Repurposing dried blood spot device technology to examine bile acid profiles in human dried fecal spot samples.

Dried blood spot (DBS) analysis has existed for >50 years, but application of this technique to fecal analysis remains limited. To address whether dried fecal spots (DFS) could be used to measure fecal bile acids, we collected feces from five subjects for each of the following cohorts: 1) healthy individuals, 2) individuals with diarrhea, and 3) Clostridioides difficile-infected patients. Homogenized fecal extracts were loaded onto quantitative DBS (qDBS) devices, dried overnight, and shipped to the bioanalytical lab at ambient temperature. For comparison, source fecal extracts were shipped on dry ice and stored frozen. After 4 mo, frozen fecal extracts and ambient DFS samples were processed and subjected to targeted liquid chromatography-tandem mass spectrometry (LC-MS/MS)-based metabolomics with stable isotope-labeled standards. We observed no differences in the bile acid levels measured between the traditional extraction and the qDBS-based DFS methods. This pilot data demonstrates that DFS-based analysis is feasible and warrants further development for fecal compounds and microbiome applications.NEW & NOTEWORTHY Stool analysis in remote settings can be challenging, as the samples must be stored at -80°C and transported on dry ice for downstream processing. Our work indicates that dried fecal spots (DFS) on Capitainer quantitative DBS (qDBS) devices can be stored and shipped at ambient temperature and yields the same bile acid profiles as traditional samples. This approach has broad applications for patient home testing and sample collection in rural communities or resource-limited countries.

Mechanical power in decelerating flow versus square flow ventilation in pediatric ARDS.

BACKGROUND: Mechanical power (MP) is a summary variable quantifying the risk of ventilator-induced lung injury (VILI). The original MP equation was developed using square flow ventilation. However, most children are ventilated using decelerating flow. It is unclear whether MP differs according to mode of flow delivery. We compared MP in children with acute respiratory distress syndrome (ARDS) who received both square and decelerating flow ventilation. METHODS: This was a secondary analysis of a prospectively enrolled cohort of pediatric ARDS. Patients were ventilated on decelerating flow, and then placed in square flow and allowed to stabilize. Ventilator metrics from both modes were collected within 24 hours of ARDS onset. Paired t-tests were used to compare differences in MP between the modes. RESULTS: We enrolled 185 subjects with a median oxygenation index of 9.5 (IQR 7, 13) and median age 8.3 years (IQR 1.8, 14). MP was lower in square flow (mean 0.46 J・min-1·Kg-1, SD 0.25, 95% CI 0.42-0.50) than in decelerating flow modes (mean 0.49 J・min-1·Kg-1, SD 0.28, 95% CI 0.45-0.53) with a mean difference of 0.03 J・min-1·Kg-1 (SD 0.08, 95% CI 0.014-0.038) (p<0.001). This result remained statistically significant when stratified by age < 2 years in square flow compared to decelerating flow and also when stratified by age >/= 2 years in square flow compared to decelerating flow. The elastic contribution in square flow was 70% and the resistive contribution was 30%. CONCLUSIONS: MP was marginally lower in square flow than in decelerating flow, although the clinical significance of this is unclear. Upward of 30% of MP may go towards overcoming resistance, regardless of age. This is nearly three-fold greater resistance compared to what has been reported in adults.

Acute respiratory failure-related excess mortality in pediatric sepsis.

Excess mortality risk imparted by acute respiratory failure in children is unknown. We determined excess mortality risk associated with mechanically ventilated acute respiratory failure in pediatric sepsis. Novel ICD10-based algorithms were derived and validated to identify a surrogate for acute respiratory distress syndrome to calculate excess mortality risk. Algorithm-identified ARDS was identified with specificity of 96.7% (CI 93.0 - 98.9) and sensitivity of 70.5% (CI 44.0 - 89.7). Excess risk of mortality for ARDS was 24.4% (CI 22.9 - 26.2). Development of ARDS requiring mechanical ventilation imparts modest excess risk of mortality in septic children.

