scholarly journals A rigorous evaluation of optimal peptide targets for MS-based clinical diagnostics of Coronavirus Disease 2019 (COVID-19)

2021 ◽  
Vol 18 (1) ◽  
Author(s):  
Andrew T. Rajczewski ◽  
Subina Mehta ◽  
Dinh Duy An Nguyen ◽  
Björn Grüning ◽  
James E. Johnson ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Direct Detection ◽  
Clinical Diagnostics ◽  
Clinical Proteomics ◽  
Clinical Samples ◽  
P Value ◽  
Upper Respiratory Tract ◽  
Proteomics Data ◽  
High Throughput Analysis

Abstract Background The Coronavirus Disease 2019 (COVID-19) global pandemic has had a profound, lasting impact on the world's population. A key aspect to providing care for those with COVID-19 and checking its further spread is early and accurate diagnosis of infection, which has been generally done via methods for amplifying and detecting viral RNA molecules. Detection and quantitation of peptides using targeted mass spectrometry-based strategies has been proposed as an alternative diagnostic tool due to direct detection of molecular indicators from non-invasively collected samples as well as the potential for high-throughput analysis in a clinical setting; many studies have revealed the presence of viral peptides within easily accessed patient samples. However, evidence suggests that some viral peptides could serve as better indicators of COVID-19 infection status than others, due to potential misidentification of peptides derived from human host proteins, poor spectral quality, high limits of detection etc. Methods In this study we have compiled a list of 636 peptides identified from Sudden Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) samples, including from in vitro and clinical sources. These datasets were rigorously analyzed using automated, Galaxy-based workflows containing tools such as PepQuery, BLAST-P, and the Multi-omic Visualization Platform as well as the open-source tools MetaTryp and Proteomics Data Viewer (PDV). Results Using PepQuery for confirming peptide spectrum matches, we were able to narrow down the 639-peptide possibilities to 87 peptides that were most robustly detected and specific to the SARS-CoV-2 virus. The specificity of these sequences to coronavirus taxa was confirmed using Unipept and BLAST-P. Through stringent p-value cutoff combined with manual verification of peptide spectrum match quality, 4 peptides derived from the nucleocapsid phosphoprotein and membrane protein were found to be most robustly detected across all cell culture and clinical samples, including those collected non-invasively. Conclusion We propose that these peptides would be of the most value for clinical proteomics applications seeking to detect COVID-19 from patient samples. We also contend that samples harvested from the upper respiratory tract and oral cavity have the highest potential for diagnosis of SARS-CoV-2 infection from easily collected patient samples using mass spectrometry-based proteomics assays.

scholarly journals A rigorous evaluation of optimal peptide targets for MS-based clinical diagnostics of Coronavirus Disease 2019 (COVID-19).

2021 ◽  
Author(s):  
Andrew T Rajczewski ◽  
Subina T Mehta ◽  
Dinh Duy An Ngyuen ◽  
Björn Andreas Grüning ◽  
James E Johnson ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Direct Detection ◽  
Clinical Diagnostics ◽  
Clinical Proteomics ◽  
Clinical Samples ◽  
P Value ◽  
Upper Respiratory Tract ◽  
Proteomics Data ◽  
High Throughput Analysis

The Coronavirus Disease 2019 (COVID19) global pandemic has had a profound, lasting impact on the world's population. A key aspect to providing care for those with COVID19 and checking its further spread is early and accurate diagnosis of infection, which has been generally done via methods for amplifying and detecting viral RNA molecules. Detection and quantitation of peptides using targeted mass spectrometry-based strategies has been proposed as an alternative diagnostic tool due to direct detection of molecular indicators from non-invasively collected samples as well as the potential for high-throughput analysis in a clinical setting; many studies have revealed the presence of viral peptides within easily accessed patient samples. However, evidence suggests that some viral peptides could serve as better indicators of COVID19 infection status than others, due to potential misidentification of peptides derived from human host proteins, poor spectral quality, high limits of detection etc. In this study we have compiled a list of 636 peptides identified from Sudden Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) samples, including from in vitro and clinical sources. These datasets were rigorously analyzed using automated, Galaxy-based workflows containing tools such as PepQuery, BLAST-P, and the Multi-omic Visualization Platform as well as the open-source tools MetaTryp and Proteomics Data Viewer (PDV). Using PepQuery for confirming peptide spectrum matches, we were able to narrow down the 639 peptide possibilities to 87 peptides which were most robustly detected and specific to the SARS-CoV-2 virus. The specificity of these sequences to coronavirus taxa was confirmed using Unipept and BLAST-P. Through stringent p-value cutoff combined with manual verification of peptide spectrum match quality, 4 peptides derived from the nucleocapsid phosphoprotein and membrane protein were found to be most robustly detected across all cell culture and clinical samples, including those collected non-invasively. We propose that these peptides would be of the most value for clinical proteomics applications seeking to detect COVID-19 from a variety of sample types. We also contend that samples taken from the upper respiratory tract and oral cavity have the highest potential for diagnosis of SARS-CoV-2 infection from easily collected patient samples using mass spectrometry-based proteomics assays.

