Cellular Proteomics Service

MtoZ Biolabs provides cellular proteomics service for cell samples, integrating optimized cell sample preparation workflows, high-resolution LC-MS/MS analysis, and professional bioinformatics interpretation to systematically characterize cellular protein composition, expression changes, and functional features.

List of Cellular Proteomics Service

Service Type	Research Applications	Available Technologies and Advantages
Discovery Proteomics	Suitable for studies without predefined target proteins that aim to comprehensively characterize cellular protein composition, identify potential protein changes, or establish cellular protein expression profiles.	Based on LC-MS/MS-driven large-scale protein identification and proteomics analysis, enabling global characterization of cellular protein expression patterns.
Quantitative Proteomics	Suitable for studies requiring comparison of protein expression changes between experimental groups, such as before and after drug treatment, gene modification studies, different cellular states, or different experimental conditions.	Supports multiple quantitative strategies, including Label-Free, DIA, and TMT-based quantification. The appropriate approach can be selected based on sample number, experimental design, and quantitative requirements.
PTM Proteomics	Suitable for studies focusing on protein regulation, signal transduction, or functional changes that require analysis of protein modifications beyond protein abundance changes.	Supports analysis of multiple PTMs, including phosphorylation, ubiquitination, acetylation, and glycosylation, providing insights into protein regulation at the modification level.
Interaction Proteomics	Suitable for studies investigating protein interaction networks, including identification of protein complex components, discovery of candidate interacting proteins, and analysis of regulatory networks.	Supports Co-IP/MS, Pull-Down/MS, AP-MS, and XL-MS for protein interaction analysis.

Analysis Workflow

1. Cell Sample Preparation

Cell samples are processed according to cell type, sample condition, and experimental objectives to prepare suitable protein samples for downstream proteomics analysis.

2. Protein Digestion and Peptide Preparation

Extracted proteins are enzymatically digested into peptides, followed by peptide preparation procedures prior to mass spectrometry analysis.

3. LC-MS/MS Analysis

High-resolution LC-MS/MS technology is used for peptide detection to generate cellular proteomics datasets. Different data acquisition and quantitative strategies can be applied according to project requirements.

4. Protein Identification and Quantification

Mass spectrometry data are processed through database searching and quantitative analysis to obtain protein identification results, protein abundance information, and expression changes between experimental groups.

5. Bioinformatics Analysis

Bioinformatics analysis is performed based on protein identification and quantification results, including quality control, differential protein analysis, GO enrichment analysis, KEGG pathway analysis, and protein-protein interaction (PPI) network analysis.

Figure 1. Workflow of Cellular Proteomics

Service Advantages

1. Advanced LC-MS/MS Platforms

Utilizing high-performance Thermo Fisher Orbitrap and Bruker timsTOF mass spectrometry platforms combined with advanced liquid chromatography systems, MtoZ Biolabs provides high-resolution and highly reproducible mass spectrometry analysis for cellular proteomics projects.

2. Optimized Cell Sample Processing

Customized sample preparation workflows are developed for different cell types. Protein extraction strategies are optimized according to cell characteristics and sample conditions to improve protein recovery and downstream LC-MS/MS analysis performance.

3. Support for Complex and Low-Input Cell Samples

Beyond conventional cell samples, MtoZ Biolabs provides workflow evaluation and sample preparation optimization for low-input cells, difficult-to-lyse cells, membrane protein-rich cells, cytoskeleton-rich samples, and samples containing potential interfering components such as high nucleic acid content, high lipid content, residual culture medium/FBS, or detergent contamination.

4. Flexible Experimental Design Support

Based on research objectives, sample characteristics, and experimental designs, MtoZ Biolabs helps select suitable proteomics strategies and supports analysis of various cellular models, including drug treatment, genetic modification, and cell differentiation studies.

Cell Sample Requirements for Proteomics Analysis

Item	Recommendation
Supported Cell Types	Supports various cell types, including adherent cells, suspension cells, cell lines, primary cells, immune cells, and stem cells. In principle, there are no species restrictions. For non-model organisms, species information should be provided to enable selection of appropriate protein databases for identification analysis.
Recommended Sample Submission Format	Supports cell pellets, frozen cells, cell lysates, and extracted protein samples. Suitable proteomics analysis strategies can be evaluated based on sample condition and research objectives.
Required Cell Amount	For cellular proteomics analysis, a minimum of approximately 5 × 10⁶ cells/sample is recommended, while approximately 1 × 10⁷ cells/sample is preferred to achieve more reliable protein identification and quantification results.
Cell Collection Requirements	Cells should be washed with PBS before collection to remove residual culture medium and FBS. For adherent cells, trypsin treatment should be carefully controlled, and residual trypsin should be minimized to reduce potential effects on downstream proteomics analysis.
Storage and Transportation	Cell samples should preferably be snap-frozen in liquid nitrogen or stored at -80°C and shipped on dry ice. Repeated freeze-thaw cycles should be avoided, with no more than 1–2 cycles recommended to minimize protein degradation and sample variation.

Deliverables

Deliverable	Analysis Content
Data Quality Control	Evaluation of mass spectrometry data quality, including data stability and sample analysis quality assessment.
Protein Identification and Quantification	Provides protein identification and quantitative analysis results, including cellular protein composition and abundance information.
Sample Correlation and Multivariate Analysis	Includes sample correlation analysis, principal component analysis (PCA), and clustering analysis to evaluate sample relationships and overall expression patterns among experimental groups.
Differential Protein Analysis	Statistical analysis of protein expression changes between experimental groups to identify differentially expressed proteins.
Functional Enrichment and Pathway Analysis	Includes GO enrichment analysis and KEGG pathway analysis to interpret biological processes, functional categories, and pathways associated with differential proteins.
Protein-Protein Interaction (PPI) Network Analysis	Constructs PPI networks based on protein interaction information to analyze protein associations and potential functional relationships.

Note: Standard cellular proteomics analysis does not include subcellular localization analysis. Additional subcellular localization analysis can be performed separately if required.

FAQs

Q1. What is the typical turnaround time for cellular proteomics analysis?

The typical turnaround time for standard cellular proteomics projects is 3–4 weeks. The timeline may vary depending on sample number, experimental design, and analysis requirements. Complex projects, such as TMT-based quantitative proteomics or PTM proteomics, may require 4–5 weeks.

Q2. Do I Need to Extract Proteins Before Submitting Cell Samples?

No. We accept cell pellets, frozen cells, cell lysates, and extracted protein samples. Cell pellets are recommended, allowing flexible optimization of protein extraction and downstream analysis workflows.

Q3. What Factors Should Be Considered Before Starting a Cellular Proteomics Project?

Project design should consider research objectives, experimental groups, sample quality, and analysis requirements. Providing information about treatment conditions and expected outcomes helps select the most suitable proteomics strategy.

Related Services

Start Your Cellular Proteomics Project

From cell sample preparation to LC-MS/MS-based protein analysis and bioinformatics interpretation, MtoZ Biolabs provides comprehensive cellular proteomics service to support your research.

Contact us to discuss your sample requirements and select the most suitable proteomics strategy for your project.