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White Papers and Videos

Transitioning Biomarkers from Discovery to Validation at Unprecedented Scale with the Stellar Mass Spectrometer

White Paper

This white paper from Thermo Fisher Scientific details the design and capabilities of the Stellar mass spectrometer, as well as how it can be used for transitioning putative biomarker candidates from discovery to validation for translational proteomics, metabolomics, and lipidomics research.

High-Throughput High-Resolution Data-Independent Acquisition Workflow on an Orbitrap Ascend Multiomics Tribrid Mass Spectrometer for Accurate Label-Free Quantitation

White Paper

Accurately quantifying the abundances of proteins of interest in complex samples is a prerequisite for developing suitable statistical models to gain biological insights from experimental data sets. Statistical significance is improved by decreasing variability in measurements and/or increasing the sample set. However, increasing throughput means decreasing acquisition time, which often comes at a cost to measurement quality. Therefore, acquisition methods must be extensively optimized and validated to ensure that the data will produce meaningful biological insights. Traditional data-dependent analysis (DDA) approaches have been widely employed for LFQ experiments, but they suffer from run-to-run inconsistencies due to intensity-based stochastic triggering of precursors, often leading to under sampling, especially of low-abundance proteins. Missing values become more likely as sample size increases, and so DIA has emerged as a popular technique for large-scale quantitative analyses.

This technical note from Thermo Fisher Scientific details the development and assessment of label-free quantitation with an optimized data-independent acquisition method on an Orbitrap Ascend MultiOmics Tribrid mass spectrometer using a long, short, and ultra-high throughput gradient for large-scale proteomics analysis.

Low-Input and Single-Cell Samples on the Orbitrap Ascend MultiOmics Tribrid Mass Spectrometer

White Paper

In recent years, there has been a shift to analyzing smaller sample quantities, driven by an interest in profiling the proteome of individual cells. This increased focus on LC-MS analysis of limited sample amounts requires the highest possible sensitivity. At the same time, throughput, chromatographic performance, quantitative accuracy, and precision must be preserved to generate sufficiently high-quality data from large data sets to draw meaningful biological insights. This trend toward analyzing smaller sample quantities reflects the need to understand the heterogeneous nature of biological systems through the dissection of complex systems into their individual parts, or specifically, individual cells.

This technical note from Thermo Fisher Scientific assesses proteome coverage and sample throughput for low-input and single-cell samples using a library-free data-independent acquisition method on the Orbitrap Ascend MultiOmics Tribrid mass spectrometer.

Unveiling Hidden Protein Depths: A High-Throughput Plasma Proteomics Workflow for Enhanced Biomarker Discovery

White Paper

The analysis of blood plasma for cancer biomarkers presents a promising avenue for early detection, but the complexity of the associated workflows has hindered progress in this area. The analysis of plasma presents a substantial challenge due to the vast concentration range of proteins in blood plasma. Detecting low-abundance proteins, which hold potential as biomarkers, proves challenging as they are often greatly overshadowed by high-abundance proteins. In fact, approximately 99 percent of the plasma proteome is composed of proteins such as albumin, globulins, and coagulants, effectively overshadowing potentially less abundant protein biomarkers. Therefore, there is a pressing need to develop methods that can accurately identify and quantify these low-abundance proteins in plasma samples.

This application note from Thermo Fisher Scientific describes the development of a robust plasma proteomics workflow with different sample preparation and throughput methods for deep plasma proteomics and superior quantitation by a label-free data-independent acquisition strategy on the Orbitrap Astral mass spectrometer.

Navigating Neuroscience Through Spatial Biology

White Paper

Neuroscience is a multidisciplinary field that focuses on the structure, function, development, and pathology of the nervous system. Thus, it has far-reaching applications from basic brain functions to the development of novel treatments for cancer, neurodegenerative diseases, and psychiatric disorders.

This infographic from Lunaphore shows how spatial biology brings new tools to the field of neuroscience to reveal the arrangement of molecules in space and the relationships between spatial organization and cellular and tissular functions.