scholarly journals Could Chlamydia Pneumoniae Be Considered an Infectious Risk Factor for Inflammatory Diseases Such as Atherosclerosis ?

2005 ◽  
Vol 3 (3) ◽  
pp. 109-112
Author(s):  
R. Sessa ◽  
M. Di Pietro ◽  
G. Schiavoni ◽  
I. Santino ◽  
M. Del Piano
Keyword(s):  
Risk Factor ◽  
Chlamydia Pneumoniae ◽  
Direct Detection ◽  
Inflammatory Diseases ◽  
Cell Types ◽  
Chronic Inflammatory Disease ◽  
Upper Respiratory Tract ◽  
Infectious Risk ◽  
Tract Infections

Chlamydia pneumoniae, a Gram-negative intracellular obligate bacteria, is recognised as a common cause of upper respiratory tract infections, and accounts for ∼10% of community-acquired pneumonia. In recent years, chronic and persistent infection with C. pneumoniae has been implicated in the pathogenesis of atherosclerosis. Atherosclerosis is regarded as a chronic inflammatory disease that results from complex interactions between a variety of cell types such as endothelial cells, vascular smooth muscle cells, monocytes/macrophages and inflammatory mediators. Involvement of C. pneumoniae in the pathogenesis of atherosclerosis has been supported by findings from seroepidemiologic studies, direct detection of chlamydial DNA, experimental animal and in vitro studies, and antibiotic intervention trials. The spectrum of cell biological, animal, and human clinical data suggests that C. pneumoniae may be considered an infectious risk factor for atherosclerosis but further studies are needed to clarify the etiopathogenetic role of C. pneumoniae in atherosclerotic vessel walls.

scholarly journals Comparative Transcriptomic Analysis of Temozolomide Resistant Primary GBM Stem-Like Cells and Recurrent GBM Identifies Up-Regulation of the Carbonic Anhydrase CA2 Gene as Resistance Factor

Cancers ◽  
2019 ◽  
Vol 11 (7) ◽  
pp. 921 ◽  
Author(s):  
Ricarda Hannen ◽  
Martin Selmansberger ◽  
Maria Hauswald ◽  
Axel Pagenstecher ◽  
Andrea Nist ◽  
...  
Keyword(s):  
Carbonic Anhydrase ◽  
Patient Survival ◽  
Clinical Samples ◽  
P Value ◽  
Sequencing Analysis ◽  
First Line ◽  
Recurrent Tumors ◽  
Comparative Transcriptomic Analysis ◽  
Recurrent Gbm

About 95% of patients with Glioblastoma (GBM) show tumor relapse, leaving them with limited therapeutic options as recurrent tumors are most often resistant to the first line chemotherapy standard Temozolomide (TMZ). To identify molecular pathways involved in TMZ resistance, primary GBM Stem-like Cells (GSCs) were isolated, characterized, and selected for TMZ resistance in vitro. Subsequently, RNA sequencing analysis was performed and revealed a total of 49 differentially expressed genes (|log2-fold change| > 0.5 and adjusted p-value < 0.1) in TMZ resistant stem-like cells compared to their matched DMSO control cells. Among up-regulated genes, we identified carbonic anhydrase 2 (CA2) as a candidate gene correlated with glioma malignancy and patient survival. Notably, we describe consistent up-regulation of CA2 not only in TMZ resistant GSCs on mRNA and protein level, but also in patient-matched clinical samples of first manifest and recurrent tumors. Co-treatment with the carbonic anhydrase inhibitor Acetazolamid (ACZ) sensitized cells to TMZ induced cell death. Cumulatively, our findings illustrate the potential of CA2 as a chemosensitizing target in recurrent GBM and provide a rationale for a therapy associated inhibition of CA2 to overcome TMZ induced chemoresistance.

