Mass Spectrometry-based Quantification Method Research Articles

A candidate reference measurement procedure for the quantification of α-synuclein in cerebrospinal fluid using an SI traceable primary calibrator and multiple reaction monitoring.

α-synuclein aggregation is an important hallmark of neurodegenerative diseases such as Parkinson's disease (PD) and Lewy body dementia. α-synuclein has been increasingly used as a diagnostic biomarker in PD and other synucleinopathies. Current clinical assays rely on antibody-based immunoassays to detect α-synuclein, which possess high sensitivity, afford high throughput and require small sample volumes. The utility of these assays, however, may be compounded by the specificity, selectivity and batch-to-batch heterogeneity of the antibody used, which can lead to deviations in the total amount of the protein measured when comparing results among different laboratories. Similarly, current mass spectrometry-based quantification methods for α-synuclein lack well-defined, value assigned calibrators to ensure comparability of measurements. Therefore, there is still an unmet need for the standardisation of clinical measurements for α-synuclein that can be achieved by the development of reference measurement procedures (RMPs) utilising calibrators traceable to the SI (International System of Units). Here, we report a candidate RMP for α-synuclein, using an SI traceable primary calibrator and an isotope dilution mass spectrometry (IDMS) approach to address this need. The gravimetrically prepared primary calibrator was traceably quantified utilising a combination of amino acid analysis (AAA) and quantitative nuclear magnetic resonance (qNMR) for value assignment. An optimised targeted sample clean-up procedure involving a non-denaturing Lys-C digestion and solid-phase extraction strategy was devised, followed by the development of a targeted multiple reaction monitoring (MRM) method for the quantification of α-synuclein in cerebrospinal fluid (CSF). This candidate RMP was then deployed for the sensitive detection and accurate quantification of multiple proteotypic α-synuclein peptides in patient derived CSF samples. The LC-MS based results were subsequently compared to immunoassay data to assess the overall performance of our approach. The development and adoption of this candidate RMP, along with the availability of the SI traceable primary calibrator will allow for reliable quantifications of α-synuclein in CSF by an LC-MS based assay. The RMP will potentially contribute towards the standardisation of this important biomarker and may lead to future interlaboratory comparisons.

Development of a Mass Spectrometry-Based Method for Quantification of Total Cashew Protein in Roasting Oil.

Food allergen cross-contact during food preparation and production is one of the causes of unintentional allergen presence in packaged foods. However, little is known about allergen cross-contact in shared frying or roasting oil, which prevents the establishment of effective allergen controls and may put allergic individuals at risk. To better understand the quantity of allergen transferred to frying oil and subsequent products, an analytical method is needed for quantifying protein in oil that has been exposed to frying/roasting conditions. The goal of this study was to develop a parallel reaction monitoring LC-MS/MS method to quantify the amount of cashew protein in shared roasting oil. The sample preparation method was evaluated to improve protein extractability and peptide performance. Four quantitative peptides representing cashew 2S and 11S proteins were selected as targets based on their sensitivity, heat stability, and specificity. A calibration strategy was developed to quantify the amount of total cashew protein in oil. Method performance was evaluated using a heated cashew-in-oil model system. The method showed high recovery in oil samples spiked with 100 or 10 parts per million (ppm) total cashew protein heated at 138 or 166°C for 2-30 min. Samples (100 ppm total cashew protein) heated for 30 min had more than 90% recovery when treated at 138°C and more than 50% when heated at 166°C. The method is fit-for-purpose for the analysis of cashew allergen cross-contact in oil. A novel MS-based method was developed that can accurately quantify the amount of cashew protein present in heated oil.

Applied Clinical Tandem Mass Spectrometry-Based Quantification Methods for Lipid-Derived Biomarkers, Steroids and Cannabinoids: Fit-for-Purpose Validation Methods.