Comet Streamlines Hyperplex Immunofluorescence at Single-Cell Resolution

White Paper

In immuno-oncology, spatial biology is used to study immune cells and tumoral cells in their spatial context. Understanding immune cell phenotypes, functional activities, and spatial relationships inside or around the tumoral mass is crucial to understanding immune response and resistance.

This technical note from Lunaphore describes the development of a 40-plex panel for studying tumors and the tumor microenvironment across basic and translational research at single-cell resolution on the Comet tissue-staining and imaging platform.

Uncovering the Spatial Dynamics of the Tumor Microenvironment: Integrated RNA and Protein Profiling on the Same Section Through Automated Spatial Multiomics Analysis

White Paper

Spatial biology techniques have revolutionized the study of the tumor microenvironment (TME). By preserving the spatial information and allowing analyses at single-cell resolution, an unprecedented understanding of the cellular composition of cancer tissues has been made possible. On the one hand, multiplex immunofluorescence (mIF) methods have enabled precise profiling of immune cells and other key cellular players of the TME while uncovering their spatial distribution and interactions. On the other hand, in situ hybridization (ISH) technologies have been shown to provide complementary information to protein profiling, such as the mapping of cytokine- and chemokine-expressing cells, which are essential to comprehend signaling networks and immune activation statuses.

This poster from Lunaphore highlights the potential of spatial multiomics to enhance research on immune cell biology and improve the understanding of the cellular interplay within the TME, using full automation of RNA and protein co-detection on the Comet tissue-staining and imaging platform.

Antibody and Panel Validation to Advance Spatial Biology Research

White Paper

Multiplexed immunofluorescence (mIF) has emerged as a powerful technique for investigating complex biological systems and cellular interactions. By simultaneously detecting multiple targets within a single tissue or cell sample, mIF enables researchers to gain a deeper understanding of cellular dynamics, spatial relationships, and biomarker expression patterns.

This white paper from Lunaphore discusses the challenges that can impact the accuracy and reliability of mIF results, including antibody specificity, sensitivity, signal crosstalk, and reproducibility, and it explains the antibody and panel validation processes implemented by Lunaphore.

The Evolving Role of Diagnostic Labs in Oncology: Navigating Biomarker-Driven Therapies

White Paper

In the past decade, oncology care has witnessed a transformative shift, significantly propelled by the growing field of precision medicine. This transformation has been catalyzed by a deeper understanding of cancer’s underlying biological drivers, unveiling new avenues to combat this multifaceted disease. This rising significance of biomarkers has recalibrated the role of and expectations from diagnostic labs, ushering them into a more proactive and collaborative role in oncology care.

This white paper from Quest Diagnostics delves into the rise of biomarker-driven therapies in oncology, examining how this shift is reshaping the drug and therapy development landscape and exploring the evolving role of diagnostic labs as they transition into active partners in these advancements.

The Epigenome Could be More Actionable Than the Genome, says Bret Barnes, Illumina

White Paper

Bret Barnes has spent his career at Illumina developing the DNA methylation Infinium arrays that have become the workhorse of epigenomic studies around the world.

Barnes says he was torn as a young person between biochemistry and computer science, and he fortuitously ended up at UC Santa Cruz when they launched the first bioinformatics degree. Early on, he was interested in protein structure prediction. “There are 20 amino acids,” he said. Way more exciting than DNA with only four bases." At the time of the Solexa acquisition, Illumina recruited Bret to do bioinformatics work on DNA methylation.

“Methylated cystine is considered the fifth base. So five not four — a little better,” he says. He jumped on board Illumina’s team. “If the king and queen of DNA methylation at Illumina were Kevin Gunderson and Marina Bibikova, then you could think of me as the prince, or maybe the joker,” he admits.

In this podcast, Mendelspod’s Theral Timpson speaks to Bret Barnes from Illumina about the current state of epigenomics, the applications Barnes sees for the actionable epigenome, and how he sees the field developing.