Mechanical Power Is Associated With Mortality in Pediatric Acute Respiratory Distress Syndrome.

OBJECTIVES: Mechanical power (MP) transferred from the ventilator to the lungs has been proposed as a summary variable that may impact mortality in children with acute respiratory distress syndrome (ARDS). To date, no study has shown an association between higher MP and mortality in children with ARDS. DESIGN: Secondary analysis of a prospective observational study. SETTING: Single-center, tertiary, academic PICU. PATIENTS: Five hundred forty-six intubated children with ARDS enrolled between January 2013 and December 2019 receiving pressure-controlled ventilation. INTERVENTIONS: None. MEASUREMENTS AND MAIN RESULTS: Higher MP was associated with increased mortality (adjusted hazard ratio [HR] 1.34 per 1 sd increase, 95% CI 1.08-1.65; p = 0.007). When assessing the contribution of individual components of MP, only positive end-expiratory pressure (PEEP) was associated with mortality (HR 1.32; p = 0.007), whereas tidal volume, respiratory rate, and driving pressure (ΔP = [peak inspiratory pressure (PIP)-PEEP]) were not. Finally, we tested whether there remained an association when specific terms were removed from the MP equation by calculating MP from static strain (remove ΔP), MP from dynamic strain (remove PEEP), and mechanical energy (remove respiratory rate). MP from static strain (HR 1.44; p < 0.001), MP from dynamic strain (HR 1.25; p = 0.042), and mechanical energy (HR 1.29; p = 0.009) were all associated with mortality. MP was associated with ventilator-free days only when using MP normalized to predicted body weight, but not when using measured weight. CONCLUSIONS: Higher MP was associated with mortality in pediatric ARDS, and PEEP appears to be the component most consistently driving this association. As higher PEEP is used in sicker patients, the association between MP and mortality may reflect a marker of illness severity rather than MP itself being causal for mortality. However, our results support future trials testing different levels of PEEP in children with ARDS as a potential means to improve outcome.

Reference materials for MS-based untargeted metabolomics and lipidomics: a review by the metabolomics quality assurance and quality control consortium (mQACC).

INTRODUCTION: The metabolomics quality assurance and quality control consortium (mQACC) is enabling the identification, development, prioritization, and promotion of suitable reference materials (RMs) to be used in quality assurance (QA) and quality control (QC) for untargeted metabolomics research. OBJECTIVES: This review aims to highlight current RMs, and methodologies used within untargeted metabolomics and lipidomics communities to ensure standardization of results obtained from data analysis, interpretation and cross-study, and cross-laboratory comparisons. The essence of the aims is also applicable to other 'omics areas that generate high dimensional data. RESULTS: The potential for game-changing biochemical discoveries through mass spectrometry-based (MS) untargeted metabolomics and lipidomics are predicated on the evolution of more confident qualitative (and eventually quantitative) results from research laboratories. RMs are thus critical QC tools to be able to assure standardization, comparability, repeatability and reproducibility for untargeted data analysis, interpretation, to compare data within and across studies and across multiple laboratories. Standard operating procedures (SOPs) that promote, describe and exemplify the use of RMs will also improve QC for the metabolomics and lipidomics communities. CONCLUSIONS: The application of RMs described in this review may significantly improve data quality to support metabolomics and lipidomics research. The continued development and deployment of new RMs, together with interlaboratory studies and educational outreach and training, will further promote sound QA practices in the community.

Hepatomegaly and short stature in a 14-year-old with type 1 diabetes mellitus: case report.