The emergence of metabolomics and quantification approaches is revealing new biomarkers applied to drug discovery. In this context, tandem mass spectrometry is the method of choice, requiring a specific validation process for preclinical and clinical applications. Research on the two classes of lipid mediators, steroids and cannabinoids, has revealed a potential interaction in cannabis addiction and metabolism-related disorders. Here we present the development of GC-MS/MS and LC-MS/MS methods for routine quantification of targeted steroids and cannabinoids, respectively. The methods were developed using an isotopic approach, including validation for linearity, selectivity, LLOQ determination, matrix effect, carryover, between- and within-run accuracy and precision, and stability tests to measure 11 steroids and seven cannabinoids in human plasma. These methods were satisfactory for most validity conditions, although not all met the acceptance criteria for all analytes. A comparison of calibration curves in biological and surrogate matrices and in methanol showed that the latter condition was more applicable for our quantification of endogenous compounds. In conclusion, the validation of our methods met the criteria for GLP-qualified rather than GLP-validated methods, which can be used for routine analytical studies for dedicated preclinical and clinical purposes, by combining appropriate system suitability testing, including quality controls in the biological matrix.

Targeted Method for Quantifying Air-Borne Pesticide Residues from Conventional Seed Coat Treatments to Better Assess Exposure Risk During Maize Planting.

Agricultural seed-coat treatments are prone to drift as seed coatings may scuff off and become incorporated into field particles during planting. Vacuum planters release exhaust and kick up field dust, laden with systemic pesticides that blow across the landscape, is taken up, and later expressed in the nectar and pollen of surrounding plants. Offsite movements and nontarget exposure to systemic pesticides need attention and determining how and at what exposure levels pollinators are exposed is of critical importance. Unfortunately, this requires extensive and costly instrumental analyses. Here, we describe dust sampling and a modified, rapid method based on liquid chromatography in tandem with mass spectrometry-based method for quantification of a broad array of agrochemicals in captured dust particles. This method increases ability to detect potential exposure to multiple agrochemicals and allows researchers to better address critical knowledge gaps in the environmental fate, off-target movement, and persistence of conventional seed treatments.

Quantification of Parathyroid Hormone and its Fragments in Serum by Liquid Chromatography-High-Resolution Mass Spectrometry.

Parathyroid hormone (PTH), an 84-amino acid peptide hormone, is a major regulator of calcium homeostasis. Quantification of PTH in serum is used clinically to investigate calcium imbalances and for monitoring osteodystrophy in patients with renal failure. In addition to intact PTH, several PTH fragments are found in circulation. Recent studies have shown that accurate quantification of PTH fragments may provide valuable clinical information in certain scenarios. In this chapter, a high-resolution mass spectrometry-based method for quantification of PTH (1-84) and its fragments is described. This method involves immunoaffinity capture of intact PTH and PTH-fragments followed by liquid chromatography-high-resolution mass spectrometry (LC-HRMS).

Development of a novel nanoflow liquid chromatography-parallel reaction monitoring mass spectrometry-based method for quantification of angiotensin peptides in HUVEC cultures.

BackgroundThis study aimed to develop an analytical method using liquid chromatography tandem mass spectrometry (LC-MS/MS) for the determination of angiotensin (Ang) I, Ang (1-9), Ang II, Ang (1-7), Ang (1-5), Ang III, Ang IV in human umbilical vein endothelial cell (HUVEC) culture supernatant.MethodsHUVEC culture supernatant was added with gradient concentrations (0.05–1,000 ng/ml) of standard solutions of the Ang peptides. These samples underwent C18 solid-phase extraction and separation using a preconcentration nano-liquid chromatography mass spectrometry system. The target peptides were detected by a Q Exactive quadrupole orbitrap high-resolution mass spectrometer in the parallel reaction monitoring mode. Ang converting enzyme (ACE) in HUVECs was silenced to examine Ang I metabolism.ResultsThe limit of detection was 0.1 pg for Ang II and Ang III, and 0.5 pg for Ang (1-9), Ang (1-7), and Ang (1-5). The linear detection range was 0.1–2,000 pg (0.05–1,000 ng/ml) for Ang II and Ang III, and 0.5–2,000 pg (0.25–1,000 ng/ml) for Ang (1-9) and Ang (1-5). Intra-day and inter-day precisions (relative standard deviation) were <10%. Ang II, Ang III, Ang IV, and Ang (1-5) were positively correlated with ACE expression by HUVECs, while Ang I, Ang (1-7), and Ang (1-9) were negatively correlated.ConclusionThe nanoflow liquid chromatography-parallel reaction monitoring mass spectrometry-based methodology established in this study can evaluate the Ang peptides simultaneously in HUVEC culture supernatant.

