PROTEIN BIOMARKER analysis

High-Throughput Laboratory Services for Proteomics Analysis

Cutting-Edge

Protein Biomarker Profiling

Protein biomarkers play an important role in disease diagnosis, prognosis, and treatment. At BioXpedia we excel in high-throughput omics analyses, utilising a diverse range of state-of-the-art technologies to uncover meaningful markers within collections of clinical samples. We offer a high-multiplex proteomics approach for screening protein expression across 5300+ potential biomarkers. Moreover, our customisable screening panels empower researchers  to explore subsets of biomarkers in clinical and preclinical samples.

BioXpedia offers high throughput, high multiplex protein analyses, as well as single-plex custom analyses of biological samples. In other words, we support projects spanning from large-scale biomarker discovery down to low- and mid-plex absolute protein quantification and biomarker validation.

Technologies for Protein Biomarker Screening

For screening large collections of clinical samples against a large number of potential protein biomarkers, we typically apply high multiplex assays such as Olink Explore 3072 or Olink Explore HT. For validation, for screening in lower plex, or for screening against a more defined panel of biomarkers, we offer ELISA, Meso Scale Discovery (MSD), or Olink intermediate formats, such as Olink Target 96 or Olink Flex.

Hamilton Vantage system.Liquid handling for Olink protein biomarker assays on Hamilton Vantage system.

Genomics, Transcriptomics, and Proteomics

Proteomics, transcriptomics, and genomics are interconnected disciplines, all part of the broader realm of multiomics.

Genomics focuses on studying an organism’s genetic material by employing DNA sequencing to distinguish genetic variations and their relevance to diseases.

Transcriptomics looks at the complete set of RNA molecules (the transcriptome) produced by a cell or tissue, providing insights into gene expression patterns.

Finally, proteomics deals with the proteome; the complete set of proteins present in a cell or tissue, their chemical modifications, their degradation, and their changes in response to external factors, such as disease.

Collectively, multiomics allows researchers to investigate the intricate relationship between genetic information, gene expression, proteomic fingerprints, and phenotype-level changes. In this way, the multi-omics approach facilitates a comprehensive understanding of biological processes and disease mechanisms.

Protein Biomarker Profiling

Protein biomarker profiling refers to the comprehensive identification and quantification of proteins, in order to identify potential biomarkers associated with a particular disease, physiological condition, or biological process. The analysis assesses protein expression levels within biological samples, which may vary, for instance, between different patient cohorts and healthy controls. Through the comparison of protein profiles, researchers can pinpoint potential diagnostic or prognostic biomarkers. In essence, protein biomarker profiling is a subset or specific application of proteomics.

The information gained, once verified, can be used to guide personalised medicine, monitor treatment response, and improve disease detection and management. Typical sample materials include blood-derived liquids (human or animal) such as plasma, serum, cerebrospinal fluid (CSF), or other biofluids.

Supporting your projects

We welcome your project at BioXpedia.

We support biological and clinical research, by offering our expertise and laboratory analyses to the pharma industry and the medical research community. We offer a wide variety of services and technologies.

The Proximity Extension Assay

The cornerstone of our protein biomarker discovery service is the proximity extension assay (PEA) from Olink Proteomics. This assay is a powerful and very sensitive immunoassay for the simultaneous detection and quantification of multiple protein biomarkers in a sample.

In the PEA assay, a pair of antibodies initially targets the specific protein of interest and binds to its surface. Each of these antibodies is covalently bound to a DNA oligo. When two antibodies bind to the same target protein, the oligos are brought into close proximity. Under these conditions, the oligos will hybridise, allowing polymerase to bind to the short stretch of double-stranded DNA. The polymerases will synthesise a longer double-stranded DNA, with a sequence that uniquely identifies the antibodies that found their target. The DNA product is quantified either by qPCR or NGS, and the amount of product correlates with the amount of target protein in the sample. Using specifically tailored DNA oligos on individual antibodies in the assay, it is possible to multiplex the reactions. In this way we can run a large number of assays on the same sample material and in the same reaction volume. The output of most PEA assay formats is provided in normalised units, referred to as normalised protein expression (NPX) units. Exceptions to this are the Olink Flex and Target 48 assays, which provide an absolute concentration readout.