BACKGROUND: Mauriac syndrome is a rare consequence of poorly controlled insulin-dependent diabetes, characterized by hepatomegaly, growth failure, delayed onset of puberty, and cushingoid features. Case reports of patients with Mauriac syndrome are found infrequently in the literature given historic improvements in diabetes management due to readily available insulin therapy. METHODS: We describe a case of a 14-year-old girl who presented with acute onset abdominal pain, distention, and orthopnea. RESULTS: She had a history of poorly controlled insulin-dependent diabetes as well as short stature. Abdominal imaging revealed impressive hepatomegaly. Laboratory testing showed markedly elevated triglycerides and cholesterol. Mauriac syndrome was suspected and diagnosed by liver biopsy, which demonstrated significant glycogenic hepatopathy. CONCLUSIONS: This case provides an illustrative example of Mauriac syndrome in a child who did not experience delayed onset of puberty and continued to have regular menses unlike what has been previously described. Furthermore, this case highlights the important consideration for significant dyslipidemia in patients with Mauriac syndrome and discusses the challenges of controlling insulin-dependent diabetes in the adolescent population.

Absolute Quantification of Apolipoproteins Following Treatment with Omega-3 Carboxylic Acids and Fenofibrate Using a High Precision Stable Isotope-labeled Recombinant Protein Fragments Based SRM Assay.

Stable isotope-labeled standard (SIS) peptides are used as internal standards in targeted proteomics to provide robust protein quantification, which is required in clinical settings. However, SIS peptides are typically added post trypsin digestion and, as the digestion efficiency can vary significantly between peptides within a protein, the accuracy and precision of the assay may be compromised. These drawbacks can be remedied by a new class of internal standards introduced by the Human Protein Atlas project, which are based on SIS recombinant protein fragments called SIS PrESTs. SIS PrESTs are added initially to the sample and SIS peptides are released on trypsin digestion. The SIS PrEST technology is promising for absolute quantification of protein biomarkers but has not previously been evaluated in a clinical setting. An automated and scalable solid phase extraction workflow for desalting and enrichment of plasma digests was established enabling simultaneous preparation of up to 96 samples. Robust high-precision quantification of 13 apolipoproteins was achieved using a novel multiplex SIS PrEST-based LC-SRM/MS Tier 2 assay in non-depleted human plasma. The assay exhibited inter-day coefficients of variation between 1.5% and 14.5% (median = 3.5%) and was subsequently used to investigate the effects of omega-3 carboxylic acids (OM3-CA) and fenofibrate on these 13 apolipoproteins in human plasma samples from a randomized placebo-controlled trial, EFFECT I (NCT02354976). No significant changes were observed in the OM3-CA arm, whereas treatment with fenofibrate significantly increased apoAII and reduced apoB, apoCI, apoE and apoCIV levels. The reduction in apoCIV following fenofibrate treatment is a novel finding. The study demonstrates that SIS PrESTs can facilitate the generation of robust multiplexed biomarker Tier 2 assays for absolute quantification of proteins in clinical studies.

An Examination of the Longer-Term Impact of a Combined Classroom and Parental Intervention on Alcohol-Related Harms and Heavy Episodic Drinking.

Although fewer adolescents are consuming alcohol than was the case in previous decades, those who are consuming alcohol are still exposed to alcohol-related harms. While the evidence for the effectiveness of universal, school-based interventions is limited, a recent cluster randomised controlled trial (The STAMPP Trial) reported a significant effect at 10 months post-intervention of a combined classroom/parental intervention on heavy episodic drinking (HED) in the previous 30 days, but no significant effect on the number of self-reported alcohol-related harms (ARH) experienced in the previous 6 months. This follow-up study sought to examine intervention effects 24 months after delivery of the intervention (+ 57 months from baseline, or + 34 months post-intervention). Participants were 5029 high school students in STAMPP (38% of 12,738 pupils originally randomised into the trial), from 87 schools (82.3% of schools recruited in the original STAMPP trial). Outcomes were assessed using two-level random intercepts models (logistic regression for HED and negative binomial for number of ARH). Results of the present study show that the intervention effect for HED deteriorated over the following 2 years (OR declined from 0.60 to 0.97), and there was still no difference in ARH. This was due to an increase in the prevalence of intervention students' HED rather than a reduction in prevalence in control students. Results are discussed in the context of prevention initiatives.