Development of a Mass Spectrometry-Based Method for Quantification of Ustekinumab in Serum Specimens.

Ustekinumab (UST) is a human monoclonal antibody used to treat moderate-to-severe Crohn disease by blocking the interleukin-12/23 pathway. Although an optimized therapeutic concentration of UST is associated with clinical response and improved prognosis, the availability of clinical laboratory methods for UST monitoring is limited. Furthermore, the commercially available methods are immunoassays that are prone to interference of antidrug antibodies. This study aimed to develop a liquid chromatography-tandem mass spectrometry method for quantification of UST in human serum specimens. A tryptic peptide that is specific to the heavy chain variable region of UST was selected. Quantification of UST was performed by selective reaction monitoring on a quadrupole TQ-XS with an internal standard. After digestion with trypsin, peptides were separated by reverse-phase C18 liquid chromatography; peptides were detected by MS/MS, and analyte to internal standard peak area ratios were used for the quantification. Finally, serum samples from patients treated with UST were collected at trough levels (n = 66). The assay showed a broad dynamic range with linearity between 0.4 and 20 mg/L (R = 0.995). The lower limit of quantification was found to be 0.4 mg/L. The reproducibility was tested with 3 different UST concentrations (2, 8, and 16 mg/L). The coefficients of intra-assay and interassay variations were 2.2%-4.0% and 2.7%-5.3%, respectively. UST serum concentrations of 2-16 mg/L were stable for up to 14 days when specimens were left at room temperature (20°C). The newly developed LC/MS-based method was shown to be feasible for UST quantification. This analytical approach may lead to individualized dosing and improved patient care.

Development and validation of an assay for a novel ghrelin receptor inverse agonist PF-5190457 and its major hydroxy metabolite (PF-6870961) by LC-MS/MS in human plasma

PF-5190457 is a selective and potent ghrelin receptor inverse agonist presently undergoing clinical trials to treat alcohol use disorder (AUD). We describe the development and validation of a selective and sensitive liquid chromatography-tandem mass spectrometry-based method for quantification of PF-5190457 and its recently discovered hydroxy metabolite PF-6870961 in human plasma. Analytes were extracted after simple protein precipitation using methanol (2.5 ng mL−1 tacrine as an internal standard). A gradient liquid chromatography method was used to separate the analytes on an Acquity UPLC BEH C18 analytical column. The separation was achieved at a flow rate of 0.25 mL min−1 and the total chromatographic runtime was 11.30 min. Positive electrospray ionization and multiple reaction monitoring mode were used for the quantification of all the analytes. The calibration curves from six validation runs were linear with a correlation coefficient of ≥0.996 for the concentration range of 1–1000 ng mL−1 and 2–250 ng mL−1 for PF-5190457 and PF-6870961, respectively. The retention time for PF-5190457, PF-6870961 and tacrine were 4.4, 3.8, and 4.6 min, respectively. The lower limit of quantification for PF-5190457 and PF-6870961 was 1 and 2 ng mL−1, respectively. The inter-assay precision and accuracy results obtained were within the Food and Drug Administration recommended ±15% limit of nominal values. All the analytes were found to be stable under varied stability conditions. The recovery of PF-5190457 and PF-6870961 ranged from 95 to 103%. Further, the application of the method was demonstrated by measuring the concentration of PF-5190457 and its hydroxy metabolite in patient plasma samples from 100 mg dose.

A New Quantification Method Using Electrochemical Mass Spectrometry.

