Protein Biomarker Discovery Service

Protein biomarker discovery is the process of identifying specific proteins that can serve as measurable indicators of biological or pathological states, which can be used for disease diagnosis, prognosis, and treatment monitoring. This process involves using advanced techniques such as mass spectrometry and high-throughput proteomics to analyze biological samples and identify proteins that are differentially expressed or modified in disease states. Protein biomarkers are crucial for understanding disease mechanisms, detecting diseases early, monitoring disease progression, and assessing treatment efficacy. They can provide valuable molecular signatures that reflect the underlying biology of diseases, enabling clinicians to make more accurate decisions and develop personalized treatment strategies.

 

The need for protein biomarker discovery arises from the limitations of current diagnostic tools, which often rely on invasive procedures, imaging, or nonspecific clinical markers. These methods are insufficient for early-stage detection or for monitoring the progression of diseases, especially complex conditions such as cancer, neurodegenerative diseases, and metabolic disorders. Protein biomarker discovery can address these challenges by providing non-invasive, highly specific markers that can be detected in easily accessible body fluids like blood or urine. By identifying disease-specific biomarkers, this process enables earlier and more precise detection, better disease stratification, and more tailored treatments. It also bridges the gap between clinical symptoms and molecular pathophysiology, offering insights into disease progression and therapeutic response, ultimately improving patient outcomes and advancing precision medicine.

 



Del, Boccio, P. et al. Proteomics Clin Appl. 2016.

Figure 1. Workflow for Protein Biomarker Discovery

 

Service at MtoZ Biolabs

MtoZ Biolabs, an integrated Chromatography and Mass Spectrometry (MS) Services Provider, provides advanced proteomics, metabolomics, and biopharmaceutical analysis services to researchers in biochemistry, biotechnology, and biopharmaceutical fields. MtoZ Biolabs offers specialized protein biomarker discovery service including the entire process from sample collection and data analysis to biomarker validation. We are committed to helping clients identify disease-related protein biomarkers using advanced mass spectrometry and proteomics technologies. If you are interested in our service, please contact us freely.

 

Service Advantages

Advantages of MtoZ Biolabs Protein Biomarker Discovery Service:  

1. High Sensitivity and Specificity  

MtoZ Biolabs leverages advanced mass spectrometry technologies and innovative proteomics approaches to detect low-abundance protein biomarkers in complex samples, ensuring the precise identification of biomarkers and overcoming the challenge of low biomarker abundance in tissues and serum.

 

2. Optimized Sample Handling and Stability Assurance  

To address protein degradation during sample processing, MtoZ Biolabs employs protease inhibitors and optimized storage conditions to minimize interference in biomarker detection. Additionally, advanced fractionation techniques are used to enhance the detection of protein biomarkers, ensuring protein biomarker integrity and stability, and delivering high-quality research data to clients.

 

3. Comprehensive Protein Biomarker Discovery and Validation  

By integrating untargeted mass spectrometry with specific protein detection technologies, MtoZ Biolabs enables the broad protein biomarkers discovery and provides subsequent validation services. Our streamlined process not only reduces the cost of biomarker development but also minimizes time wasted due to specificity issues or validation failures, offering clients an efficient and cost-effective solution.

 

4. Expert Team with Extensive Experience  

MtoZ Biolabs boasts a professional team of proteomics and protein biomarker discovery experts with extensive experience in mass spectrometry and biomarker research. Our specialists provide tailored experimental designs and in-depth data analysis, ensuring that every project meets the highest scientific standards.