scholarly journals Fuzzy-FishNet: A highly precise distribution-free network approach for feature selection in clinical proteomics

2015 ◽  
Author(s):  
Wilson Wen Bin Goh
Keyword(s):  
Feature Selection ◽  
Small Sample Size ◽  
Small Sample ◽  
Clinical Proteomics ◽  
P Value ◽  
Fisher Exact Test ◽  
Proteomics Data ◽  
Exact Test ◽  
Genomics And Proteomics ◽  
T Distribution

Network-based analysis methods can help resolve coverage and inconsistency issues in proteomics data. Previously, it was demonstrated that a suite of rank-based network approaches (RBNAs) provides unparalleled consistency and reliable feature selection. However, reliance on the t-statistic/t-distribution and hypersensitivity (coupled to a relatively flat p-value distribution) makes feature prioritization for validation difficult. To address these concerns, a refinement based on the fuzzified Fisher exact test, Fuzzy-FishNet was developed. Fuzzy-FishNet is highly precise (providing probability values that allows exact ranking of features). Furthermore, feature ranks are stable, even in small sample size scenario. Comparison of features selected by genomics and proteomics data respectively revealed that in spite of relative feature stability, cross-platform overlaps are extremely limited, suggesting that networks may not be the answer towards bridging the proteomics-genomics divide.

scholarly journals In Vivo Pharmacokinetic Analysis Utilizing Non-Targeted and Targeted Mass Spectrometry and In Vitro Assay against Transient Receptor Potential Channels of Maobushisaishinto and Its Constituent Asiasari Radix

Molecules ◽  
2020 ◽  
Vol 25 (18) ◽  
pp. 4283
Author(s):  
Takashi Matsumoto ◽  
Mikina Takiyama ◽  
Shou Sanechika ◽  
Akiko Nakayama ◽  
Katsuyuki Aoki ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Transient Receptor Potential ◽  
Receptor Potential ◽  
Pharmacokinetic Analysis ◽  
Upper Respiratory Tract ◽  
Vitro Assay ◽  
Targeted Analysis ◽  
Transient Receptor ◽  
Tract Infections

The Japanese traditional medicine maobushisaishinto (MBST) has been prescribed for treating upper respiratory tract infections, such as a common cold. However, its mode of action is poorly understood, especially concerning the MBST constituent Asiasari Radix (AR). In this study, we focused on AR, with an objective of clarifying its bioavailable active ingredients and role within MBST by performing pharmacokinetic and pharmacological studies. Firstly, we performed qualitative non-targeted analysis utilizing high-resolution mass spectrometry to explore the bioavailable ingredients of AR as well as quantitative targeted analysis to reveal plasma concentrations following oral administration of MBST in rats. Secondly, we performed in vitro pharmacological study of bioavailable AR ingredients in addition to other ingredients of MBST to confirm any agonistic activities against transient receptor potential (TRP) channels. As a result, methyl kakuol and other compounds derived from AR were detected in the rat plasma and showed agonistic activity against TRPA1. This study suggests that methyl kakuol as well as other compounds have the potential to be an active ingredient in AR and thus presumably would contribute in part to the effects exerted by MBST.

