Low-Input Quantitative Proteomics
Low-Input Quantitative Proteomics
What Is Low-Input Proteomics?
MetwareBio's Low-Input (Micro-DIA) Quantitative Proteomics Service overcomes this limitation by integrating the SISPROT (Single-Tube Sample Preparation for Proteomics) technology, which performs protein extraction and enzymatic digestion in a streamlined, single-tube workflow. This minimizes handling steps and sample loss while preserving protein recovery and digestion efficiency. Combined with diaPASEF® acquisition on the Bruker timsTOF platform, this workflow delivers deep proteome coverage, high sensitivity, and excellent reproducibility, even from microgram-scale inputs. The micro-DIA platform is ideally suited for low-input clinical studies, microenvironment-specific proteomics, and high-throughput small-sample investigations, expanding the reach of proteomics into challenging yet highly valuable biological systems.
Schematic workflow of 3D-SISPROT for deep proteome profiling (Chen et al., 2017)
Why Choose MetwareBio for Low-Input Proteomics





Low-Input DIA Proteomics Deliverables
Extensive Low-Input Proteomics Experience
Number of proteins identified from various medical and animal samples via micro-DIA assay
Applications of Low-Input DIA Proteomics Across Life Sciences
Ideal for low-input clinical samples such as needle biopsies, fine-needle aspirates, or patient-derived organoids. Enables biomarker discovery, treatment response profiling, and disease subtype analysis in oncology, immunology, and precision medicine.
Supports proteomic analysis of microdissected tissues, developing organs, or rare cell populations in plants. Facilitates research on hormone signaling, stress adaptation, and developmental regulation, even from minimal plant material.
Applicable to low-biomass microbial cultures, co-culture models, or specific strains within microbial communities. Enables investigation of metabolism, virulence regulation, and antibiotic resistance mechanisms in microbiology and synthetic biology.
Enables proteomic profiling of small model organisms (e.g., zebrafish embryos, Daphnia, nematodes) exposed to environmental stressors. Supports toxicological assessment, stress pathway analysis, and biomarker identification in ecological and pollution research.
Sample Requirements for Low-Input Quantitative Proteomics Service
Sample Type | Samples | Recommended Sample Size | Minimum Sample Size |
Tissue Samples | Fresh or frozen tissue | 1 mg | 0.2 mg |
Cryosectioned tissue | 3 | 1 | |
FFPE sections | 5 | 2 | |
Liquid Samples | Plasma / serum | 1μL | / |
Cells | Mammalian cells (~250 pg protein per cell) |
10000 | 2000 |
Oocytes | 10 | 5 |
Biological duplicates: A minimum of 3 replicates is required; 3-6 replicates for animal samples; 6-10 for clinical samples. For other sample types not listed, please contact us for consultation.
FAQ on Low-Input DIA Proteomics
Our Micro-DIA workflow is optimized for small sample proteomics, enabling reliable analysis from as little as 1–10 µg of total protein, ideal for clinical biopsies, sorted cells, or organoids.
Unlike conventional workflows, SISPROT technology integrates protein extraction and tryptic digestion in a single tube. This minimizes handling steps and improves protein recovery in low-input proteomics applications.
Yes. Our workflow is compatible with challenging sample types including FFPE sections, microdissected tissues, and fine-needle aspirates, making it ideal for clinical proteomics.
Despite using less starting material, our platform powered by diaPASEF acquisition achieves high proteome coverage, quantitative accuracy, and reproducibility, with thousands of proteins reliably identified.
We include comprehensive QC analysis—such as peptide yield checks, PCA, sample correlation, and technical replicate assessment—to ensure high-quality results from low-yield input.
Yes. Protein quantification data from Micro-DIA can be seamlessly integrated with metabolomics, lipidomics, or transcriptomics, supporting multi-omics systems biology studies.
Reference
Chen, W., Adhikari, S., Chen, L., Lin, L., Li, H., Luo, S., Yang, P., & Tian, R. (2017). 3D-SISPROT: A simple and integrated spintip-based protein digestion and three-dimensional peptide fractionation technology for deep proteome profiling. Journal of chromatography. A, 1498, 207–214.https://doi.org/10.1016/j.chroma.2017.01.033
Next-Generation Omics Solutions:
Proteomics & Metabolomics
Ready to get started? Submit your inquiry or contact us at support-global@metwarebio.com.