Interplay Between Sensation Seeking and Parental Rules in the Emergence of Heavy Episodic Drinking.

This study examined the parallel mediational processes between sensation seeking and parental rules on alcohol, in the emergence of heavy episodic drinking (HED) in adolescents. Data were drawn from a U.K. clustered randomized control trial (control arm only, N ≈ 6,300, Mage at baseline = 12.5). Using parallel process latent growth curve analysis, stricter parental rules at baseline were found to be associated with greater declines in sensation seeking over time and a lower risk of HED at follow-up (+33 months). Higher initial levels of sensation seeking predicted a faster relaxation of parental rules and a greater risk of HED. By maintaining strict rules about alcohol, parents may promote a positive reduction in sensation seeking and a lower risk of HED.

Recanting of Previous Reports of Alcohol Consumption within a Large-Scale Clustered Randomised Control Trial.

The aim of this study was to examine the extent of recanting (inconsistencies in reporting of lifetime alcohol use) and its impact on the assessment of primary outcomes within a large-scale alcohol prevention trial. One hundred and five post-primary schools in were randomised to receive either the intervention or education as normal. Participants (N = 12,738) were secondary school students in year 8/S1 (mean age 12.5) at baseline. Self-report questionnaires were administered at baseline (T0) and at T1 (+ 12 months post-baseline), T2 (+ 24 months) and T3 (+ 33 months). The primary outcomes were (i) heavy episodic drinking (consumption of ≥ 6 units in a single episode in the previous 30 days for males and ≥ 4.5 units for females) assessed at T3 and (ii) the number of alcohol-related harms experienced in the last 6 months assessed at T3. Recanting was defined as a negative report of lifetime alcohol consumption that contradicted a prior positive report. Between T1 and T3, 9.9% of students recanted earlier alcohol consumption. Recanting ranged from 4.5 to 5.3% across individual data sweeps. While recanting was significantly associated (negatively) with both primary outcomes, the difference in the rate of recanting across trial arms was small, and adjusting for recanting within the primary outcome models did not impact on the primary outcome effects. Males were observed to recant at a greater rate than females, with a borderline small-sized effect (V = .09). While differential rates of recanting have the potential to undermine the analysis of prevention trial outcomes, recanting is easy to identify and control for within trial primary outcome analyses. Adjusting for recanting should be considered as an additional sensitivity test within prevention trials.Trial Registration: ISRCTN47028486 ( http://www.isrctn.com/ISRCTN47028486 ). The date of trial registration was 23/09/2011, and school recruitment began 01/11/2011.

Multiplexed panel of precisely quantified salivary proteins for biomarker assessment.

An increasingly popular "absolute" quantitative technique involves the SRM or MRM approach with stable isotope-labeled standards (SIS). Using this approach, many proteins in human plasma/serum have been quantified for biomarker assessment and disease stratification. Due to the complexity of plasma and the invasive nature of its collection, alternative biosamples are currently being explored. Here, we present the broadest panel of multiplexed MRM assays with SIS peptides for saliva proteins developed to date. The validated panel consists of 158 candidate human saliva protein biomarkers, inferred from 244 interference-free peptides. The resulting concentrations were reproducibly quantified over a 6 order-of-magnitude concentration range (from 218 µg/mL to 88 pg/mL; average CVs of 12% over analytical triplicates). All concentrations were determined from reverse standard curves, which were generated using a constant concentration of endogenous material with varying concentrations of spiked-in SIS peptides. The large-scale screening of the soluble and membrane-associated proteins contained within the 158-plex assay could present new opportunities for biomarker assessment and clinical diagnostics.

Multiplexed MRM-based assays for the quantitation of proteins in mouse plasma and heart tissue.