From “Clinical Proteomics” to “Clinical Chemistry Proteomics”: considerations using quantitative mass-spectrometry as a model approach

2012 ◽  
Vol 50 (2) ◽  
Author(s):  
Sylvain Lehmann ◽  
Pauline Poinot ◽  
Laurent Tiers ◽  
Christophe Junot ◽  
François Becher ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Biomarker Discovery ◽  
Clinical Chemistry ◽  
Biological Fluids ◽  
Clinical Proteomics ◽  
Detection Methods ◽  
Patient Treatment ◽  
Quantitative Detection ◽  
New Biomarkers

AbstractClinical Proteomics biomarker discovery programs lead to the selection of putative new biomarkers of human pathologies. Following an initial discovery phase, validation of these candidates in larger populations is a major task that recently started relying upon the use of mass spectrometry approaches, especially in cases where classical immune-detection methods were lacking. Thanks to highly sensitive spectrometers, adapted measurement methods like selective reaction monitoring (SRM) and various pre-fractionation methods, the quantitative detection of protein/peptide biomarkers in low concentrations is now feasible from complex biological fluids. This possibility leads to the use of similar methodologies in clinical biology laboratories, within a new proteomic field that we shall name “Clinical Chemistry Proteomics” (CCP). Such evolution of Clinical Proteomics adds important constraints with regards to the in vitro diagnostic (IVD) application. As measured values of analytes will be used to diagnose, follow-up and adapt patient treatment on a routine basis; medical utility, robustness, reference materials and clinical feasibility are among the new issues of CCP to consider.

scholarly journals Multicentre Evaluation of a Newly Developed Anti-Calcium Dobesilate-Enzymatic Creatinine Assay Based on Real-World Data in China

2020 ◽  
Author(s):  
Xiuzhi Guo ◽  
Li’an Hou ◽  
Zhongxin Lu ◽  
Guiru Zhi ◽  
Xiaoyan Li ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Real World ◽  
Isotope Dilution Mass Spectrometry ◽  
Reference Method ◽  
Ultra Performance Liquid Chromatography ◽  
Clinical Samples ◽  
Calcium Dobesilate ◽  
Real World Data ◽  
Precision And Accuracy

Abstract BackgroundPreviously, we reported that calcium dobesilate (CaD), a vasoprotective agent mainly used for diabetic retinopathy, negatively interferes with enzymatic creatinine assays. Anewly developed enzymatic creatinine assay, the “Cr-R assay”, is commercially available and claims to have no interference from CaD. This study aimed to verify the performance of the Cr-R assay on clinical samples and to investigate the degree of CaD interference in a multicentre, real-world study.MethodsThe precision and accuracy ofthe Cr-R assay was evaluated in 23 hospitals in different regions of China. Interference was then calculated both in vitro and in clinical samples. Samples with potential interference were screened based on the different creatinine results between Cr-R and the creatinine assays commonly used in each participating hospital (Cr-C). Interference was confirmed by determining serum CaD concentration by directly using ultra-performance liquid chromatography (UPLC) methodand by assessing the “true” creatinine levels using the standard isotope dilution mass spectrometry (ID-MS/MS) method. ResultsTheprecision and bias and anti-interference ability of Cr-R assay on most platforms fulfilled the specification criteria. In the clinical setting, 67,469 samples were tested in 23 centres, and CaD concentration was measured in 818 samples, of which 257 contained CaD, accounting for 0.38% of the total and 31% of screened patients. In these 257 cases, the median CaD concentration was 11.356 (range, 1.350–121.519; IQR, 7.162–21.175) μg/mL. Creatinine levels measured using Cr-C assay were up to 35.1% (95%CI, 37.9–32.4 %; P < 0.001) lower than the “real” creatinine levels using the ID-MS/MSmethod. For Cr-R reagent, the average bias from the reference method was -6.2% (95%CI, -7.9–4.6%; P < 0.001), ranging from -17.9% to 7.1%.ConclusionsMulticentre tests confirmed that the precision, bias, and anti-CaD ability of the Cr-R assay met clinical needs. The prevalence of CaD interference should be considered when performing clinical enzymatic creatinine measurements.Other manufacturers should improve the anti-interference performance of creatinine reagents.

scholarly journals Antibacterial Activity of Sudanese Propolis Extract Against Methicillin-susceptible and Methicillin-resistant Staphylococcus aureus isolates in Khartoum State, Sudan

2019 ◽  
pp. 07-12
Author(s):  
Islam Abbas ◽  
Musa Abdulla Ali
Keyword(s):  
Staphylococcus Aureus ◽  
Clinical Medicine ◽  
Inhibition Zone ◽  
University Hospital ◽  
Clinical Samples ◽  
P Value ◽  
Upper Respiratory Tract ◽  
Methicillin Resistant ◽  
Propolis Extract ◽  
Upper Respiratory