Mass spectrometry-based quantification method has advanced rapidly. In general, the methods for accurate quantification rely on the use of authentic target compounds or isotope-labeled compounds as standards, which might be not available or difficult to synthesize. To tackle this grand challenge, this paper presents a novel approach, based on electrochemistry (EC) combined with mass spectrometry (MS). In this approach, a target compound is allowed to undergo electrochemical oxidation and then subject to MS analysis. The oxidation current recorded from electrochemistry (EC) measurement provides information about the amount of the oxidized analyte, based on the Faraday's Law. On the other hand, the oxidation reaction yield can be determined from the analyte MS signal changes upon electrolysis. Therefore, the total amount of analyte can be determined. In combination with liquid chromatography (LC), the method can be applicable to mixture analysis. The striking strength of such a method for quantitation is that neither standard compound nor calibration curve is required. Various analyte molecules such as dopamine, norepinephrine, and rutin as well as peptide glutathione in low quantity were successfully quantified using our method with the quantification error ranging from - 2.6 to +4.6%. Analyte in a complicated matrix (e.g., uric acid in urine) was also accurately measured. Graphical Abstract.

Methods to measure ubiquitin chain length and linkage.

To understand the biological roles of different ubiquitin chains, it is important to determine the types of ubiquitin linkages, the lengths of the polymers, and the combinations of ubiquitin chains attached to substrates. In this chapter, we describe a mass spectrometry-based quantification method of ubiquitin chains, named Ub-AQUA/PRM (ubiquitin-absolute quantification/parallel reaction monitoring), for direct and highly sensitive measurement of the stoichiometry of all eight ubiquitin-ubiquitin linkage types simultaneously. We also show a method to quantify the K48/K63 branched ubiquitin chain, a recently identified ubiquitin signal with a complex topology. In addition, we describe a method to measure ubiquitin chain length of ubiquitylated substrates using a chain protector and limited digestion of ubiquitin chains, named Ub-ProT (ubiquitin chain protection from trypsinization). These strategies will contribute to our knowledge of polymeric ubiquitin signals and permit investigation of new mechanisms concerning the ubiquitin code.

Optimization of sample preparation for transporter protein quantification in tissues by LC–MS/MS

BackgroundReproducible quantification of drug transporter protein expression in tissues is important for predicting transporter mediated drug disposition. Many mass-spectrometry based transporter protein quantification methods result in high variability of the estimated transporter quantities. Therefore, we aimed to evaluate and optimize mass spectrometry-based quantification method for drug transporter proteins in tissues. Materials and methodsPlasma membrane (PM) proteins from mouse tissues were isolated by applying three extraction protocols: commercial plasma membrane extraction kit, tissue homogenization by Potter-Elvehjem homogenizer in combination with sucrose-cushion ultracentrifugation, and PM enrichment with Tween 40. Moreover, five different protein digestion protocols were applied on the same PM fraction. PM isolation and digestion protocols were evaluated by measuring the amount of transporter proteins by liquid chromatography-tandem mass spectrometry in selected reaction monitoring mode. ResultsMouse liver homogenization by Potter-Elvehjem homogenizer in combination with sucrose-cushion ultracentrifugation and PM enrichment with Tween 40 resulted in two times higher transporter protein quantity (Breast cancer resistance protein (Bcrp) 18.0 fmol/μg protein) in comparison with the PM samples isolated by extraction kit (Bcrp 9.8 fmol/μg protein). The evaluation of protein digestion protocols revealed that the most optimal protocol for PM protein digestion is with Lys-C and trypsin, in combination with trypsin enhancer and heat denaturation. Overall, quantities of Bcrp and Na+/K + ATPase proteins evaluated in mouse liver and kidney cortex by using our optimized PM isolation method, as well as, established digestion protocol were two to three times higher than previously reported and coefficient of variation (CV) for technical replicates was below 10%. ConclusionWe have established an improved transporter protein quantification methodology by optimizing PM isolation and protein digestion procedures. The optimized procedure resulted in a higher transporter protein yield and improved precision.

Quantitative Proteomic Approach for MicroRNA Target Prediction Based on 18O/16O Labeling.