The mouse is the most commonly used laboratory animal, with more than 14 million mice being used for research each year in North America alone. The number and diversity of mouse models is increasing rapidly through genetic engineering strategies, but detailed characterization of these models is still challenging because most phenotypic information is derived from time-consuming histological and biochemical analyses. To expand the biochemists' toolkit, we generated a set of targeted proteomic assays for mouse plasma and heart tissue, utilizing bottom-up LC/MRM-MS with isotope-labeled peptides as internal standards. Protein quantitation was performed using reverse standard curves, with LC-MS platform and curve performance evaluated by quality control standards. The assays comprising the final panel (101 peptides for 81 proteins in plasma; 227 peptides for 159 proteins in heart tissue) have been rigorously developed under a fit-for-purpose approach and utilize stable-isotope labeled peptides for every analyte to provide high-quality, precise relative quantitation. In addition, the peptides have been tested to be interference-free and the assay is highly multiplexed, with reproducibly determined protein concentrations spanning >4 orders of magnitude. The developed assays have been used in a small pilot study to demonstrate their application to molecular phenotyping or biomarker discovery/verification studies.

Multiplexed MRM-Based Protein Quantitation Using Two Different Stable Isotope-Labeled Peptide Isotopologues for Calibration.

When quantifying endogenous plasma proteins for fundamental and biomedical research - as well as for clinical applications - precise, reproducible, and robust assays are required. Targeted detection of peptides in a bottom-up strategy is the most common and precise mass spectrometry-based quantitation approach when combined with the use of stable isotope-labeled peptides. However, when measuring protein in plasma, the unknown endogenous levels prevent the implementation of the best calibration strategies, since no blank matrix is available. Consequently, several alternative calibration strategies are employed by different laboratories. In this study, these methods were compared to a new approach using two different stable isotope-labeled standard (SIS) peptide isotopologues for each endogenous peptide to be quantified, enabling an external calibration curve as well as the quality control samples to be prepared in pooled human plasma without interference from endogenous peptides. This strategy improves the analytical performance of the assay and enables the accuracy of the assay to be monitored, which can also facilitate method development and validation.

Clinical Use of Expanded Prostate Cancer Index Composite for Clinical Practice to Assess Patient Reported Prostate Cancer Quality of Life Following Robot-Assisted Radical Prostatectomy.

PURPOSE: EPIC-CP (Expanded Prostate Cancer Index Composite for Clinical Practice) is a short questionnaire that comprehensively measures patient reported health related quality of life at the point of care. We evaluated the feasibility of using EPIC-CP in the routine clinical care of patients with prostate cancer without research infrastructure. We compared longitudinal patient and practitioner reported prostate cancer outcomes. MATERIALS AND METHODS: We reviewed health related quality of life outcomes in 482 patients who underwent radical prostatectomy at our institution from 2010 to 2014. EPIC-CP was administered and interpreted in routine clinical practice without research personnel. We compared practitioner documented rates of incontinence pad use and functional erections to patient reported rates using EPIC-CP. RESULTS: A total of 708 EPIC-CP questionnaires were completed. Mean urinary incontinence domain scores were significantly higher (worse) than baseline (mean ± SD 0.6 ± 0.2) 3 and 6 months after treatment (mean 3.1 ± 2.3 and 2.2 ± 2.1, respectively, each p <0.05) but they returned to baseline at 12 months (mean 1.6 ± 1.7, p >0.05). Mean sexual domain scores were significantly worse than baseline (mean 2.4 ± 2.8) at all posttreatment time points (each p <0.05). Practitioners significantly overestimated incontinence pad-free rates at 3 months (48% vs 39%) and functional erection rates at 3 months (18% vs 12%), 6 months (38% vs 23%) and 12 months (45% vs 23%, each p <0.05). CONCLUSIONS: EPIC-CP is feasible to use in the routine clinical care of patients with prostate cancer without requiring a research infrastructure. Using EPIC-CP in clinical practice may help practitioners objectively assess and appropriately manage posttreatment side effects in patients with prostate cancer.