 

Case Study

1. Cerebrospinal Fluid Protein Biomarker Discovery in CLN3

Syndromic CLN3-Batten is a fatal pediatric neurodegenerative disease caused by CLN3 mutations, with CLN3 encoding the lysosomal transmembrane CLN3 protein. Currently, there are no approved therapies targeting CLN3. The prolonged and asynchronous nature of disease manifestation complicates the assessment of potential therapies using clinical progression parameters. Biomarkers are needed as surrogates to measure the progression and efficacy of potential treatments. Researchers conducted a proteomics discovery study using cerebrospinal fluid (CSF) samples from 28 CLN3 patients and 32 age-matched non-CLN3 patients. Proximity Extension Assay (PEA) and untargeted data-dependent mass spectrometry were used to generate an orthogonal list of protein biomarker candidates, analyzing 1,467 proteins. Under the criteria of an adjusted p-value <0.1 and a threshold CLN3/non-CLN3 fold-change ratio of 1.5, PEA identified 54 candidate biomarkers, while MS identified 233 candidates. Some of these, such as NEFL and CHIT1, have previously been associated with other neurological diseases. Others, including CLPS, FAM217B, QRICH2, KRT16, and ZNF333, appear to be novel. Both methods identified 25 candidate biomarkers, including CHIT1, NELL1, and ISLR2, which showed absolute fold-change ratios >2. NELL1 and ISLR2, known to regulate neuronal axonal development, emerge as new candidates for further CLN3 research. In addition to candidate protein biomarker discovery for CLN3 research, this study also provides a comparative evaluation of two large-scale proteomics discovery methods for analyzing CSF.

 



Dang, Do, AN. et al. J Proteome Res. 2023.

Figure 2. Workflow of Cerebrospinal Fluid Protein Biomarker Discovery in CLN3

 

2. Plasma Proteomics Identify Biomarkers Predicting Parkinson’s Disease Up to 7 Years Before Symptom Onset

Parkinson's disease is becoming increasingly prevalent. It progresses from the prodromal phase (characterized by non-motor symptoms such as REM sleep behavior disorder) to the debilitating motor stages. Objective biomarkers for early/prodromal disease stages could enable interventions to slow the underlying neurodegenerative processes. In this study, researchers validated targeted multiplexed mass spectrometry analysis of blood samples from individuals recently diagnosed with motor Parkinson's disease (n = 99), prodromal individuals with isolated REM sleep behavior disorder (two cohorts: longitudinal n = 18 and n = 54), and healthy controls (n = 36). Machine learning models analyzed the expression of eight proteins — granin precursor, mannose-binding lectin serine protease-2, endoplasmic reticulum chaperone-BiP, prostaglandin-H2-D-isomerase, intercellular adhesion molecule-1, complement C3, Dickkopf-WNT signaling pathway inhibitor-3, and plasma protease-C1 inhibitor — accurately identifying all Parkinson's disease patients and classifying 79% of prodromal individuals within seven years prior to motor onset. Many of these biomarkers were correlated with symptom severity. This specific blood test can indicate early molecular events and aid in identifying high-risk participants for clinical trials aimed at slowing or preventing motor Parkinson's disease.

 



Hällqvist, J. et al. Nat Commun. 2024.

Figure 3. Volcano Plot Showing the Protein Expression Differences Between PD and Controls

 

FAQ

Q1: What role does post-translational modification analysis play in protein biomarkers discovery?

Answer: Post-translational modification (PTM) analysis is essential in protein biomarker discovery as it reveals disease-specific changes in protein function, localization, and interactions. PTMs, such as phosphorylation, glycosylation, and acetylation, play critical roles in regulating cellular processes, and their dysregulation often reflects pathological states. By identifying unique PTM patterns, researchers can uncover biomarkers with high specificity and sensitivity, particularly in the early stages of disease. PTM analysis also provides insights into the molecular mechanisms of diseases, aiding in understanding pathogenesis and identifying therapeutic targets. Advanced proteomics technologies enable precise detection of PTMs, even at low abundance, making them valuable for early diagnosis, prognosis, and personalized treatment strategies.

 

Deliverables

1. Comprehensive Experimental Details

2. Materials, Instruments, and Methods

3. Relevant Liquid Chromatography and Mass Spectrometry Parameters

4. The Detailed Information of Protein Biomarker Discovery

5. Mass Spectrometry Image

6. Raw Data