Abstract: The 4D proteomics service represents a next-generation solution in mass spectrometry-based protein analysis, offering enhanced separation, sensitivity, and quantitative depth for complex biological samples. By incorporating ion mobility as a fourth analytical dimension—alongside retention time, mass-to-charge ratio, and intensity—4D proteomics enables precise resolution of co-eluting peptides, isobaric species, and post-translational modification isomers. This expanded analytical power supports deep proteome coverage, accurate quantification, and confident characterization of protein structure and function, making it a valuable tool across biomarker discovery, drug mechanism research, and systems biology.
Recognizing the transformative potential of this approach, MtoZ Biolabs has established a fully integrated 4D proteomics service platform powered by Bruker timsTOF Pro and advanced data processing pipelines. Our service combines high-resolution TIMS-PASEF acquisition with expert-driven workflows and AI-assisted bioinformatics, delivering actionable insights from even the most limited or complex samples. Designed for scalability and reproducibility, MtoZ Biolabs’ 4D proteomics service empowers researchers to accelerate discoveries across life science, biotechnology, and translational research.
What Sets 4D Proteomics Analysis Apart?
As the complexity of biological systems continues to challenge conventional proteomic workflows, researchers are seeking tools that can go beyond the traditional three-dimensional limitations of LC-MS. Co-eluting peptides, isobaric species, and low-abundance targets often evade detection—limiting both depth and confidence in protein identification.
4D proteomics changes the game by introducing ion mobility separation based on collisional cross section (CCS), adding a powerful fourth dimension to peptide characterization. This additional axis enables the separation of molecules not just by mass and charge, but by their shape and gas-phase behavior—offering a transformative leap in resolution and sensitivity.
At MtoZ Biolabs, we’ve integrated 4D proteomics into our analytical pipeline using TIMS-PASEF technology, which delivers:
1. Superior discrimination of isobaric and near-isobaric species
Ion mobility allows fine separation of peptides with nearly identical mass-to-charge ratios, significantly improving identification accuracy in complex or crowded spectra.
2. Deep profiling of post-translational modifications at the isomer level
4D proteomics supports the high-resolution analysis of PTMs—including phosphorylation, glycosylation, acetylation, and ubiquitination—distinguishing isomeric forms and mapping modification sites with confidence.
3. High-throughput acquisition with exceptional data completeness
The platform enables rapid data collection while preserving identification depth and spectral quality, minimizing missing values and enhancing coverage in large-scale studies.
4. Reliable quantification across diverse sample types and study scales
From single biopsies to multi-condition or cohort-based studies, 4D proteomics delivers consistent, reproducible quantification across various sample formats and research scenarios.
By expanding the analytical dimensions of proteomics, MtoZ Biolabs' 4D platform empowers researchers to uncover hidden biological insights, resolve complex proteoforms, and accelerate discovery in systems biology, translational medicine, and biomarker research.
Specialized Modules of 4D Proteomics Service
MtoZ Biolabs' 4D proteomics service is engineered to address the most pressing needs of modern life science and biomedical research through a portfolio of specialized modules, each optimized for specific scientific questions and sample types:
1. Quantitative Proteome Profiling
(1) 4D-LFQ (Label-Free Quantification): Delivers highly reproducible, missing-value-minimized protein quantification across cohorts, treatments, or time points.
(2) 4D-DIA (Data-Independent Acquisition): Utilizes CCS-aligned spectral libraries for deep, consistent quantitative data, supporting clinical, translational, or population-scale investigations.
Key uses: Biomarker discovery, drug mechanism studies, comparative cohort analyses.
2. PTMomics and Functional Proteomics
(1) 4D-PTMomics: Provides high-resolution, site-specific mapping of phosphorylation, acetylation, ubiquitination, and other critical PTMs, including confident isomer differentiation.
(2) 4D Glycoproteomics: Integrated site-specific glycosylation analysis and glycoform quantification. Supports studies in immune modulation, signaling networks, and therapeutic glycoprotein characterization.
Key uses: Signaling pathway mapping, disease mechanism research, biotherapeutic characterization.
3. Microbial and Environmental Proteomics
4D Metaproteomics: Tailored for multi-species and complex matrices such as stool, soil, fermentation broth, or environmental samples. This module allows high-confidence, high-throughput protein identification without excessive sample cleanup.
Key uses: Environmental microbiome analysis, agricultural innovation, industrial bioprocessing.
Workflow of MtoZ Biolabs 4D Proteomics Service
From project consultation to result delivery, MtoZ Biolabs offers a transparent and end-to-end service experience. We support clients at every stage, ensuring data quality, project clarity, and scientific relevance.
1. Consultation and Project Planning
Collaborate with our scientific team to define objectives, select modules, and optimize protocols to match your experimental needs.
2. Sample Preparation and Quality Control
Receive step-by-step sample preparation instructions and technical support. Every submission undergoes rigorous QC, including protein quantification and integrity assessment, prior to LC-MS analysis.
3. 4D LC-MS/MS Data Acquisition
Samples are analyzed on the Bruker timsTOF Pro, leveraging TIMS and PASEF technologies for four-dimensional, high-resolution data collection.
4. Data Processing and Quantitative Analysis
Our automated bioinformatics pipelines ensure robust peptide and protein identification, normalization, and quantification. Advanced statistical controls minimize missing values and maximize biological insight.
