DDA Quantitative Proteomics
DDA Quantitative Proteomics
What Is DDA-Based Quantitative Proteomics?
MetwareBio’s DDA-based quantitative proteomics service is powered by the Bruker timsTOF HT platform, which features a dual TIMS design and the advanced PASEF® (Parallel Accumulation–Serial Fragmentation) acquisition mode. This architecture significantly improves ion transmission efficiency and sequencing speed. The addition of ion mobility enables true four-dimensional data acquisition—including retention time, m/z, ion mobility, and intensity—greatly enhancing resolution and peptide identification accuracy. This high-performance workflow supports deep proteome coverage, robust label-free quantification, and is ideally suited for mechanistic studies, protein interaction mapping, and focused biological discovery requiring precision and depth.
Why Choose MetwareBio for DDA Proteomics?
DDA Proteomics Deliverables
DDA Proteomics Project Experience
Number of proteins identified from various medical and plant samples via DDA quantitative proteomics
Flexible Applications Across Biology, Agriculture, and Environment
Mass spectrometry-based quantitative proteomics enables in-depth profiling of protein expression changes in human diseases. It supports biomarker discovery, mechanism-of-action studies, and therapeutic target identification in oncology, neurology, metabolic disorders, and precision medicine.
Proteomics reveals the functional dynamics of microbial systems, including protein expression under stress, virulence factor regulation, and metabolic adaptation. It is also a powerful tool for studying host–pathogen interactions, immune evasion, and microbial responses in infection models.
In plant systems, proteomics facilitates the investigation of developmental processes, plant hormone signaling, and stress responses to drought, salinity, and pathogens. These insights aid in molecular breeding, trait improvement, and plant systems biology.
Quantitative proteomics is increasingly used in environmental biology to study organismal responses to pollutants, climate stress, and habitat changes. It provides valuable molecular indicators for ecotoxicology, climate adaptation, and ecosystem monitoring.
By integrating proteome profiling with genomics and transcriptomics, proteomics enables systems-level analysis of gene function, regulatory networks, and biological pathways across different species, tissues, and conditions.
DDA Quantitative Proteomics Case study
DDA Proteomics Reveals Functional Differences in Egg White Components
In a 2023 study published in Food Research International, researchers used MetwareBio’s label-free DDA quantitative proteomics service to investigate the protein composition of chicken egg white and its three major structural components: thin egg white (TNEW), thick egg white (TKEW), and chalaza (CLZ). Through high-resolution proteomic profiling, the study identified 173 proteins and revealed distinct expression patterns among the components. Key structural and functional proteins—such as mucin-5B, mucin-6, and lysozyme—were significantly enriched in TKEW and CLZ, offering molecular insight into their viscosity, gel-like properties, and functional roles in egg structure.
This case highlights the value of MetwareBio’s DDA proteomics platform in food science research, providing accurate protein-level data to support the characterization of functional food components, and enabling scientific advances in product development, ingredient optimization, and processing innovation.
Protein Composition Differentiation Across Egg White Components (Pu et al., 2023)
Sample Requirements of DDA Quantitative Proteomics
| Sample Type | Samples | Recommended Sample Size | Minimum Sample Size |
| Human/Animal Tissue | Normal tissues (heart, liver, spleen, lungs, intestines, kidneys, etc.) | 50mg | 5mg |
| Fatty tissue | 200mg | 100mg | |
| Brain tissue | 50mg | 5mg | |
| Bone | 1g | 200mg | |
| Hair | 500mg | 200mg | |
| Skin | 200mg | 100mg | |
| Plant Tissue | Young tissue (young leaf, seedling, petal, etc.) | 200mg | 100mg |
| Mature tissue (root, stem, fruit, pericarp, etc.) | 1g | 500mg | |
| Pollen | 40mg | 15mg | |
| Liquid Samples | Serum/Plasma (without removing high abundance proteins) | 20μL | 5μL |
| Serum/Plasma (remove high abundance proteins) | 200μL | 100μL | |
| Joint fluid, Lymph fluid | 200μL | 100μL | |
| Aqueous humor, Vitreous body | 300μL | 200μL | |
| Cerebrospinal fluid | 200μL | 100μL | |
| Ascites, Follicular fluid | 100μL | 50μL | |
| Alveolar lavage fluid (BALF) | 1ml | 500μL | |
| Amniotic fluid | 1ml | 500μL | |
| Milk | 20μL | 5μL | |
| Urine | 10mL | 5mL | |
| Saliva (mammals) | 1ml | 500μL | |
| Fermentation broth, Bacterial solution | 10ml | 5ml | |
| Cellular supernatant | 25mL | 10ml | |
| Exosome (sediment) | 25μl | 15μL | |
| Microorganisms | Bacteria | 200mg | 100mg |
| Fungi | 300mg | 150mg | |
| Cells | Primary Cells | 3×10^6 | 1×10^6 |
| Transmissible cells | 2×10^6 | 1×10^6 | |
| Sperm, Platelets | 2×10^7 | 1×10^7 | |
| Protein | Protein | 100μg | 50μg |
FAQ on DDA Quantitative Proteomics Analysis
DDA is a mass spectrometry-based acquisition strategy that selects the most intense precursor ions from each MS1 scan for fragmentation in MS2. This approach enables high-confidence peptide identification and is widely used for in-depth label-free proteomics and protein quantification.
DDA (Data-Dependent Acquisition) selectively fragments the most abundant precursor ions in each scan cycle, providing high-quality spectra ideal for in-depth protein identification. In contrast, DIA (Data-Independent Acquisition) fragments all ions within a predefined mass range, enabling broader but less targeted detection. DDA is ideal when precise identification and spectrum quality are prioritized.
For a more detailed comparison and to learn when to use each technique, check out our DDA vs. DIA: The Essential Guide to Label-Free Quantitative Proteomics
DDA can detect low-abundance proteins, especially with optimized sample preparation and high-sensitivity instruments. However, for samples with a wide dynamic range or highly complex matrices, DIA may offer more comprehensive coverage.
Depending on sample type and quality, DDA workflows typically identify 5,000–8,000 proteins per run. Deep proteome coverage is achievable with high-resolution instruments and extended gradients.
Our DDA proteomics workflow is powered by Bruker timsTOF HT mass spectrometry, utilizing the TIMS-PASEF (Trapped Ion Mobility Spectrometry - Parallel Accumulation Serial Fragmentation) acquisition mode. This advanced technology enables high-speed, high-sensitivity, and deep proteome coverage, making it ideal for large-scale, label-free quantitative proteomics.
We accept a wide range of biological matrices, including cell lines, tissues, blood (serum/plasma), plant samples, and microbial cultures. Contact us for tailored sample preparation guidance.
For most studies, we recommend submitting 50–100 μg of total protein. However, the required amount may vary depending on the sample type (e.g., tissue, plasma, plant material). Please refer to our Sample Requirements page for detailed guidelines, or contact our team for personalized advice.
Reference
Pu, J., Zhao, B., Liu, X., Li, S., Wang, B., Wu, D., Wang, J., & Geng, F. (2023). Quantitative proteomic analysis of chicken egg white and its components. Food research international (Ottawa, Ont.), 170, 113019. https://doi.org/10.1016/j.foodres.2023.113019
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