Plasma Proteomics Analysis Service

What is Plasma Proteomics?

Plasma proteomics is a mass spectrometry-based approach for protein identification and quantitative analysis, enabling systematic characterization of protein composition and abundance changes in plasma samples.

Due to the complex protein composition and extremely wide protein abundance range of plasma, plasma proteomics analysis presents several technical challenges. High-abundance proteins, such as albumin and immunoglobulins, may interfere with the detection of lower-abundance proteins. Therefore, optimized sample preparation strategies, sensitive LC-MS/MS analysis, and comprehensive bioinformatics workflows are required to obtain reliable plasma proteome information.

Service Overview

Our plasma proteomics workflow is designed to address the analytical challenges of plasma samples, including high-abundance protein interference, lower-abundance protein detection, and complex biological variation.

Depending on research objectives and sample characteristics, different strategies can be selected:

Research Objective	Our Service
Global plasma protein profiling	Label-free quantitative proteomics / DIA proteomics
Protein abundance comparison between groups	Quantitative proteomics using DIA, LFQ, or TMT workflows
Improved detection of lower-abundance plasma proteins	Optimized plasma proteomics workflows for enhanced protein detection
Biomarker discovery studies	Quantitative plasma proteomics combined with bioinformatics analysis
Large cohort studies	High-throughput quantitative proteomics workflows

Technical Platforms

MtoZ Biolabs utilizes advanced LC-MS/MS platforms for plasma proteomics studies, including:

• Thermo Fisher Orbitrap Exploris 480
• Thermo Fisher Q Exactive series
• Thermo Fisher Orbitrap Astral
• Bruker timsTOF Pro 2

Different platforms and acquisition methods can be selected according to study requirements, including:

• DIA-based quantitative proteomics
• Label-free quantitative proteomics
• TMT-based quantitative proteomics
• Optimized plasma proteomics workflows for improved protein detection and quantitative analysis

Plasma Proteomics Analysis Workflow

1. Plasma Protein Preparation

Plasma samples are processed using optimized preparation strategies according to sample characteristics and analytical requirements.

2. Protein Digestion and Peptide Preparation

Proteins are processed through standardized reduction, alkylation, enzymatic digestion, and purification workflows to generate peptide samples suitable for LC-MS/MS analysis.

3. LC-MS/MS Data Acquisition

Peptide samples are analyzed using high-resolution mass spectrometry platforms with DIA, DDA, or quantitative acquisition strategies according to study objectives.

4. Protein Identification and Quantification

Proteomics data are processed for peptide identification, protein inference, quantitative calculation, and quality control assessment.

5. Bioinformatics Analysis

Differential protein analysis, functional enrichment analysis, pathway analysis, protein interaction analysis, and customized downstream interpretation are performed according to research objectives.

Service Advantages

1. Plasma-Specific Sample Preparation

Customized plasma processing strategies help address high-abundance protein interference and improve protein detection performance in complex plasma samples.

2. Advanced Mass Spectrometry Platforms

High-resolution Orbitrap and timsTOF platforms enable sensitive and reproducible plasma protein identification and quantitative analysis.

3. Flexible Quantitative Strategies

DIA, label-free, and TMT-based workflows are available for different sample scales, experimental designs, and quantitative requirements.

4. Complete Data Analysis Workflow

Integrated analysis from raw MS data processing to biological interpretation supports biomarker discovery and mechanism studies.

Applications of Plasma Proteomics

1. Plasma Protein Profiling

Systematic characterization of plasma protein composition and abundance patterns to understand protein changes under different biological conditions.

2. Comparative Proteomics Research

Comparison of protein expression differences between experimental groups or biological conditions to identify potential candidate proteins.

3. Biomarker Discovery

Identification of potential biomarkers associated with disease states, biological changes, or treatment responses through plasma protein profiling.

4. Biological Mechanism Studies

Investigation of biological processes and molecular pathways associated with protein expression changes through functional and pathway analysis.

5. Treatment Response Studies

Analysis of plasma protein alterations before and after drug treatment or experimental intervention to evaluate molecular responses.

6. Translational Research

Supporting molecular characterization in preclinical and translational research using plasma proteomics data.

Deliverables

Deliverable	Description
Protein identification results	Identified proteins, peptide evidence, and protein annotation information generated from LC-MS/MS analysis
Quantitative protein matrix	Protein abundance matrix for comparative quantitative analysis across different experimental groups
Differential protein analysis	Differentially expressed protein results, statistical analysis, and visualization between comparison groups
Bioinformatics analysis	Functional enrichment analysis, including GO, KEGG, pathway analysis, protein–protein interaction (PPI) analysis, and customized analysis
Quality control analysis	Proteomics data quality assessment, including peptide length distribution, identification score evaluation, mass error analysis, and other QC metrics
Raw data and analysis report	Original mass spectrometry data, processed analysis files, and comprehensive project analysis report

Sample Submission Requirements

Item	Requirement
Sample type	Human plasma, animal plasma, and plasma samples from different experimental conditions
Plasma proteomics projects	Minimum ≥15 μL; 20–50 μL recommended
Plasma PTM proteomics	≥0.5 mL; 1 mL recommended
Anticoagulant	EDTA plasma recommended
Storage	-80°C storage recommended
Freeze-thaw cycles	Minimize repeated freeze-thaw cycles
Sample quality	Avoid severe hemolysis, precipitation, or contamination
Sample information	Provide species, anticoagulant type, experimental groups, and storage information

FAQs

Q1. What is the difference between plasma proteomics and serum proteomics?

Plasma and serum are both derived from blood but differ in preparation and protein composition. Plasma is collected after anticoagulation and retains coagulation-related proteins, while serum is obtained after clotting, which may alter some protein components. The choice between plasma and serum depends on research objectives and experimental design.

Q2. How long does a plasma proteomics project take?

A typical plasma proteomics project requires approximately 3–4 weeks, depending on sample number, workflow complexity, and data analysis requirements.

Q3. Does plasma proteomics support the detection of lower-abundance proteins?

Plasma proteins span a wide abundance range, and high-abundance proteins may interfere with the detection of lower-abundance proteins. Optimized sample preparation strategies, protein extraction workflows, and LC-MS/MS analysis approaches can improve protein detection performance. The final analytical performance depends on sample quality, experimental design, and research objectives.

Contact Us

Planning a plasma proteomics study?

Please provide your sample information and research objectives. Our technical team will help evaluate sample suitability and design an appropriate LC-MS/MS-based plasma proteomics analysis workflow according to your project requirements.