Multiple Reaction Monitoring Enables Precise Quantification of 97 Proteins in Dried Blood Spots.

The dried blood spot (DBS) methodology provides a minimally invasive approach to sample collection and enables room-temperature storage for most analytes. DBS samples have successfully been analyzed by liquid chromatography multiple reaction monitoring mass spectrometry (LC/MRM-MS) to quantify a large range of small molecule biomarkers and drugs; however, this strategy has only recently been explored for MS-based proteomics applications. Here we report the development of a highly multiplexed MRM assay to quantify endogenous proteins in human DBS samples. This assay uses matching stable isotope-labeled standard peptides for precise, relative quantification, and standard curves to characterize the analytical performance. A total of 169 peptides, corresponding to 97 proteins, were quantified in the final assay with an average linear dynamic range of 207-fold and an average R(2) value of 0.987. The total range of this assay spanned almost 5 orders of magnitude from serum albumin (P02768) at 18.0 mg/ml down to cholinesterase (P06276) at 190 ng/ml. The average intra-assay and inter-assay precision for 6 biological samples ranged from 6.1-7.5% CV and 9.5-11.0% CV, respectively. The majority of peptide targets were stable after 154 days at storage temperatures from -20 °C to 37 °C. Furthermore, protein concentration ratios between matching DBS and whole blood samples were largely constant (<20% CV) across six biological samples. This assay represents the highest multiplexing yet achieved for targeted protein quantification in DBS samples and is suitable for biomedical research applications.

Clinical translation of MS-based, quantitative plasma proteomics: status, challenges, requirements, and potential.

INTRODUCTION: Aided by the advent of advanced mass spectrometry (MS)-based technologies and methodologies, quantitative proteomics has emerged as a viable technique to capture meaningful data for candidate biomarker evaluation. To aid clinical translation, these methods generally utilize a bottom-up strategy with isotopically labeled standards and a targeted form of MS measurement. AREAS COVERED: This article reviews the status, challenges, requirements, and potential of translating current, MS-based methods to the clinical laboratory. The described methods are discussed and contrasted within a fit-for-purpose approach, while different resources for quality control, quantitative analysis, and data interpretation are additionally provided. Expert commentary: Although great strides have been made over the past five years in developing reliable quantitative assays for plasma protein biomarkers, it is crucial for investigators to have an understanding of the clinical validation process, a major roadblock in translational research. Continued progress in method design and validation of protein assays is necessary to ultimately achieve widespread adoption and regulatory approval.

Precise quantitation of 136 urinary proteins by LC/MRM-MS using stable isotope labeled peptides as internal standards for biomarker discovery and/or verification studies.

Spurred on by the growing demand for panels of validated disease biomarkers, increasing efforts have focused on advancing qualitative and quantitative tools for more highly multiplexed and sensitive analyses of a multitude of analytes in various human biofluids. In quantitative proteomics, evolving strategies involve the use of the targeted multiple reaction monitoring (MRM) mode of mass spectrometry (MS) with stable isotope-labeled standards (SIS) used for internal normalization. Using that preferred approach with non-invasive urine samples, we have systematically advanced and rigorously assessed the methodology toward the precise quantitation of the largest, multiplexed panel of candidate protein biomarkers in human urine to date. The concentrations of the 136 proteins span >5 orders of magnitude (from 8.6 µg/mL to 25 pg/mL), with average CVs of 8.6% over process triplicate. Detailed here is our quantitative method, the analysis strategy, a feasibility application to prostate cancer samples, and a discussion of the utility of this method in translational studies.

Protocol for Standardizing High-to-Moderate Abundance Protein Biomarker Assessments Through an MRM-with-Standard-Peptides Quantitative Approach.

