Performance limitations of label-free sensors in molecular diagnosis using complex samples

2016 ◽  
Author(s):  
Manoj Varma
Keyword(s):  
Molecular Diagnosis ◽  
Label Free ◽  
Complex Samples ◽  
Performance Limitations

scholarly journals Label-Free Mass Spectrometry-Based Quantification of Linker Histone H1 Variants in Clinical Samples

2020 ◽  
Vol 21 (19) ◽  
pp. 7330
Author(s):  
Roberta Noberini ◽  
Cristina Morales Torres ◽  
Evelyn Oliva Savoia ◽  
Stefania Brandini ◽  
Maria Giovanna Jodice ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Histone H1 ◽  
Histone Variants ◽  
Linker Histone ◽  
Clinical Samples ◽  
Label Free ◽  
Complex Samples ◽  
Linker Histone H1 ◽  
Ideal Tool ◽  
Free Quantification

Epigenetic aberrations have been recognized as important contributors to cancer onset and development, and increasing evidence suggests that linker histone H1 variants may serve as biomarkers useful for patient stratification, as well as play an important role as drivers in cancer. Although traditionally histone H1 levels have been studied using antibody-based methods and RNA expression, these approaches suffer from limitations. Mass spectrometry (MS)-based proteomics represents the ideal tool to accurately quantify relative changes in protein abundance within complex samples. In this study, we used a label-free quantification approach to simultaneously analyze all somatic histone H1 variants in clinical samples and verified its applicability to laser micro-dissected tissue areas containing as low as 1000 cells. We then applied it to breast cancer patient samples, identifying differences in linker histone variants patters in primary triple-negative breast tumors with and without relapse after chemotherapy. This study highlights how label-free quantitation by MS is a valuable option to accurately quantitate histone H1 levels in different types of clinical samples, including very low-abundance patient tissues.

Melanin-targeted nonlinear microscopy for label-free molecular diagnosis and staging

2016 ◽  
Author(s):  
Warren S. Warren ◽  
Francisco Robles ◽  
Martin Fischer ◽  
Jesse Wilson ◽  
Sanghamitra Deb ◽  
...  
Keyword(s):  
Molecular Diagnosis ◽  
Nonlinear Microscopy ◽  
Label Free

scholarly journals Quantitative Mass Spectrometry Imaging of Biological Systems

2021 ◽  
Vol 72 (1) ◽  
Author(s):  
Daisy Unsihuay ◽  
Daniela Mesa Sanchez ◽  
Julia Laskin
Keyword(s):  
Mass Spectrometry ◽  
Mass Spectrometry Imaging ◽  
Matrix Effects ◽  
High Sensitivity ◽  
Biological Tissues ◽  
Annual Review ◽  
Publication Date ◽  
Label Free ◽  
Complex Samples ◽  
Mass Dependent

Mass spectrometry imaging (MSI) is a powerful, label-free technique that provides detailed maps of hundreds of molecules in complex samples with high sensitivity and subcellular spatial resolution. Accurate quantification in MSI relies on a detailed understanding of matrix effects associated with the ionization process along with evaluation of the extraction efficiency and mass-dependent ion losses occurring in the analysis step. We present a critical summary of approaches developed for quantitative MSI of metabolites, lipids, and proteins in biological tissues and discuss their current and future applications. Expected final online publication date for the Annual Review of Physical Chemistry, Volume 72 is April 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

scholarly journals Quantitative mapping of triacylglycerol chain length and saturation using broadband CARS microscopy

2018 ◽  
Author(s):  
A. Paul ◽  
Y.J. Wang ◽  
C. Brännmark ◽  
S. Kumar ◽  
M. Bonn ◽  
...  
Keyword(s):  
Chain Length ◽  
High Speed ◽  
Lipid Analysis ◽  
Neutral Lipids ◽  
Cell Types ◽  
Label Free ◽  
Complex Samples ◽  
Disease States ◽  
Coherent Raman