PEA assays offers excellent sensitivity due to the PCR amplification step, and high specificity due to the inherent requirement for dual antibody recognition of each target. Taken together, this enables detection and quantification of low-abundance proteins (e.g. quantification limit of 2 pg/mL for EGF). Very small sample volumes are needed for the PEA  assays.

Olink Proteomics

Our Olink Panel Service

The Proximity Extension Assay (PEA) from Olink Proteomics allows us to quantify from 15 to 5300+ disease relevant proteins in a single analysis. The assays can either be run in predefined panels and recognise 43 to 5300+ protein targets, or in customised panels of 15 to 21 specifically selected targets. The Olink panels accommodate different a number of samples per workflow, but we accept projects of any size, up to tens of thousands of samples. The panel sizes offer a good approximate indication of the lower limit size for a project.

 

  • Olink Flex: 40 samples, readout in pg/ml or NPX.
  • Olink Target 48: 40 samples, readout in pg/ml or NPX.
  • Olink Target 96: 88 samples, readout in NPX.
  • Olink Explore 384: 88 samples, readout in NPX.
  • Olink Explore 3072: 88 samples, readout in NPX.
  • Olink Explore HT: 172 samples, readout in NPX.

Olink Explore HT Service

Explore HT is the most advanced Olink solution in protein biomarker discovery. This assay measures the levels of 5,300+ proven or potential protein biomarkers. All targets and antibody pairs in the assay have been through a rigorous validation process, in order ensure that the Olink Explore HT panel delivers reliable data. Like all Olink Explore series panels, the Explore HT panel is based on the integration of proximity extension technology and NGS.

The Olink Explore HT assay has been designed with focus on functional, actionable, druggable, and circulating proteins. With this focus Olink Explore HT accommodates basic research, as well as drug development and research in diagnostics. As an Olink service provider we can help design and conduct your Explore HT protein biomarker project.

Liquid handling for Olink protein biomarker assays on Mettler Rainin BenchSmart.

Olink Explore 3072 and Olink Explore 384

With the Olink Explore 3072, we offer the capability to assess 2900+ protein biomarkers from a single biological sample. This panel is composed of subpanels, each targeted to a specific research domain. Each subpanel can be run independently and analysed (Olink Explore 384) or can be combined with other panels in the series. The panels are designed with minimal overlap. Altogether, the eight Olink Explore 384 panels form the Olink Explore 3072 panel. As with Olink Explore HT, results from the Olink Explore 3072 panels are provided in units of normalised protein expression (NPX). The subpanels of the Explore 3072 panel are listed below:

 

Marie Holt, Project Manager

Olink Flex, ELISA, and MSD

Validation and verification in single- and low-plex.

Our service take you from the discovery stage to validation and application, by combining a range of assay types and technologies. For single- or low-plex applications we offer Olink Flex, MSD, and ELISA.

Olink Target 96 and Target 48

Each of the Target 96 panels contains 92 individual protein assays. The panels are grouped by research area, e.g., inflammation, oncology, cardiovascular disease, mouse samples, or neurology. A single Target 48 panel is also available for measuring cytokine levels.

Unlike other panels in the Target series, the Target 48 cytokine panel will give a quantitative readout, in addition to normalised protein expression (NPX) units. The panels in the Target series overlap, so the collective number of protein assays in the Target series is 1160+. The complete list of Target panels is:

 

Olink Flex Assay Service

Olink Flex is a custom protein panel that allows for the simultaneous measurement of up to 21 proteins in a single sample. The target proteins can be individually selected from the continually expanding catalogue of 200 proteins. Similar to the Olink Target 48 assay, the Olink Flex assay can provide readout in absolute concentration units. This, along with the custom design option, are the features that set the Olink Flex panel apart. The Olink Flex panel is built with a focus on inflammation markers.

