scholarly journals Noninvasive Analysis Using Data-Independent Acquisition Mass Spectrometry: New Epidermal Proteins That Reveal Sex Differences in the Aging Process

2021 ◽  
Vol 2021 ◽  
pp. 1-17
Author(s):  
Shirui Chen ◽  
Hui Zhang ◽  
Mengting Liu ◽  
Yaochi Wang ◽  
Cong Xin ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Sex Differences ◽  
Age Groups ◽  
Protein Composition ◽  
Protein Detection ◽  
High Sensitivity ◽  
Skin Aging ◽  
Protein Biomarkers ◽  
Data Independent Acquisition ◽  
Noninvasive Analysis

The development of mass spectrometry has provided a method with extremely high sensitivity and selectivity that can be used to identify protein biomarkers. Epidermal proteins, lipids, and cornified envelopes are involved in the formation of the skin epidermal barrier. The epidermal protein composition changes with age. Therefore, quantitative proteomic changes may be indicative of skin aging. We sought to utilize data-independent acquisition mass spectrometry for noninvasive analysis of epidermal proteins in healthy Chinese individuals of different age groups and sexes. In our study, we completed high-throughput protein detection, analyzed protein differences with MaxQuant software, and performed statistical analyses of the proteome. We obtained interesting findings regarding ceruloplasmin (CP), which exhibited significant differences and is involved in ferroptosis, a signaling pathway significantly associated with aging. There were also several proteins that differed between sexes in the younger group, but the sex differences disappeared with aging. These proteins, which were associated with both aging processes and sex differences, are involved in signaling pathways such as apoptosis, oxidative stress, and genomic stability and can serve as candidate biomarkers for sex differences during aging. Our approach for noninvasive detection of epidermal proteins and its application to accurately quantify protein expression can provide ideas for future epidermal proteomics studies.

scholarly journals Novel circulating protein biomarkers for thyroid cancer determined through data-independent acquisition mass spectrometry

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e9507
Author(s):  
Dandan Li ◽  
Jie Wu ◽  
Zhongjuan Liu ◽  
Ling Qiu ◽  
Yimin Zhang
Keyword(s):  
Mass Spectrometry ◽  
Area Under The Curve ◽  
High Sensitivity ◽  
Factor H ◽  
Complement Factor ◽  
Protein Biomarkers ◽  
Serum Samples ◽  
Data Independent Acquisition ◽  
Median Serum ◽  
And Control

Background Distinguishing between different types of thyroid cancers (TC) remains challenging in clinical laboratories. As different tumor types require different clinical interventions, it is necessary to establish new methods for accurate diagnosis of TC. Methods Proteomic analysis of the human serum was performed through data-independent acquisition mass spectrometry for 29 patients with TC (stages I–IV): 13 cases of papillary TC (PTC), 10 cases of medullary TC (MTC), and six cases follicular TC (FTC). In addition, 15 patients with benign thyroid nodules (TNs) and 10 healthy controls (HCs) were included in this study. Subsequently, 17 differentially expressed proteins were identified in 291 patients with TC, including 247 with PTC, 38 with MTC, and six with FTC, and 69 patients with benign TNs and 176 with HC, using enzyme-linked immunosorbent assays. Results In total, 517 proteins were detected in the serum samples using an Orbitrap Q-Exactive-plus mass spectrometer. The amyloid beta A4 protein, apolipoprotein A-IV, gelsolin, contactin-1, gamma-glutamyl hydrolase, and complement factor H-related protein 1 (CFHR1) were selected for further analysis. The median serum CFHR1 levels were significantly higher in the MTC and FTC groups than in the PTC and control groups (P < 0.001). CFHR1 exhibited higher diagnostic performance in distinguishing patients with MTC from those with PTC (P < 0.001), with a sensitivity of 100.0%, specificity of 85.08%, area under the curve of 0.93, and detection cut-off of 0.92 ng/mL. Conclusion CFHR1 may serve as a novel biomarker to distinguish PTC from MTC with high sensitivity and specificity.

