysis. A method was developed to improve the capabilities of LC-MALDI-MS/MS in terms of protein identification in a bottom-up proteomic workflow. Enhanced protein identification is achieved by an increase in the MALDI signal intensity of the precursor peptides brought about by coating the MALDI plate with a thin film of graphite powder. Using the Escherichia coli proteome, it is demonstrated that the graphite-modified MALDI plates used in an offline LC-MALDI-MS/MS bottom-up protocol led to a 50-135% increase in the number of peptide identifications, and a concomitant 21%-105% increase in the number of proteins inferred. We identify factors that lead to improvements in peptide sequence identifications and in the number of unique proteins identified when compared to using an unmodified MALDI plate. These improvements are achieved using a low cost approach that it is easy to implement, requires no hardware/protocol modification, it is compatible with LC and adds no additional analysis time.

Memory effect in isothermal crystallization of syndiotactic polypropylene - role of melt structure and dynamics?

The crystalline-memory effect on the crystallization of syndiotactic polypropylene is investigated by differential scanning calorimetry and solid-state NMR spectroscopy. The influence of several parameters in the thermal (pre-)treatment and the crystallization conditions is studied in detail. In agreement with previous reports, the power law behavior of the overall crystal growth rate is found to be remarkably different for melts with and without memory. This has previously been interpreted in terms of changes in the structure and/or the dynamics of the melt (disentangled state, local order), and a variety of NMR experiments is used to detect such potential changes. All our NMR results are identical for melts with and without memory, therefore excluding any large effect of the "memory" on melt structure or dynamics exceeding the percent level of the whole sample volume, and thus supporting more conventional interpretations in terms of persisting nuclei. Samples that were pre-crystallized at lower temperatures exhibit a larger memory effect, and the potential nuclei fraction is a non-equilibrium structure and is restricted to the 0.1% level if it is crystalline or highly ordered.

Neuronal cell nuclear factor--a nuclear receptor possibly involved in the control of neurogenesis and neuronal differentiation

We have cloned from a cDNA library of neuronal derivatives of retinoic-acid-induced embryonic carcinoma cells a nuclear receptor that may be involved in the control of late neurogenesis and early neuronal differentiation. The receptor which is practically identical in sequence with germ cell nuclear factor, has been designated neuronal cell nuclear factor (NCNF). NCNF is exclusively expressed in the neuronal derivatives of PCC7-Mz1 cells, with the expression beginning within hours of exposure to retinoic acid. In the developing mouse brain, NCNF is expressed in the marginal zones of the neuroepithelium which are known to contain young postmitotic neurons. NCNF binds to the DR0 sequence thereby silencing transcription. Because NCNF does not recognize hormone response elements of other nuclear receptors tested and does not heterodimerize with these, it probably binds exclusively as a homodimer. NCNF may induce neuronal differentiation by repressing the activity of genes that permit cell fates other than the neuronal one.