DDA Quantitative Proteomics

Accurate qualitative and quantitative analysis with excellent data stability.
High sensitivity with more low-abundance proteins detection.
High throughput, suitable for cohort studies with large sample amounts.
Small sample size, suitable for clinical projects with limited sample availability.

Technology Introduction

Label-free quantitative proteomics technology utilizes the unique dual TIMS design of the timsTOF series mass spectrometer and the ddaPASEF® acquisition mode to achieve protein qualitative and quantitative analysis. The ddaPASEF acquisition mode combines data-dependent acquisition (DDA) with PASEF (Parallel Accumulation–Serial Fragmentation) technology. In the ddaPASEF acquisition mode, precursor ions with high ion intensity are selected from the MS1 spectra to set the mass spectrum scan range to specific narrow mass windows. Subsequently, the selected target precursor ions are sequentially fragmented in the MS2 spectra, recording their retention time, mass-to-charge ratio, ion intensity, and ion mobility. Finally, protein qualitative and quantitative analysis is conducted based on this information. Label-free quantitative proteomics technology offers simplicity in operation, independence from expensive labeling reagents, reduced data analysis complexity, and approximately 12-fold improved detection sensitivity compared to traditional label-free methods.

Applications of DDA Quantitative Proteomics

Medical Research
Disease Mechanisms, Molecular Diagnosis, Biomarker Development, Drug Targets.
Animal Research
Reproductive Development, Disease Mechanisms, Nutrient Metabolism, Animal Toxicology.
Plant Research
Reproductive Development, Abiotic Stress Response, Disease Resistance, Crop Improvement.
Pathogenic Mechanisms, Drug Resistance, Stress-Related Proteins Screening, Environmental Impact Mechanisms.

Project Experience


Average number of proteins identified
Project Workflow
Sample Shipment
Protein Extraction
Trypsin Digestion
Data Acquisition
Database Search
Data Analysis

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 30μg
Biological duplicates: A minimum of 3 replicates is required; 3-6 replicates for animal samples; 6-10 for clinical samples.


Please submit a detailed description of your project. We will provide you with a customized project plan metabolomics services to meet your research requests. You can also send emails directly to support-global@metwarebio.com for inquiries.
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