Electrical Detection of Protein Biomarkers Using Nanoneedle Biosensors

2012 ◽  
Vol 1414 ◽  
Author(s):  
Rahim Esfandyarpour ◽  
Hesaam Esfandyarpour ◽  
Mehdi Javanmard ◽  
James S. Harris ◽  
Ronald W. Davis
Keyword(s):  
Physical Adsorption ◽  
Ionic Current ◽  
Microfluidic Channel ◽  
Protein Detection ◽  
High Sensitivity ◽  
Receptor Protein ◽  
Label Free ◽  
Electrical Detection ◽  
Protein Biomarkers ◽  
Impedance Modulation

Abstract:Here we present the development of an array of electrical nano-biosensors in a microfluidic channel, called Nanoneedle biosensors. Then we present the proof of concept study for protein detection. A Nanoneedle biosensor is a real-time, label-free, direct electrical detection platform, which is capable of high sensitivity detection, measuring the change in ionic current and impedance modulation, due to the presence or reaction of biomolecules such as proteins or nucleic acids. We show that the sensors which have been fabricated and characterized for the protein detection. We have functionalized Nanoneedle biosensors with receptors specific to a target protein using physical adsorption for immobilization. We have used biotinylated bovine serum albumin as the receptor and sterptavidin as the target analyte. The detection of streptavidin binding to the receptor protein is also presented.

scholarly journals Multiplex targeted mass spectrometry assay for one-shot flavivirus diagnosis

2019 ◽  
Vol 116 (14) ◽  
pp. 6754-6759 ◽  
Author(s):  
Sheena Wee ◽  
Asfa Alli-Shaik ◽  
Relus Kek ◽  
Hannah L. F. Swa ◽  
Wei-Ping Tien ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Nonstructural Protein ◽  
High Sensitivity ◽  
Single Shot ◽  
Protein Biomarkers ◽  
Diagnostic Assays ◽  
Nonstructural Protein 1 ◽  
Parallel Reaction Monitoring ◽  
Mass Spectrometry Technology ◽  
Sensitivity Specificity

Targeted proteomic mass spectrometry is emerging as a salient clinical diagnostic tool to track protein biomarkers. However, its strong analytical properties have not been exploited in the diagnosis and typing of flaviviruses. Here, we report the development of a sensitive and specific single-shot robust assay for flavivirus typing and diagnosis using targeted mass spectrometry technology. Our flavivirus parallel reaction monitoring assay (fvPRM) has the ability to track secreted flaviviral nonstructural protein 1 (NS1) over a broad diagnostic and typing window with high sensitivity, specificity, extendibility, and multiplexing capability. These features, pivotal and pertinent to efficient response toward flavivirus outbreaks, including newly emerging flavivirus strains, circumvent the limitations of current diagnostic assays.fvPRM thus carries high potential in positioning itself as a forerunner in delivering early and accurate diagnosis for disease management.

MosaicNeedles: A tool for multi-omic liquid biopsy sensitivity and specificity enhancement.

2021 ◽  
Vol 39 (15_suppl) ◽  
pp. e15019-e15019
Author(s):  
Qimin Quan ◽  
Joe Wilkinson ◽  
Joshua Ritchey ◽  
Alaina Kaiser ◽  
John Geanacopoulos ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Single Molecule ◽  
Liquid Biopsy ◽  
Dynamic Range ◽  
Color Change ◽  
Protein Detection ◽  
Target Sequence ◽  
Label Free ◽  
Protein Biomarkers ◽  
Oncology Research

e15019 Background: Liquid biopsy has evolved to be an important method complementary to tissue biopsy. It is not only non-invasive, but also has the potential to detect cancer in its earliest stages and monitor patients in remission. The integration of proteomics into liquid biopsy may transform the molecular diagnostics of cancer and accelerate basic and clinical oncology research. A recent study showed that adding just 8 protein biomarkers to a panel of circulating DNA biomarkers increased the diagnostic accuracy up to 98% sensitivity and 99% specificity. Proteomics also bridges the gaps of functional information lost due to post-transcriptional and post-translational modifications in the genomic approach. However, the proteogenomic approach normally requires the use of multiple different assay technologies and laboratory workflows, including mass spectrometry. Methods: NanoMosaic’s Tessie platform employs a densely integrated nanoneedle sensor array (thus named MosaicNeedles) which can be used to detect both nucleic acids and proteins in a single assay process with reduced workflow complexity, without the need for mass spectrometry. Results: The NanoMosaic platform is a label-free, digital, single molecule counting technology using nanoneedles. It achieves sub-pg/ml (̃fM) level sensitivity with 7 logs of dynamic range. An array of nanoneedles is densely integrated and manufactured with CMOS-compatible nanofabrication processes. Each nanoneedle is a single molecule biosensor that is functionalized with capture probes. The capture probe can be either an antibody for protein detection or an oligonucleotide with a specific target sequence to a DNA fragment, mRNA, or miRNA of interest. The scattering spectrum of each nanoneedle changes when an analyte binds to its surface. At low abundance, analytes that are captured can be quantitated by counting the presence or absence of a color change on each individual nanoneedle in a binary fashion. As an analyte concentration increases the binding events increase accordingly and achieve saturation. In this range, an analog analysis on the spectrum shift will be performed, thus providing a wider dynamic range, up to 7 logs. Ultrahigh level multiplex can be achieved by parallelizing each analyte specific sensing area without loss of sensitivity or dynamic range. A 10,000-plex study can be achieved with a total of 2.5 billion nanoneedles on a 50mm by 50mm consumable. In this consumable, a 2,000-plex proteome and 8,000 cell-free DNA fragments can be detected. Conclusions: In conclusion, a full proteogenomic quantification can be performed on the NanoMosaic platform in one reaction, with higher sensitivity, lower cost and higher throughput than is currently possible by traditional methods. In addition, the high-plexibility of the NanoMosaic platform allows the discovery of new biomarkers across the whole proteome without the need for mass spectrometry.