MOTIVATIONAmong many large-scale proteomic quantification methods, 18O/16O labeling requires neither specific amino acid in peptides nor label incorporation through several cell cycles, as in metabolic labeling; it does not cause significant elution time shifts between heavy- and light-labeled peptides, and its dynamic range of quantification is larger than that of tandem mass spectrometry-based quantification methods. These properties offer 18O/16O labeling the maximum flexibility in application. However, 18O/16O labeling introduces large quantification variations due to varying labeling efficiency. There lacks a processing pipeline that warrants the reliable identification of differentially expressed proteins (DEPs). This motivates us to develop a quantitative proteomic approach based on 18O/16O labeling and apply it on Kaposi sarcoma-associated herpesvirus (KSHV) microRNA (miR) target prediction. KSHV is a human pathogenic γ-herpesvirus strongly associated with the development of B-cell proliferative disorders, including primary effusion lymphoma. Recent studies suggest that miRs have evolved a highly complex network of interactions with the cellular and viral transcriptomes, and relatively few KSHV miR targets have been characterized at the functional level. While the new miR target prediction method, photoactivatable ribonucleoside-enhanced cross-linking and immunoprecipitation (PAR-CLIP), allows the identification of thousands of miR targets, the link between miRs and their targets still cannot be determined. We propose to apply the developed proteomic approach to establish such links.METHODWe integrate several 18O/16O data processing algorithms that we published recently and identify the messenger RNAs of downregulated proteins as potential targets in KSHV miR-transfected human embryonic kidney 293T cells. Various statistical tests are employed for picking DEPs, and we select the best test by examining the enrichment of PAR-CLIP-reported targets with seed match to the miRs of interest among top ranked DEPs returned by statistical tests. Subsequently, the list of DEPs picked by the selected statistical test is filtered with the criteria that they must have downregulated gene expressions, must have reported as targets by an miR target prediction algorithm SVMcrio, and must have reported as targets by PAR-CLIP.RESULTWe test the developed approach in the problem of finding targets of KSHV miR-K1. The RNAs of three DEPs are identified as miR-K1 targets, among which RAB23 and HNRNPU are novel. Results from both Western blotting and Luciferase reporter assays confirm the novel targets. These results show that the developed quantitative approach based on 18O/16O labeling can be combined with genomic, PAR-CLIP, and target prediction algorithms for the confident identification of KSHV miR targets. The developed approach could also be applied in other applications.

AB0161 Identification and validation of a protein combination including s100a9 able to predict the response to the mtx/etanercept association in rheumatoid arthritis patients

BackgroundThe number of biologic agents in Rheumatoid Arthritis (RA) is continuously increasing. However, clinicians observe that around 30 to 40% of treated patients fail to respond to TNFα blocking agents....

Rapid analysis of avenacosides in grain and husks of oats by UPLC–TQ–MS

Avenacosides A (AA) and B (AB) as well as 26-desglucoavenacoside A (26dAA) were quantified in oats using rapid and sensitive method utilising UPLC–TQ–MS. In the grain, AA and AB were revealed as the primary saponins, whereas in the husks, dAA was predominant. Inconsistent with the published data, observed concentrations of AA and AB in the grain were very similar. Presumably, this is due to higher sensitivity and better selectivity of the mass spectrometry-based quantification method, thus allowing for more precise measurements. Elevated level of an active fungicidal form of saponin, dAA in the husks possibly indicates they are more prone to fungal attacks.

Quantification of lactosylation of whey proteins in stored milk powder using multiple reaction monitoring

Lactosylation in stored milk powder was quantified by multiple reaction monitoring (MRM), a mass spectrometry-based quantification method. The MRM method was developed from a knowledge of peptide fragmentation. The neutral losses of 162Da (cleavage of galactose) and 216Da (the formation of furylium ion) which were representative of lactosylated peptides were specifically selected as MRM transitions. Quantification of lactosylated protein was based on the peak areas of these fragmentation ions. The MRM results showed an increase in peak areas of the two transition fragments from tryptic digests of whey proteins in stored milk protein concentrate powder. A good correlation between the MRM and furosine results indicated that MRM based on tryptic digests of whole products was a feasible method for quantification of modified milk proteins.