Quantitative mass spectrometry (MS)-based approaches are emerging as a core technology for addressing health-related queries in systems biology and in the biomedical and clinical fields. In several 'omics disciplines (proteomics included), an approach centered on selected or multiple reaction monitoring (SRM or MRM)-MS with stable isotope-labeled standards (SIS), at the protein or peptide level, has emerged as the most precise technique for quantifying and screening putative analytes in biological samples. To enable the widespread use of MRM-based protein quantitation for disease biomarker assessment studies and its ultimate acceptance for clinical analysis, the technique must be standardized to facilitate precise and accurate protein quantitation. To that end, we have developed a number of kits for assessing method/platform performance, as well as for screening proposed candidate protein biomarkers in various human biofluids. Collectively, these kits utilize a bottom-up LC-MS methodology with SIS peptides as internal standards and quantify proteins using regression analysis of standard curves. This chapter details the methodology used to quantify 192 plasma proteins of high-to-moderate abundance (covers a 6 order of magnitude range from 31 mg/mL for albumin to 18 ng/mL for peroxidredoxin-2), and a 21-protein subset thereof. We also describe the application of this method to patient samples for biomarker discovery and verification studies. Additionally, we introduce our recently developed Qualis-SIS software, which is used to expedite the analysis and assessment of protein quantitation data in control and patient samples.

Qualis-SIS: automated standard curve generation and quality assessment for multiplexed targeted quantitative proteomic experiments with labeled standards.

Multiplexed targeted quantitative proteomics typically utilizes multiple reaction monitoring and allows the optimized quantification of a large number of proteins. One challenge, however, is the large amount of data that needs to be reviewed, analyzed, and interpreted. Different vendors provide software for their instruments, which determine the recorded responses of the heavy and endogenous peptides and perform the response-curve integration. Bringing multiplexed data together and generating standard curves is often an off-line step accomplished, for example, with spreadsheet software. This can be laborious, as it requires determining the concentration levels that meet the required accuracy and precision criteria in an iterative process. We present here a computer program, Qualis-SIS, that generates standard curves from multiplexed MRM experiments and determines analyte concentrations in biological samples. Multiple level-removal algorithms and acceptance criteria for concentration levels are implemented. When used to apply the standard curve to new samples, the software flags each measurement according to its quality. From the user's perspective, the data processing is instantaneous due to the reactivity paradigm used, and the user can download the results of the stepwise calculations for further processing, if necessary. This allows for more consistent data analysis and can dramatically accelerate the downstream data analysis.

Advances in multiplexed MRM-based protein biomarker quantitation toward clinical utility.

Accurate and rapid protein quantitation is essential for screening biomarkers for disease stratification and monitoring, and to validate the hundreds of putative markers in human biofluids, including blood plasma. An analytical method that utilizes stable isotope-labeled standard (SIS) peptides and selected/multiple reaction monitoring-mass spectrometry (SRM/MRM-MS) has emerged as a promising technique for determining protein concentrations. This targeted approach has analytical merit, but its true potential (in terms of sensitivity and multiplexing) has yet to be realized. Described herein is a method that extends the multiplexing ability of the MRM method to enable the quantitation 142 high-to-moderate abundance proteins (from 31mg/mL to 44ng/mL) in undepleted and non-enriched human plasma in a single run. The proteins have been reported to be associated to a wide variety of non-communicable diseases (NCDs), from cardiovascular disease (CVD) to diabetes. The concentrations of these proteins in human plasma are inferred from interference-free peptides functioning as molecular surrogates (2 peptides per protein, on average). A revised data analysis strategy, involving the linear regression equation of normal control plasma, has been instituted to enable the facile application to patient samples, as demonstrated in separate nutrigenomics and CVD studies. The exceptional robustness of the LC/MS platform and the quantitative method, as well as its high throughput, makes the assay suitable for application to patient samples for the verification of a condensed or complete protein panel. This article is part of a Special Issue entitled: Biomarkers: A Proteomic Challenge.