scholarly journals Development of Targeted Mass Spectrometry-Based Approaches for Quantitation of Proteins Enriched in the Postsynaptic Density (PSD)

Proteomes ◽  
2019 ◽  
Vol 7 (2) ◽  
pp. 12 ◽  
Author(s):  
Rashaun Wilson ◽  
Navin Rauniyar ◽  
Fumika Sakaue ◽  
TuKiet Lam ◽  
Kenneth Williams ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Postsynaptic Density ◽  
Protein Composition ◽  
Protein Abundance ◽  
Large Network ◽  
Glutamatergic Synapses ◽  
Data Independent Acquisition ◽  
Parallel Reaction Monitoring ◽  
Biochemical Fractionation ◽  
Internal Peptide

The postsynaptic density (PSD) is a structural, electron-dense region of excitatory glutamatergic synapses, which is involved in a variety of cellular and signaling processes in neurons. The PSD is comprised of a large network of proteins, many of which have been implicated in a wide variety of neuropsychiatric disorders. Biochemical fractionation combined with mass spectrometry analyses have enabled an in-depth understanding of the protein composition of the PSD. However, the PSD composition may change rapidly in response to stimuli, and robust and reproducible methods to thoroughly quantify changes in protein abundance are warranted. Here, we report on the development of two types of targeted mass spectrometry-based assays for quantitation of PSD-enriched proteins. In total, we quantified 50 PSD proteins in a targeted, parallel reaction monitoring (PRM) assay using heavy-labeled, synthetic internal peptide standards and identified and quantified over 2100 proteins through a pre-determined spectral library using a data-independent acquisition (DIA) approach in PSD fractions isolated from mouse cortical brain tissue.

scholarly journals Protein Biomarker Quantification by Immunoaffinity Liquid Chromatography–Tandem Mass Spectrometry: Current State and Future Vision

2020 ◽  
Vol 66 (2) ◽  
pp. 282-301 ◽  
Author(s):  
Hendrik Neubert ◽  
Christopher M Shuford ◽  
Timothy V Olah ◽  
Fabio Garofolo ◽  
Gary A Schultz ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Hybrid Methods ◽  
High Sensitivity ◽  
Binding Assays ◽  
Protein Biomarkers ◽  
Affinity Capture ◽  
Ms Detection ◽  
Liquid Chromatography Tandem Mass ◽  
Significant Uptake ◽  
Future Vision

Abstract Immunoaffinity–mass spectrometry (IA-MS) is an emerging analytical genre with several advantages for profiling and determination of protein biomarkers. Because IA-MS combines affinity capture, analogous to ligand binding assays (LBAs), with mass spectrometry (MS) detection, this platform is often described using the term hybrid methods. The purpose of this report is to provide an overview of the principles of IA-MS and to demonstrate, through application, the unique power and potential of this technology. By combining target immunoaffinity enrichment with the use of stable isotope-labeled internal standards and MS detection, IA-MS achieves high sensitivity while providing unparalleled specificity for the quantification of protein biomarkers in fluids and tissues. In recent years, significant uptake of IA-MS has occurred in the pharmaceutical industry, particularly in the early stages of clinical development, enabling biomarker measurement previously considered unattainable. By comparison, IA-MS adoption by CLIA laboratories has occurred more slowly. Current barriers to IA-MS use and opportunities for expanded adoption are discussed. The path forward involves identifying applications for which IA-MS is the best option compared with LBA or MS technologies alone. IA-MS will continue to benefit from advances in reagent generation, more sensitive and higher throughput MS technologies, and continued growth in use by the broader analytical community. Collectively, the pursuit of these opportunities will secure expanded long-term use of IA-MS for clinical applications.

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