Top-down Proteomics Analysis Service

The top-down proteomics analysis service is a mass spectrometry-based proteomics approach that analyzes intact proteins without complete digestion. This method enables the study of protein bioactive conformations, post-translational modification (PTM) types, and modification sites. The emergence of high-sensitivity, high-resolution mass spectrometers and advancements in separation technologies have paved the way for high-throughput top-down proteomics. Instruments such as Fourier transform (FT) mass spectrometers, Fourier transform ion cyclotron resonance (FTICR) mass spectrometers, and Orbitrap mass spectrometers have enabled isotopic resolution of intact proteins for the first time. These instruments remain among the highest-resolution mass spectrometers available today. Furthermore, the application of multidimensional separation techniques, such as orthogonal separation platforms (RPLC), capillary electrophoresis (CE), and size-exclusion chromatography (SEC) coupled with tandem mass spectrometry, has significantly improved sample separation efficiency. This allows for a more in-depth characterization of protein conformations at the intact protein level.

 

With technological advancements, top-down proteomics analysis service faces multiple challenges. Key research directions include:

 

1. Protein Solubilization: For membrane proteins and extracellular proteins that are difficult to extract and solubilize, surfactants can effectively dissolve membrane proteins. However, due to mass spectrometry incompatibility, multiple washing steps are required, leading to significant protein loss. Developing novel mass spectrometry-compatible surfactants has become a major focus of research.

 

2. High Dynamic Range: The protein dynamic range (10⁸–10¹²) in proteomics makes detecting low-abundance protein conformations highly challenging. Thus, developing affinity enrichment strategies for low-abundance proteins is a primary approach to overcoming the challenge of high dynamic range.

 

3. Protein Complexity: The complexity of the proteome remains a significant challenge for top-down proteomics. The broad molecular weight distribution of proteins within the proteome spans over five orders of magnitude, making comprehensive top-down coverage difficult. This necessitates intact protein separation before mass spectrometry analysis. Proteins can first be fractionated by molecular weight and further separated based on hydrophobicity to detect a greater number of proteins.

 

4. Data Analysis: The data analysis process for top-down proteomics analysis service is complex and labor-intensive, posing a major barrier for new users. Therefore, developing software optimized for top-down deconvolution and data processing is critical.

 

5. High Throughput: High-throughput omics technologies are becoming a driving force in precision medicine, enabling highly detailed molecular characterization of patients. However, the sheer number of required samples necessitates the development of higher-throughput experimental workflows.

 



Melby, J A. et al. Journal of the American Society for Mass Spectrometry, 2021.

Figure 1. Challenges of Top-down Proteomics.

 

Services at MtoZ Biolabs

Leveraging multiple Orbitrap series mass spectrometers, MtoZ Biolabs provides top-down proteomics analysis service that maintain high resolution, high accuracy, and high sensitivity while ensuring high-throughput sample processing and high-quality data acquisition. Utilizing advanced characterization software, MtoZ Biolabs can efficiently analyze complex mass spectrometry data and generate detailed reports tailored to research needs.

 

Analysis Workflow

 



Xu, T. et al. Anal Methods, 2024.

Figure 2. Flow Chart of Top-down Proteomics Detection.

 

Service Advantages

1. Multiple Mass Spectrometers

MtoZ Biolabs operates multiple high-resolution Thermo mass spectrometers, ensuring fast data acquisition and highly accurate service outcomes.

 

2. Transparent Pricing

Our pricing structure is transparent, with no hidden or additional fees.

 

3. High Data Quality

MtoZ Biolabs employs optimized experimental protocols to deliver high-quality data along with comprehensive data reports and graphical representations.

 

4. Customized Research Solutions

We offer personalized services based on sample characteristics, addressing diverse research questions and experimental needs.

 

Sample Submission Suggestions

1. Sample Types

Tissue samples, Cell samples.

 

2. Sample Amount

Sample quantity requirements vary based on the sample type.

Note: If you have any special requests or need assistance with sample preparation, please contact us.

 

Applications

1. Structural Analysis

Top-down proteomics analysis service enables detailed structural characterization of proteins, including the detection of variants and post-translational modifications (PTMs).

 

2. Biomarker Discovery

Comparative top-down proteomics allows for the identification of potential biomarkers by analyzing protein expression differences across various samples.

 

3. Drug Development

Top-down proteomics analysis service helps evaluate drug-induced changes in protein expression, assisting researchers in understanding drug efficacy.

 

Case Study

1. Challenges in Top-Down Proteomics and the Characterization of True Protein Isoforms

Top-down proteomics analysis service is designed to identify and analyze intact proteins extracted from biological samples. Accurately characterizing true protein isoforms requires determining the primary amino acid sequence and precisely mapping mass shifts to their specific locations within the protein sequence. By utilizing top-down proteomics data, researchers can comprehensively elucidate protein isoforms, providing critical insights into their biological significance and functional roles.

 



Allen Po. et al.Journal of Proteome Research, 2023.

Figure 3. Top-down Proteomics Flowchart.

 

Deliverables

1. Experimental Process

 

2. Materials, Instruments, and Methods

 

3. Total Ion Chromatogram & Quality Control Assessment

 

4. Data Analysis 

 

5. Raw Data Files

 

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. Our ultimate aim is to provide more rapid, high-throughput, and cost-effective analysis, with exceptional data quality and minimal sample consumption. Free project evaluation, welcome to learn more details!