Label-Free DIA Quantitative Proteomics

What Is Label-Free DIA Quantitative Proteomics?

Label-Free DIA Quantitative Proteomics combines label-free relative quantification with data-independent acquisition. Unlike label-based approaches such as TMT, each sample is analyzed separately without isotope or isobaric labeling, while DIA systematically acquires fragment-ion data across predefined precursor windows.

Protein abundance is compared using quantitative peptide signals extracted across LC-MS/MS runs. Because DIA repeatedly samples the defined mass range rather than selecting only a subset of precursor ions, the approach supports consistent protein quantification across multiple samples with fewer missing values than conventional DDA-based label-free workflows.

When This Service Is a Good Fit

Label-Free DIA is a good fit when your study needs flexible, reproducible protein quantification across multiple samples without labeling.

• You have a large sample set.

Label-Free DIA is particularly suitable for studies with more than 20 samples.

• You may add samples later.

New samples can be incorporated without redesigning a predefined multiplex.

• You need consistent comparison across groups.

DIA provides systematic peptide sampling and helps reduce missing quantitative values across repeated LC-MS/MS runs.

• You are comparing multiple conditions or time points.

The workflow is well suited to multi-group, treatment-response, longitudinal, and time-course studies.

Label-Free DIA can also be useful when available protein amounts make labeling workflows less practical. If your study involves a small number of samples and requires tightly controlled multiplexed comparison, TMT may be worth considering instead. For absolute quantification of predefined targets, PRM or MRM is more appropriate.

Hamzelou S. et al. Critical Reviews in Biotechnology. 2023.

Figure 1. Workflow of three acquisition modes of quantitative proteomics

Label-Free DIA Quantitative Proteomics Service at MtoZ Biolabs

MtoZ Biolabs provides Label-Free DIA Quantitative Proteomics Service for large-scale protein identification, relative quantification, differential protein analysis, and downstream biological interpretation.

The service supports tissues, cells, microorganisms, biofluids, and other biological samples with an available reference database. DIA acquisition is performed on high-resolution Orbitrap Exploris 480 or Astral platforms, followed by DIA-NN processing for protein identification and quantitative analysis.

MtoZ Biolabs can tailor the analytical strategy to sample type, sample number, group design, available material, and planned comparisons. Quantitative results can be extended to statistical analysis, functional annotation, and pathway enrichment.

Workflow of Label-Free DIA Quantitative Proteomics Service

1. Protein Extraction and Digestion

Proteins are extracted, reduced, alkylated, and enzymatically digested into peptides.

2. LC Separation and DIA Acquisition

Peptides are separated by liquid chromatography and analyzed by high-resolution mass spectrometry using DIA acquisition.

3. DIA Data Processing

DIA-NN is used for peptide and protein identification, signal extraction, and relative quantification.

4. Differential Protein Analysis

Protein abundance is compared across predefined groups to identify differential proteins and evaluate quantitative consistency.

5. Bioinformatics Analysis

Differential proteins are further evaluated through visualization, functional annotation, pathway enrichment, and other applicable analyses.

Figure 2. Workflow of Label-Free DIA Quantitative Proteomics Service

Why Choose MtoZ Biolabs?

1. High-Resolution DIA Platforms

Orbitrap Exploris 480 and Astral platforms support high-resolution DIA proteome analysis.

2. One-Stop Service

MtoZ Biolabs integrates sample preparation, DIA LC-MS/MS, quantitative analysis, bioinformatics, and reporting.

3. High Throughput and Cost-Effective

Eliminates the need for expensive isotope labeling. Compared to TMT/iTRAQ labeling methods, it offers higher sample throughput, making it ideal for large-scale proteomics studies.

4. Enhanced Detection of Low-Abundance Proteins

The full-scan DIA acquisition mode ensures that all peptide ions are collected. Combined with deep-learning-based predicted spectral libraries, it optimizes data processing and improves the detection rate of low-abundance proteins.

5. High Quantitative Accuracy and Reproducibility

Label-Free DIA overcomes the stochastic sampling limitations of DDA-based approaches, resulting in higher data reproducibility.

6. One-Time-Charge

Our pricing is transparent, no hidden fees or additional costs.

Applications

The Label-Free DIA Quantitative Proteomics Service can support a broad range of discovery and comparative proteomics studies.

1. Biomarker Candidate Discovery

Identify differential proteins for subsequent candidate prioritization and targeted verification.

2. Disease Mechanism Research

Characterize protein abundance changes and biological pathways associated with disease models or phenotypes.

3. Drug Response and Pharmacology

Compare proteomic responses across treatment groups, doses, or time points.

4. Cell Signaling Research

Analyze coordinated protein changes associated with signaling pathways and cellular responses.

5. Plant and Microbial Research

Compare proteomic responses across environmental conditions, developmental stages, or experimental treatments.

Sample Submission Suggestions

1. Sample Amount

The following values are general recommendations for Label-Free DIA quantitative proteomics. Exact requirements may vary with sample characteristics and analytical objectives. Please contact MtoZ Biolabs for study-specific submission guidance.

Sample Type	Recommended Quantity	Minimum Quantity
Animal Tissue	20-100 mg	10-50 mg
Plant Tissue	0.1-5 g	0.05-2 g
Cell Pellet	1 × 10⁷ cells	2 × 10⁶ cells
Microbial Samples	50 mg or 50 μL	20 mg or 20 μL
Serum/Plasma	10-50 μL	5-25 μL
Urine	1 mL	0.5 mL
Cerebrospinal Fluid	0.1 mL	0.05 mL
Culture Supernatant	10 mL	5 mL
Extracted Protein	≥50 μg	>20 μg

For extracted protein, a concentration above 0.5 μg/μL is recommended for analysis.

2. Storage and Shipping

• Samples should be stored at -80°C when applicable and shipped on dry ice. 
• Avoid repeated freeze-thaw cycles and keep collection and processing conditions consistent across experimental groups. 
• Extracted protein solutions should contain minimal salt and detergent, and the buffer composition should be provided before submission.

Deliverables

The Label-Free DIA Quantitative Proteomics Service typically provides:

1. Protein and Peptide Identification

Protein and peptide identification results with supporting quantitative information.

2. Relative Protein Quantification

Protein abundance matrices across submitted samples and experimental groups.

3. Differential Protein Analysis

Statistical comparison of protein abundance changes between predefined groups.

4. Quality Control and Visualization

Quantitative quality assessment, PCA, clustering heatmaps, volcano plots, and other applicable figures.

5. Functional Analysis

GO annotation, KEGG pathway enrichment, PPI analysis, and other database-supported analyses when applicable.

6. Raw Data and Final Report

Raw mass spectrometry files, processed result tables, and a structured analysis report.

Start Your Project with MtoZ Biolabs

Planning a large-cohort or comparative proteomics study? Share your species, sample type, sample number, group design, available sample amount, planned comparisons, and research objective with MtoZ Biolabs.

MtoZ Biolabs provides free project consultation for Label-Free DIA Quantitative Proteomics Service. We can discuss sample suitability and quantitative strategy and provide a project quote based on your specific study requirements.