Introduction: Staphylococcus aureus is a Gram-positive round shaped bacterium frequently found in the upper respiratory tract and on the skin. The emergence of antibiotic-resistant strains of S. aureus such as methicillin-resistant S. aureus (MRSA) is a worldwide problem in clinical medicine. It is resistant to various antibiotic medications. Propolis is (bee glue) a flavonoid-rich product of honey comb, derives from the Greek pro “before” and polis “city”, it exhibits antibacterial and anti-inflammatory properties which indicate that it can be an extremely powerful natural antibiotic and useful when fighting off upper respiratory infections. Materials and Methods: This was a descriptive cross-sectional study conducted at Soba University Hospital, Sudan. Following ethical consideration, 100 isolates of Staphylococcus aureus from different clinical samples, 50 samples of MSSA and 50 samples of MRSA were enrolled. subculture were used to re-identified the Staphylococcus aureus based on colonial morphology, Gram’s stain, and other biochemical test were used for MSSA and MRSA detection. Perforated plastic plate’s technique used for propolis collection and measurement of the inhibition zone were used for detection of sensitivy or resistant reaction. Results: All of the study MSSA samples (50/50; 100%) and MRSA (50/50; 100%) samples which cultured with a different concentrations of Al-Gelly propolis extract were shown a resistant inhibition zone while (50/50; 100%) of the study MSSA samples and (50/50; 100%) of the study MRSA samples which cultured with a different concentrations of Al-Fao propolis extract were shown sensitive inhibition zone at different sensitivity levels. The sensitivity levels of both MSSA and MRSA to the Al-Fao propolis extract was significantly correlate with the concentration of the propolis extract (P value 0.000, 0.000 respectively). The greatest effect will be a product of 20% concentration.

scholarly journals Efektivitas Ekstrak Nanas (Ananas comosus(L.) pada Pertumbuhan Streptococcus beta-hemolitycus

2019 ◽  
Vol 10 (3) ◽  
pp. 390
Author(s):  
Sri Ujiani ◽  
Marhamah Marhamah
Keyword(s):  
Traditional Medicine ◽  
Ananas Comosus ◽  
P Value ◽  
Healthy Children ◽  
Upper Respiratory Tract ◽  
Significant Difference ◽  
Experimental Laboratory ◽  
Group A ◽  
The One

<p><span>Prevalence of Group A <em>beta-hemolyticus Streptococcus</em> in the upper respiratory tract in healthy children is 10-35%, and at most high, in children aged 3-15 years Career <em>Streptococcus beta-hemolyticus</em> Group A can cause throat infections. The use of traditional medicine in the world is part of the history of human culture for thousands of years. One of the natural ingredients that can be used as traditional medicine is pineapple. The effectiveness of pineapple (<em>Ananas comosus (L</em>.) extract on the growth of <em>beta-hemolitycus Streptococcus</em> has been carried out. The purpose of this study was to determine the effectiveness of pineapple extract (<em>Ananas comosus (L.</em>) on the growth of <em>Streptococcus beta-hemolitycus</em>. This study was an experimental laboratory study) pure in vitro. In this study, the inhibitory and killing power of <em>Ananas comosus (L.</em>) extract against the growth of <em>Streptococcus β haemolyticus</em> at various concentrations of 0.5%; 1%; 2%; 4%; 8%; 10%; 20%; 30%; 40%; 50%; 60%; 70%; 80%; 90%; 100% .. The research was conducted at the Lampung Provincial Health Laboratory Hall conducted from June to November 2018. The results of the One-way Anova test obtained p-value=0,000 so that p-value&lt;0.05 which means that the concentration of pineapple extract tested had an effect on growth of <em>Streptococcus beta hemolyticus</em> bacteria and the results of the Least Significant Difference (LSD) or Post hoc LSD (Least Significance Different) test (p-value&lt;0,05) showed that pineapple extract was effective in inhibiting and killing germs of <em>Streptococcus β haemolyticus</em> at a concentration of 8%.</span></p>

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