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Low-Input Quantitative Proteomics

Low-Input Quantitative Proteomics

SISPROT One-Pot Workflow for Minimal Sample Loss
Advanced 4D LC-MS/MS Platform with High Sensitivity
Deep Proteome Coverage from Ultra-Low Inputs
High Throughput and Reproducibility in Large Sample Sets

What Is Low-Input Proteomics?

Proteomics analysis of clinical or rare samples is often limited by insufficient protein input. Traditional workflows involve multiple steps—protein extraction, digestion, and cleanup—that can lead to significant sample loss and poor recovery, making standard DIA-based proteomics unsuitable for low-input scenarios. This presents a major barrier for studies using biopsy tissues, sorted cells, laser-microdissected regions, or other precious samples where only nanogram to low-microgram quantities are available.

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

Tailored for Low-Input and Precious Samples
Designed specifically for micro-scale samples such as biopsies, sorted cells, organoids, and other rare or clinical specimens, our workflow requires as little as 1–10 µg of total protein. The use of SISPROT single-tube processing minimizes sample loss during extraction and digestion, ensuring high recovery and compatibility with limited or irreplaceable materials.
Ultra-Fast Acquisition with TIMS + PASEF
Powered by Bruker timsTOF HT and advanced TIMS-PASEF® technology, our platform enables rapid and high-resolution ion separation and acquisition, ensuring confident protein identification even in highly complex samples.
Deep Proteome Coverage
With optimized DIA workflows, our platform is capable of quantifying over 10,000 proteins, depending on sample type and database quality — enabling sensitive detection of low-abundance proteins often missed by conventional approaches.
High Sensitivity, Accuracy, and Throughput
By combining ion mobility separation with broad precursor sampling, our DIA pipeline delivers high analytical sensitivity without sacrificing quantification accuracy, ideal for capturing subtle yet biologically meaningful protein changes.
Excellent Reproducibility for Large-Scale Studies
DIA captures fragment spectra from all ions within defined m/z windows, ensuring unbiased and comprehensive data acquisition across replicates, time points, and cohorts—making it ideal for clinical and longitudinal studies.
Comprehensive Bioinformatics & Expert Support
We provide fully processed datasets with differential expression, clustering, enrichment, and pathway analysis, along with expert support from experimental design through to biological interpretation, accelerating your research outcomes.
Multi-Omics Integration Ready
As a leading multi-omics CRO, MetwareBio offers not only advanced proteomics, but also fully integrated metabolomics, lipidomics, and transcriptomics services—enabling comprehensive multi-omics analysis and systems-level biological insights through a unified, end-to-end platform.
Workflow for DIA-Based Low-Input Proteomics Service
1
Sample Shipment
2
One-Step Sample Preprocessing
3
LC-MS/MS Detection
4
Database Search
5
Data Analysis

Low-Input DIA Proteomics Deliverables

Low-input proteomics deliverables include full data quality reports, differential protein analysis, visualization, and advanced downstream interpretation such as enrichment, PPI networks, and WPCNA. Contact Us for Demo
Volcano Plot
Cluster Heatmap
K-means Analysis
GO Enrichment
KEGG Enrichment
COG/KOG Annotation
PPI Network
WPCNA Analysis
Subcellular Localization

Extensive Low-Input Proteomics Experience

We have extensive experience applying Micro-DIA proteomics across a wide range of sample types. Depending on sample complexity and input amount, our platform typically identifies several thousand to over 10,000 proteins.

Number of proteins identified from various medical and animal samples via micro-DIA assay

Applications of Low-Input DIA Proteomics Across Life Sciences

Clinical and Translational Research

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.

Plant Biology and Stress Response

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.

Microbial and Host–Microbe Systems

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.

Environmental and Ecotoxicology Studies

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

What is the minimum protein amount required for 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.

How does SISPROT single-tube sample preparation reduce sample loss?

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.

Can low-input DIA proteomics be used on FFPE tissue or laser-microdissected samples?

Yes. Our workflow is compatible with challenging sample types including FFPE sections, microdissected tissues, and fine-needle aspirates, making it ideal for clinical proteomics.

How does data quality from Micro-DIA compare to standard DIA 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.

What quality control steps are applied in small sample proteomics?

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.

Is low-input DIA proteomics compatible with multi-omics data integration?

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

Have a project in mind? Tell us about your research, and our team will design a customized proteomics or metabolomics plan to support your goals.
Ready to get started? Submit your inquiry or contact us at support-global@metwarebio.com.
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