Individual Olink Flex panels can accommodate down to 40 samples, providing scalability. Orders down to a single custom-designed panel can be fulfilled, allowing for tailored research needs and experimental design flexibility. The current list of avaiable Olink Flex assays is below:

Meso Scale Discovery Service

Meso Scale Discovery (MSD) assays use a specialised protein detection platform and a unique assay methodology in order to quantify proteins, such as biomarkers, in complex samples.

The technology involves capture antibodies that are coated on a special MSD plate. Addition of a complex biological sample will allow the target of interest to be adsorbed on the coated surface. After the initial incubation, a mix of detection antibodies is added. These antibodies are conjugated with an electrochemiluminescent label, which will emit light in response to electricity. When an electrical current is applied to the plate, it triggers electron excitation in the labels attached to the detection antibodies. As the electrons in the label return to their ground state, they emit light. The amount of emitted light is proportional to the amount of target protein bound by the detection antibodies.

Using MSD immunoassays, we can perform absolute protein quantification of up to 10 targets in a single reaction. The assay is run in plates of 96 or 384 wells. A 96-well version of the MSD plate will accommodate 40 samples and provide duplicare readout. The MSD approach not only conserves sample volume, it also significantly reduces the time required for low- to mid-plex analyses.

ELISA Assay Service

The enzyme-linked immunosorbent assay (ELISA) and the sandwich ELISA are cornerstone assays for the simple and affordable quantification of selected proteins in complex samples.

Assays of this type are performed by first immobilising a mixed sample of proteins onto a surface. If a capture antibody is used, the surface will adsorb only the protein of interest. This is the method used in the sandwich ELISA. In a basic ELISA, the surface is treated to adsorb all proteins. A second antibody specific to the target protein is then added and allowed to bind. This second antibody is conjugated to an enzyme, and the enzyme facilitates the quantification of bound antigen, typically by means of a colorimetric reaction.

ELISA is an excellent and versatile method for validation of biomarker hits resulting from multiplex panel screening.

Compatible Sample Types

The protein analyses we offer are primarily validated for human and murine samples, although assays for other species are also available. The sample amount input is very low, down to 1 µl, allowing you to get the most out of your samples.

Our comprehensive range of assays ensures accurate and reliable results for various research applications and protein targets. Typically, our assays are compatible with any biofluid. A comprehensive but non-exhaustive list of compatible sample matrices can be found below:
 

  • Plasma
  • Serum
  • Cell culture supernatant
  • Tape strips
  • Urine
  • Tissue homogenate
  • Synovial fluid
  • Dialysate
  • Cerebrospinal fluid (CSF)
  • Cell lysate
  • Bone marrow plasma

For more information about our protein analyses services, please contact us here:

Frequently Asked Questions

What is a protein biomarker?

A protein biomarker is a measurable indicator consisting of, or derived from, proteins, revealing a particular biological state or condition.

Biomarkers play a pivotal role in disease detection, diagnosis, and monitoring, and also play a role in predicting treatment response within the context of personalised medicine strategies. Protein biomarkers offer a valuable asset for healthcare practitioners and researchers alike.

What is biomarker validation?

Biomarker validation is a process in biomarker research. It entails confirming the clinical relevance of a potential biomarker and its reliability and predictive capacity for specific diseases or conditions.

Once a novel biomarker has been identified through high throughput screening, a process of validation follows. Validation is important to ascertain the suitability of the biomarker for diagnostic, prognostic, or personalised medicine applications.

What is absolute protein quantification?

Absolute protein quantification determines the concentration of a specific protein in a sample, typically by using a calibration curve, and provides a result, including a unit of concentration. Relative protein abundance refers to the comparison of protein levels between different samples or conditions, without providing specific concentration values. It involves comparing the protein abundance in one sample relative to another sample or a control group.

Both approaches are valuable and serve different purposes in protein biomarker analysis. Absolute quantification provides dimensioned concentration values, allowing for accurate comparisons of protein levels across different studies. Relative abundance analysis, on the other hand, focuses on understanding changes in protein expression between conditions, providing insights into biological processes and disease mechanisms.