MtoZ Biolabs provides SWATH-MS Quantitative Proteomics Service for researchers who need reproducible, large scale protein quantification across complex biological samples. By integrating SWATH-MS data independent acquisition with optimized sample preparation and bioinformatics pipelines, we deliver deep, consistent quantitative proteome profiles suitable for discovery studies and targeted follow up work.

What Is SWATH-MS?

SWATH-MS (Sequential Window Acquisition of All Theoretical Fragment ion Mass Spectra) is a data independent acquisition strategy for quantitative proteomics that aims to measure virtually all detectable peptides in a sample in a single run. Instead of selecting only a few precursor ions per cycle, SWATH-MS is designed to capture comprehensive fragment information suitable for large cohort and longitudinal studies where data completeness and reproducibility are critical.

In SWATH-MS, the full m/z range is divided into a series of sequential isolation windows. The instrument cycles through these windows, fragments all ions within each window, and records the corresponding MS/MS spectra throughout the LC gradient. Peptide specific fragment traces are then extracted and matched against a spectral library or predicted peptide information to identify and quantify proteins across samples. This window based, systematic acquisition provides broader coverage and more consistent quantification than traditional data dependent acquisition.

Ludwig, C. et al. Mol Syst Biol. 2018.

Figure 1. The Principle of Sequentially Windowed Data-Independent Acquisition in SWATH-MS

SWATH-MS Quantitative Proteomics Service at MtoZ Biolabs

MtoZ Biolabs has established a robust SWATH-MS platform for quantitative proteomics projects that require consistent, large scale protein measurement. Our service is designed to support discovery and hypothesis driven studies across cells, tissues, and clinical biofluids. You only need to provide your samples and study objectives. MtoZ Biolabs handles protein extraction, digestion, MS analysis, data processing, statistical evaluation, and biological interpretation, returning a complete package of results.

Workflow of SWATH-MS Quantitative Proteomics Service

Why Choose MtoZ Biolabs

• Extensive SWATH-MS experience with optimized window schemes and library strategies for different species and sample types
• High depth and high reproducibility quantitative workflows suitable for large cohorts, time course studies, and complex matrices
• Flexible experimental design and data analysis tailored to biomarker discovery, mechanism studies, and bioprocess monitoring
• Rigorous QC throughout sample preparation, LC-MS acquisition, and data processing to ensure consistent performance
• Professional proteomics and bioinformatics team delivering clear reports, publication ready figures, and actionable biological insight

Applications of SWATH-MS Quantitative Proteomics Service

1. Biopharmaceutical Research and Drug Development

Quantitative profiling of signaling and pathway changes in cell lines, organoids, and animal models to support target validation, mechanism of action studies, and pharmacodynamic evaluation.

2. Clinical and Translational Medicine

Large scale, reproducible protein quantification in plasma, serum, CSF, urine, and tissues for biomarker discovery, patient stratification, and longitudinal disease monitoring.

3. Agricultural and Plant Sciences

Proteome level analysis of crops, model plants, and plant associated microbes to investigate stress responses, yield traits, pathogen resistance, and quality related pathways.

4. Food, Environmental, and Microbiome Studies

Quantitative analysis of proteins in food matrices, environmental samples, and complex microbial communities to monitor quality, safety, contamination, and ecosystem function.

5. Bioprocess and Biotechnology Applications

Monitoring host cell proteins, product related variants, and process impurities in biologics manufacturing to support process optimization and quality control.

FAQ

Q1: What types of samples are suitable?

We support a wide range of samples for SWATH-MS quantitative proteomics, including:

• Cell pellets from adherent or suspension cell lines

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

• Fresh frozen tissues and small biopsies

• Biofluids such as plasma, serum, CSF, and urine

• Purified protein

If you have a special sample type or low-yield materials, we can evaluate feasibility based on your project needs.

Q2: How should I prepare my samples?

• Snap freeze samples 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, glycerol, 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 Excel or CSV
• Differential expression and pathway or functional enrichment results in spreadsheet format
• Publication-ready figures such as heatmaps, volcano plots, PCA and clustering plots in high resolution PNG or TIFF
• A structured PDF report summarizing workflow, QC metrics, main quantitative findings, and biological interpretation
• Additional formats or customized deliverables can be provided on request.

Start Your Project with MtoZ Biolabs

Whether your focus is biomarker discovery, mechanism research, drug development, or bioprocess monitoring, our SWATH-MS platform can help you convert samples into high quality quantitative insights.

Contact us to discuss your study design and receive a tailored proposal.