5. Bioinformatics Annotation and Visualization
Benefit from detailed functional annotation (GO, KEGG, COG), pathway analysis, PTM mapping, network modeling, and customizable data visualizations that support manuscript preparation or strategic decisions.
6. Report Delivery and Scientific Support
Receive a publication-ready report and all supporting data. Our team remains available for interpretation support, further analysis, and guidance on next steps.
Sample Submission Suggestion
Our platform is optimized to accommodate a broad range of biological and environmental sample types:
1. Supported Sample Types
(1) Animal and human tissues
(2) Cultured or primary cells
(3) Biofluids (plasma, serum, CSF, urine)
(4) Environmental or agricultural samples (soil, plant tissue, microbiome pellets)
(5) Microbial communities or complex mixtures
2. Submission and Transport Recommendations
(1) Use dry ice and insulated containers for shipping
(2) Avoid freeze-thaw cycles; prefer same-day express shipping
(3) For high-salt/SDS buffers, conduct buffer exchange or contact us for assistance
(4) Pre-submission technical consultation is encouraged to optimize outcomes
What Could Be Included in the 4D Proteomics Service Report?
1. Comprehensive Experimental Details
Detailed description of experimental design, including sample source, preparation procedures, and all analytical protocols applied.
2. Materials, Instruments, and Methods
Transparent documentation of all reagents and consumables used, instrumentation details (such as timsTOF Pro parameters), and the full set of standard operating procedures followed during the study.
3. Total Ion Chromatogram and Quality Control Assessment (project-dependent)
Inclusion of total ion chromatograms and relevant quality control metrics specific to the project, with thorough documentation and assessment of data quality.
4. Data Analysis, Preprocessing, and Estimation (project-dependent)
Comprehensive workflow outlining raw data processing steps, normalization, quantification strategies, and initial biological interpretation as appropriate for the project.
5. Bioinformatics Analysis
Advanced bioinformatics results encompassing functional annotation, pathway and network analysis, statistical evaluations, and data visualization outputs.
Why Choose MtoZ Biolabs' 4D Proteomics Service?
1. Advanced Analytics Platform
The advanced 4D proteomics platform at MtoZ Biolabs utilizes cutting-edge instrumentation and automated pipelines to deliver reliable, rapid, and highly accurate analysis, regardless of project complexity or sample type. Continuous optimization ensures best practices in 4D proteomics analysis are always met.
2. One-Time-Charge
Transparent, all-inclusive pricing means every 4D quantitative proteomics service is offered as a clear, upfront package. There are no hidden fees or additional costs, allowing researchers to plan and manage budgets with confidence for projects of any size.
3. High Data Quality
Deep data coverage and rigorous quality control are maintained at every stage, from sample preparation to data reporting. MtoZ Biolabs' AI-powered bioinformatics platform integrates all 4D proteomics data, delivering clients a comprehensive and actionable data report suitable for publication and further research.
Scientific Discovery Enabled by MtoZ Biolabs' 4D Proteomics Service
Across disease research, functional biology, and environmental science, MtoZ Biolabs' 4D proteomics service has empowered a wide range of groundbreaking studies, including:
1. Confident Biomarker Discovery
High-sensitivity profiling in heterogeneous clinical cohorts, supporting both validation and scientific advancement.
2. Advanced PTMomics
Comprehensive mapping of phosphorylation, glycosylation, and ubiquitination, leading to the identification of novel therapeutic targets and deeper mechanistic insights.
3. Single-Cell and Low-Yield Analysis
Delivering data-rich proteomic insights from precious or limited samples, including rare cells and micro-dissected tissues.
4. Integrated Multi-Omics
Supporting systems biology by aligning proteome data with genomics and metabolomics, fueling holistic understanding and innovative discoveries.
Each research project is supported through customized analytical pipelines, expert consultation, and a rigorous quality-first approach that reflects MtoZ Biolabs’ dedication to scientific advancement.
Contact MtoZ Biolabs for Your 4D Proteomics Service
MtoZ Biolabs, an integrated chromatography and mass spectrometry (MS) services provider, provides advanced proteomics, metabolomics, and biopharmaceutical analysis services to researchers in biochemistry, biotechnology, and biopharmaceutical fields. Our ultimate aim is to provide more rapid, high-throughput, and cost-effective analysis, with exceptional data quality and minimal sample consumption.
As life sciences and biomedical research continue to evolve, harnessing the full power of next-generation proteomics is essential for innovation and impact. MtoZ Biolabs' 4D proteomics service delivers the analytical depth, reliability, and flexibility your research demands, whether you seek high-throughput biomarker discovery, advanced PTM mapping, or integrated multi-omics solutions. Our team of mass spectrometry experts and bioinformatics professionals will support your project from initial consultation to data interpretation and beyond. With transparent pricing, rigorous quality control, and actionable reporting, MtoZ Biolabs is your trusted partner for advanced 4D proteomics service and scientific success.
To learn more about our 4D quantitative proteomics analysis, request a customized quote, or start your next project, contact us today.
Contact Information:
Name: Terry
Company: MtoZ Biolabs
Email: marketing@mtoz-biolabs.com
Phone: +1-857-362-9535
Address: 155 Federal Street, Suite 700, Boston, MA 02110, USA
Country: United States
Website: https://www.mtoz-biolabs.com/
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