Membrane Protein Quantification by Peptide-Based Mass Spectrometry Approaches: Studies on the Organic Anion-Transporting Polypeptide Family

The reliable quantification of drug transport proteins is a key element that is necessary to establish relative scaling factors for human pharmacokinetic predictions and to account for pharmacokinetic variations across populations. Herein, we report a detailed evaluation of targeted mass spectrometry-based quantification methods from the perspective of sample preparation for three major organic anion-transporting polypeptide (OATP) membrane proteins. We also demonstrate the first implementation of stable isotope labeling by amino acids in cell culture (SILAC) into the OATP quantification scheme, which hinges on label incorporation at the protein level to allow for a substantially accelerated sample preparation process with precise results. These methods will enable comparable quantifications to provide individual scaling factors as well as address potential inter-individual variability in OATP proteins that are central to transporter-mediated hepatic drug clearance. The evaluation procedures can also serve as a model for other proteolytically resistant transporters that have not been adequately detected by higher-throughput quantifications. In addition, results derived from various sample preparation conditions explicitly illustrate how the conditions have a differential impact on the quantification of different proteins. Consequently, the ratio between different proteins can be an artifact of the conditions rather than a reflection of the endogenous ratio for typical peptide-based quantifications where a stoichiometrical relationship between the proteolytic peptide and the protein is not established. To the extent that ratios determined under different sets of conditions can underlie different conclusions, our results highlight important limitations that have been underappreciated in recent drug transporter quantifications that extend peptide-based mass spectrometry tools beyond relative quantifications in order to directly compare the abundance of multiple drug transporters.

The dynamic protein partnership of RNA polymerase inBacillus subtilis

In prokaryotes, transcription results from the activity of a 400 kDa RNA polymerase (RNAP) protein complex composed of at least five subunits (2α, β, β', ω). To ensure adequate responses to changing environmental cues, RNAP activity is tightly controlled by means of interacting regulatory proteins. Here, we report the affinity-purification of the Bacillus subtilis RNAP complexes from cells in different growth states and stress conditions, and the quantitative assessment by mass spectrometry of the dynamic changes in the composition of the RNAP complex. The stoichiometry of RNA polymerase was determined by a comparison of two mass spectrometry-based quantification methods: a label-based and a label-free method. The validated label-free method was then used to quantify the proteins associated with RNAP. The levels of sigma factors bound to RNAP varied during growth and exposure to stress. Elongation factors, helicases such as HelD and PcrA, and novel unknown proteins were also associated with RNAP complexes. The content in 6S RNAs of purified RNAP complexes increased at the onset of the stationary phase. These quantitative variations in the protein and RNA composition of the RNAP complexes well correlate with the known physiology of B. subtilis cells under different conditions.

Mass Spectrometric Analysis of Multiple Pertussis Toxins and Toxoids

Bordetella pertussis (Bp) is the causative agent of pertussis, a vaccine preventable disease occurring primarily in children. In recent years, there has been increased reporting of pertussis. Current pertussis vaccines are acellular and consist of Bp proteins including the major virulence factor pertussis toxin (Ptx), a 5-subunit exotoxin. Variation in Ptx subunit amino acid (AA) sequence could possibly affect the immune response. A blind comparative mass spectrometric (MS) analysis of commercially available Ptx as well as the chemically modified toxoid (Ptxd) from licensed vaccines was performed to assess peptide sequence and AA coverage variability as well as relative amounts of Ptx subunits. Qualitatively, there are similarities among the various sources based on AA percent coverages and MS/MS fragmentation profiles. Additionally, based on a label-free mass spectrometry-based quantification method there is differential relative abundance of the subunits among the sources.

Dosage et pistage de peptides Troyens dans les cellules

Trojan peptides or cell-penetrating peptides (CPP) are natural or designed peptides identified as cellular membrane-crossing molecules, in particular through their potency to vehiculate various kinds of compounds to the cytoplasm and nucleus of living cells. The indirect methods used so far to detect these peptides in cells led to controversial hypotheses on the mechanism of their cell entry. Therefore, we have developed a MALDI-TOF mass spectrometry-based quantification method to track these peptides inside cells. This new method is presented in this review.