MtoZ Biolabs offers the advanced 4D-DIA Quantitative Proteomics Analysis Service combining Data-Independent Acquisition (DIA) with ion mobility spectrometry (IMS) to deliver deeper, more precise, and highly reproducible proteomic data. Our service uses cutting-edge technology to capture, identify, and quantify proteins across diverse sample types, enabling insightful biological interpretation for discovery, biomarker validation, and mechanistic studies.

What Is 4D-DIA Quantitative Proteomics?

4D-DIA Quantitative Proteomics is an advanced technique that incorporates a fourth dimension, ion mobility, into the traditional DIA workflow. This approach enhances peptide separation by adding an extra layer of ion analysis based on the collision cross-section (CCS), providing more comprehensive data compared to conventional DIA. By utilizing the TIMS (Trapped Ion Mobility Spectrometry) technology, 4D-DIA improves data acquisition, peptide detection, and quantification, especially for complex proteomic samples.

Unlike conventional DIA, which focuses on mass-to-charge ratios (m/z) and intensity for quantification, 4D-DIA leverages ion mobility to distinguish peptides with similar m/z but different shapes or conformations. This additional layer of separation allows for enhanced sensitivity, better resolution, and reduced interferences, especially in highly complex samples.

Principle of 4D-DIA Quantitative Proteomics Analysis

4D-DIA integrates traditional DIA with ion mobility spectrometry, offering four key dimensions for proteomic analysis:

1. Retention Time (RT)

The first dimension where peptides are separated based on their hydrophobicity in liquid chromatography (LC).

2. M/Z (Mass-to-Charge Ratio)

The second dimension, where peptides are detected by their mass-to-charge ratio during the MS1 scan.

3. Ion Mobility (CCS)

The third dimension, where peptides are separated based on their shape and size using ion mobility spectrometry. The collision cross-section (CCS) is a measure of the peptide's geometry and size in the gas phase, which enhances peptide separation.

Mucha, E. et al. Chem Sci. 2019.

Figure 1. Principle of Ion Mobility Spectrometry (IMS)

4. Intensity

The fourth dimension, where peptides are quantified based on their intensity, which reflects their abundance in the sample.

4D-DIA Quantitative Proteomics Analysis Service at MtoZ Biolabs

MtoZ Biolabs offers comprehensive 4D-DIA Quantitative Proteomics Analysis using the high-resolution mass spectrometry platform, combined with nano-LC systems to provide high sensitivity and reproducibility for proteomics projects. Our workflow integrates the latest in ion mobility and DIA technologies to enhance proteome coverage and quantitative robustness. You only need to provide your experimental objectives and send us your samples. MtoZ Biolabs takes care of everything, from sample preparation to LC-MS/MS analysis, data processing, and bioinformatics interpretation.

Why Choose MtoZ Biolabs

1. Superior Sensitivity and Resolution

The addition of ion mobility separation allows for higher peptide resolution, enabling the detection of low-abundance proteins that would be missed with traditional DIA or DDA methods.

2. High Reproducibility

Systematic and unbiased data acquisition ensures consistent and reproducible results across multiple samples, improving confidence in large cohort studies or longitudinal analyses.

3. Improved Quantification Accuracy

The integration of ion mobility with DIA provides better ion utilization and higher accuracy in quantifying proteins, especially for complex proteomes.

4. Flexible Experimental Design

Supports a wide range of study designs, including multi-group comparisons, time-course studies, and dose-response assessments, making it ideal for both discovery and targeted proteomics.

5. Experienced Proteomics Team

An experienced team of proteomics specialists oversees each project, optimizing experimental setup and analysis to match your specific scientific objectives.

Applications of 4D-DIA Quantitative Proteomics Analysis Service

4D-DIA Quantitative Proteomics at MtoZ Biolabs can be applied across a broad spectrum of biological research areas:

1. Biomarker Discovery and Validation

Identify and validate protein biomarkers for early diagnosis, disease progression monitoring, and therapeutic efficacy evaluation.

2. Disease Mechanism and Pathway Analysis

Investigate complex disease mechanisms, uncover novel targets, and map regulatory networks associated with diseases such as cancer, neurodegeneration, and cardiovascular conditions.

3. Drug Development and Pharmacodynamics

Monitor global proteomic responses to drug treatments, identifying mechanism of action, resistance, or off-target effects.

4. Longitudinal and Multi-group Studies

Track protein changes over time or across experimental groups in clinical, preclinical, or model systems for better understanding of disease progression or treatment responses.

5. Functional Proteomics

Assess post-translational modifications (PTMs) and protein interactions, shedding light on the regulatory mechanisms driving cellular functions.

6. Clinical and Translational Research

Apply 4D-DIA for large-scale proteomics studies in clinical cohorts, enabling better patient stratification, personalized medicine, and precision oncology applications.

FAQ

Q1: What types of samples are suitable?

We support a wide range of samples for 4D-DIA Quantitative Proteomics, including:

• Cell pellets from adherent or suspension cell lines

• Primary cells from blood, bone marrow, or tissues

• Fresh frozen tissues or biopsies

• Biofluids such as serum, plasma, CSF, and urine

• Preclinical animal samples and other complex biological matrices

For unusual sample types or low-yield materials, please contact MtoZ Biolabs in advance for customized preparation guidance.

Q2: How should I prepare my samples?

• Use clean, low binding tubes and avoid repeated freeze thaw cycles
• Snap freeze samples after collection and store at −80 °C
• Avoid strong detergents, very high salt, and large amounts of reducing agents
• Ship on dry ice with a clearly labeled sample list

Detailed requirements and recommendations can be found in the Sample Submission Guidelines for Proteomics.

Q3: What is the service general workflow?

Q4: What data formats are provided?

• Raw 4D-DIA LC-MS/MS files in instrument specific formats.
• Peptide and protein identification and quantification tables in .xlsx or .csv, including normalized intensities and group comparisons.
• Statistical and functional analysis outputs such as differential expression and pathway enrichment in spreadsheet formats.
• Publication ready figures, including heatmaps, volcano plots, and PCA or clustering plots, in high resolution PNG or TIFF.
• A structured PDF report summarizing workflow, QC metrics, main quantitative results, and key biological interpretations.
• Additional formats or custom analysis outputs can be provided on request.

Start Your Project with MtoZ Biolabs

Contact MtoZ Biolabs to discuss your study requirements, receive a tailored experimental plan, and start your 4D-DIA Quantitative Proteomics project. Our team of experts is here to guide you from sample submission to actionable data interpretation.