Troubleshooting Magnetic Beads

White Paper

Understanding the intricate properties and behaviors of magnetic beads is crucial for optimizing nucleic acid isolation. Each characteristic plays a role in ensuring the efficiency and reliability of nucleic acid isolation protocols.

This troubleshooting guide from Cytiva explains some of the considerations and tips behind magnetic bead characteristics, and it includes strategies to understand and measure surface area, bead size, sedimentation, parking area, magnetic response, concentration, and aggregation issues for optimal performance.

Automated DNA Clean-Up Using the Zymo Research DNA Clean and Concentrator Magbead Kit

White Paper

DNA clean-up methods are used to purify samples of DNA by removing any unwanted components. This is crucial for the success of downstream processes in genomics, biotechnology, molecular biology, clinical research, and other fields of biology.

Zymo Research’s DNA Clean and Concentrator (DCC) MagBead kit offers a magnetic bead-based DNA clean-up for PCR and next-generation sequencing (NGS). Its single buffer system can recover DNA from enzymatic reactions, impure extractions, library preparations, and other sources.

This application note from Integra describes how Zymo Research’s DNA Clean and Concentrator (DCC) MagBead kit can be used with the Voyager adjustable tip spacing pipette on the Assist Plus pipetting robot to automate DNA purification and concentration, enabling high-throughput processing.

Master the Art of Pipetting and Learn How to Perform Serial Dilutions With our Comprehensive Guide

White Paper

A serial dilution is the step-wise reduction of a concentration using a constant dilution factor and similar volumes. This highly standardized procedure has applications in drug discovery, microbiology, and molecular biology.

This application guide from Integra discusses how to perform serial dilutions with optimized liquid handling parameters to prevent common issues leading to accumulated errors during inter-dependent steps, using data from a water-based serial dilution set-up to isolate key parameters and demonstrate how they influence reliability.

Western Blot Protocol Automation with the Assist Plus Pipetting Robot and Simple Western

White Paper

Automated western blotting is a cutting-edge technology revolutionizing traditional protein detection and analysis. Employing robotic systems, microscale separation, and advanced imaging technologies streamlines the labor-intensive and time-consuming process of western blotting. Automating the multiple workflow steps increases efficiency, making it an invaluable tool in various fields of biological research. Simple Western — developed by ProteinSimple, a Bio-Techne brand — is the only fully automated western blotting solution on the market. The capillary-based technology enables efficient and accurate high throughput protein separation, detection, and quantification, with all assay reagents and samples in one plate. Simple Western assays are advancing research and development in many applications, including cancer and immuno-oncology, cell and gene therapy, regenerative medicine, and targeted protein degradation.

This application note from Integra provides a protocol for using the Assist Plus pipetting robot and D-One single-channel pipetting module, together with the Simple Western Jess, to automate all the liquid handling steps required to analyze 24 samples, providing a complete walk-away solution for western blot protocol automation.

How to Improve Accessibility to Testing for GI Infections

White Paper

Infectious diarrhea, or gastroenteritis, continues to be a significant health threat worldwide, causing numerous deaths, especially among vulnerable populations in the US. This condition is largely attributed to foodborne pathogens domestically, as highlighted by the US Food and Drug Administration, which reports millions suffering from foodborne illnesses annually. Recent developments in nucleic acid amplification testing (NAAT) via PCR have transformed gastroenteritis diagnostics, moving away from slower, less reliable stool cultures to rapid, accurate tests. Multiplex syndromic NAAT panels, capable of detecting multiple pathogens simultaneously, have further advanced the field, especially in hospital settings. However, these tests are costly, prompting outpatient clinics to rely on reference labs that offer more affordable and still timely diagnostics.

In this article from Applied BioCode, Anami Patel, chief scientific officer of molecular diagnostics and genomics at PathAI, discusses the evolution of gastrointestinal infection testing and how newer, efficient testing methods can significantly enhance patient care.

This article was originally published in the August 2024 issue of Clinical Lab Products, pages 12-15, and is provided here with permission from Clinical Lab Products.