MtoZ Biolabs provides GPF-DIA Quantitative Proteomics Service using Gas-Phase Fractionation (GPF) combined with Data-Independent Acquisition (DIA) to deliver deep, sensitive, and highly reproducible protein quantification in complex biological samples. This service is designed for discovery proteomics, biomarker research, and large-scale quantitative studies across cells, tissues, and clinical biofluids.

What Is GPF-DIA?

Gas-Phase Fractionation Data-Independent Acquisition (GPF-DIA) is an advanced DIA-based proteomics strategy that improves peptide detection and quantitative accuracy by fractionating the precursor space in the gas phase. Instead of running one standard wide-window DIA method and relying only on a pre-existing spectral library, GPF-DIA performs several injections of a pooled sample with narrower, tiled precursor windows across the mass range. These narrow window runs are then combined to build a high quality, experiment specific chromatogram library.

Cai, X. et al. J Proteome Res. 2021.

Figure 1. Principle of Conventional DIA-MS and GPF-DIA

These GPF runs generate cleaner fragment ion patterns with reduced co-fragmentation, allowing more precise characterization of peptide spectra. The resulting chromatogram library captures realistic fragment intensities and retention times under the same LC-MS conditions as the study samples. In the quantitative phase, each individual sample is analyzed with a single-injection DIA method using wider windows, and the data are searched against the GPF-derived library for peptide identification and protein quantification.

By combining gas-phase fractionation with DIA, GPF-DIA:

• Enhances detection of low-abundance peptides in high dynamic range matrices
• Improves library quality compared with generic DDA-based spectral libraries
• Increases peptide and protein identification rates without the need for extensive offline fractionation
• Preserves the core DIA advantages of systematic sampling and reproducible quantification

GPF-DIA Quantitative Proteomics Service at MtoZ Biolabs

MtoZ Biolabs' GPF-DIA Quantitative Proteomics Service improves protein identification and quantification in complex samples. Using an optimized GPF-DIA workflow, we enhance proteome depth and data quality while maintaining strong quantitative reproducibility across large studies. You only need to provide your samples and project goals, and MtoZ Biolabs will complete the rest, including protein extraction, enzymatic digestion, peptide separation, MS analysis, raw data processing, and bioinformatics analysis.

Pino, L. K. et al. Mol Cell Proteomics. 2020.

Why Choose MtoZ Biolabs

1. Proven GPF-DIA Expertise

Extensive experience designing gas-phase fractionation strategies and DIA schemes for complex tissues, biofluids, and bioprocess samples.

2. High-Quality, Project-Specific Libraries

Experiment-specific chromatogram libraries built from GPF runs improve identification confidence and quantitative robustness across the entire cohort.

3. Robust and Reproducible Quantification

Standardized workflows, strict QC, and consistent LC-MS conditions deliver stable, comparable data suitable for large studies and longitudinal designs.

4. Customizable Study Design

Flexible configuration for different species, sample types, dose or time-course studies, and biomarker discovery or mechanism-focused projects.

5. End-to-End Support

From study planning and sample strategy to data interpretation, our proteomics and bioinformatics team works closely with you to align results with your scientific goals.

Applications of GPF-DIA Quantitative Proteomics Service

1. Biomarker Discovery in Clinical Cohorts

Deep profiling of plasma, serum, CSF, or tissue samples to identify low abundance protein signatures for diagnosis, prognosis, and treatment response evaluation.

2. Disease Mechanism and Pathway Research

Quantitative mapping of dysregulated pathways and protein networks in cancer, cardiovascular, neurological, inflammatory, and metabolic diseases.

3. Drug Target and Pharmacodynamic Studies

Assessing target engagement, off target effects, and global proteome shifts under different compounds, doses, and time points to support drug development.

4. Host Cell Protein and Bioprocess Monitoring

Sensitive detection and quantification of host cell proteins and process related impurities in biologics development and manufacturing.

5. Longitudinal and Time Course Experiments

Tracking proteome dynamics across developmental stages, differentiation, or treatment regimens with high data completeness and reproducibility.

FAQ

Q1: What types of samples are suitable?

We support a wide range of sample types, including:

• Cell pellets from adherent or suspension cell lines

• Primary cells isolated from blood, bone marrow, or tissues

• Fresh frozen tissues and biopsies

• Biofluids such as plasma, serum, cerebrospinal fluid, and urine

• Preclinical animal samples and other complex biological matrices

If you work with an unusual sample type, we can evaluate feasibility based on your project requirements.

Q2: How should I prepare my samples?

• Ensure samples are freshly prepared
• Snap freeze cells, tissues, or biofluids in liquid nitrogen when possible and store at −80 °C.
• Avoid repeated freeze thaw cycles and use low binding tubes.
• Do not add high concentrations of harsh detergents, salts, or stabilizers.
• Transport samples on dry ice to maintain stability during delivery.

For more information, please refer to Sample Submission Guidelines for Proteomics.

Q3: What is the service general workflow?

Q4: What data formats are provided?

• Raw data files in instrument specific formats
• Peptide and protein identification and quantification tables in .xlsx or .csv, including normalized intensities and group comparisons
• Statistical and bioinformatics outputs such as differential expression and pathway or functional enrichment in spreadsheet format
• Publication ready figures, for example heatmaps, volcano plots, PCA and clustering plots, in high resolution PNG or TIFF
• A structured PDF report summarizing the workflow, QC metrics, main quantitative results, and key biological interpretations
• Additional formats or customized deliverables can be provided on request.

Start Your Project with MtoZ Biolabs

Contact MtoZ Biolabs to discuss your project, receive a tailored proposal, and start transforming your samples into high-quality, actionable proteomic insights.