AbstractLipid droplets (LDs) are highly dynamic organelles that store neutral lipids, primarily triacylglycerols (TAGs), and are found in many cell types. While their primary function is to store excess energy, LDs are also modified in different disease states and during developmental processes. In many cases, not only the presence, but also the composition, of LDs can be equally important. In humans, LD composition has been linked to diseases such as type 2 diabetes; in plants and yeast, LD composition is relevant for engineering these organisms into biological factories in, e.g., algal bioenergy or food oil production. Therefore, lipid analysis of biological LDs with high speed and accuracy in situ is a very active area of research. Here we present an approach for in situ, quantitative TAG analysis using label-free, coherent Raman microscopy to decipher LD TAG composition in different biochemically complex samples. Our method allows direct visualization of inter-LD compositional heterogeneity of physiological quantities – TAG chain length and number of C=C bonds – with sub-micrometer spatial resolution within 5-100 milliseconds. Combined with virtually no sample preparation, this approach should enable rapid and accurate TAG LD analysis for a variety of applications.

scholarly journals Current Status and Advances in Quantitative Proteomic Mass Spectrometry

2013 ◽  
Vol 2013 ◽  
pp. 1-12 ◽  
Author(s):  
Valerie C. Wasinger ◽  
Ming Zeng ◽  
Yunki Yau
Keyword(s):  
Mass Spectrometry ◽  
Quantitative Proteomics ◽  
Biomarker Discovery ◽  
Current Status ◽  
Label Free ◽  
Stable Isotope Labelling ◽  
Complex Samples ◽  
Bioinformatic Tools ◽  
Critical Overview ◽  
Proteins And Peptides

The accurate quantitation of proteins and peptides in complex biological systems is one of the most challenging areas of proteomics. Mass spectrometry-based approaches have forged significant in-roads allowing accurate and sensitive quantitation and the ability to multiplex vastly complex samples through the application of robust bioinformatic tools. These relative and absolute quantitative measures using label-free, tags, or stable isotope labelling have their own strengths and limitations. The continuous development of these methods is vital for increasing reproducibility in the rapidly expanding application of quantitative proteomics in biomarker discovery and validation. This paper provides a critical overview of the primary mass spectrometry-based quantitative approaches and the current status of quantitative proteomics in biomedical research.

An Aptamer-Functionalized Microfluidic Platform for Biomolecular Purification and Sensing

2009 ◽  
Author(s):  
Thai Huu Nguyen ◽  
Qiao Lin
Keyword(s):  
Small Molecules ◽  
Label Free ◽  
Temperature Dependent ◽  
Synthetic Process ◽  
Microfluidic Platform ◽  
Thermally Induced ◽  
Complex Samples ◽  
Target Binding ◽  
External Stimuli

Aptamers are oligonucleotides (DNA or RNA) that bind to chemical and biological analyte targets via affinity interactions. Through an in vitro synthetic process, aptamers can be developed for an extremely broad spectrum of analytes, such as small molecules, proteins, cells, viruses, and bacteria. Target recognition by aptamers is highly selective, as affinity interactions result in secondary aptamer conformational structures that specifically fit the target. The aptamer-target binding is also reversible and depends strongly on external stimuli such as pH and temperature. The specificity and stimuli-responsiveness of aptamers are highly attractive to biological purification and sensing, which generally involve isolating minute quantities of targets from complex samples with non-specific molecules and impurities present at orders-of-magnitude higher concentrations. We present an aptamer-functionalized microfluidic platform that by design exploits the specificity and temperature-dependent reversibility of aptamers to enable biomolecular purification and sensing. Using the specificity of aptamers, we demonstrate highly selective capture and enrichment of biomolecules. Employing thermally induced, reversible disruption of aptamer-target binding, we accomplish isocratic elution of the captured analytes and regeneration of the aptamer surfaces, thereby eliminating the use of potentially harsh reagents. Using integrated microfluidic control, the eluted analytes are detected in a label-free fashion by mass spectrometric methods.

Label-free LC-MS/MS quantitative proteomics for large-scale biomarker discovery in complex samples

2007 ◽  
Vol 30 (14) ◽  
pp. 2198-2203 ◽  
Author(s):  
Yishai Levin ◽  
Emanuel Schwarz ◽  
Lan Wang ◽  
F. Markus Leweke ◽  
Sabine Bahn
Keyword(s):  
Quantitative Proteomics ◽  
Large Scale ◽  
Biomarker Discovery ◽  
Label Free ◽  
Complex Samples
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