MtoZ Biolabs’ 4D Proteomics Service Powers High-Throughput, PTM-Aware Research
Boston, MA, United States, 1st May 2025 – 4D proteomics service is an advanced analytical offering designed to push the boundaries of protein characterization through enhanced separation, sensitivity, and speed. Built upon conventional 3D proteomics (retention time, mass-to-charge ratio, and intensity), 4D proteomics introduces ion mobility as a fourth dimension, enabling precise separation of peptide ions based on their collisional cross-section and shape. This concept gained momentum in 2018 with the launch of the Bruker timsTOF Pro system, which integrates Trapped Ion Mobility Spectrometry (TIMS) and Parallel Accumulation–Serial Fragmentation (PASEF) technologies. Together, these innovations significantly improve the detection of low-abundance proteins and the resolution of post-translational modification (PTM) isomers, offering an unparalleled depth of proteomic analysis.
To meet the growing demand for high-throughput, modification-aware proteomics from limited sample input, MtoZ Biolabs has launched a dedicated 4D proteomics service powered by the timsTOF Pro platform. Our streamlined workflow translates complex ion mobility data into high-confidence proteomic insights, enabling researchers to explore dynamic proteome changes with exceptional clarity. Whether for biomarker discovery, drug mechanism investigation, systems biology, or clinical metaproteomics, MtoZ Biolabs delivers expert-guided, scalable solutions that accelerate your research with precision and reliability.
What Makes 4D Proteomics Different?
Beyond adding ion mobility as a fourth analytical dimension, 4D proteomics fundamentally redefines how proteomic data is acquired and interpreted. Unlike conventional workflows that may suffer from peptide co-elution, signal interference, or limited depth, 4D proteomics enhances analytical resolution and throughput through precise ion separation and high-speed MS/MS sequencing. Key performance advantages of 4D proteomics include:
- Discrimination of isobaric and near-isobaric peptides through shape-based ion
- Superior sensitivity for detecting low-abundance proteins in complex biological
- Accelerated scan cycles, capturing over 100 MS/MS spectra per second without compromising data quality.
- Reproducible collisional cross-section (CCS) values, offering a new dimension of molecular specificity.
- Consistent performance across large sample sets, ensuring reliable quantification and cohort comparability.
Together, these attributes translate into deeper proteome coverage, improved confidence in peptide identification, and enhanced ability to resolve post-translational modification variants—all critical for systems biology, clinical research, and biomarker-driven studies.
Scientific and Technological Applications of 4D Proteomics Analysis
The combination of high resolution, speed, and reproducibility makes 4D proteomics analysis uniquely suited for a variety of scientific applications:
1. Biomarker Discovery in Clinical Proteomics
In disease research, particularly oncology and neurology, sensitivity is paramount. 4D proteomics allows for confident identification and quantification of differentially expressed proteins in limited patient samples—accelerating biomarker validation in multi-sample clinical studies.
2. Functional Proteomics and Drug Mechanism Studies
By quantifying proteome dynamics under drug treatment or gene modulation (e.g., knockout, knockdown, or overexpression), researchers can map signaling pathways, monitor off-target effects, and evaluate downstream consequences of therapeutic interventions.
3. Environmental and Agricultural Proteomics
From studying drought resistance in crops to characterizing microbiome shifts in polluted ecosystems, 4D proteomics enables the tracking of subtle protein expression changes, even from trace biological samples like plant exudates or microbial pellets.
4. Systems Biology and PTMomics
With its ability to differentiate between similar peptides and modification isomers, 4D proteomics is ideally positioned to support large-scale PTM mapping projects. Phosphorylation, glycosylation, acetylation, and ubiquitination can be tracked at high throughput and high site resolution.
Core Modules of 4D Proteomics Analysis
To address a wide range of proteomic research needs—from global expression profiling to site-specific modification analysis and microbial community studies—MtoZ Biolabs offers a suite of specialized 4D proteomics service modules. These modules are designed to fully leverage the advantages of ion mobility-enhanced mass spectrometry, while maintaining flexibility, depth, and scalability.
1. Quantitative Proteome Profiling
Modules: 4D Label-Free Quantification (4D-LFQ), 4D Data-Independent Acquisition (4D-DIA) These foundational modules support comprehensive protein expression analysis across multiple samples, conditions, or timepoints.
- 4D-LFQ enhances classical label-free quantification with improved reproducibility and reduced missing values, making it ideal for large-cohort or comparative studies.
- 4D-DIA integrates data-independent acquisition with CCS-aligned spectral libraries to deliver deep coverage and high consistency across replicates.
2. Post-Translational Modification Mapping
Modules: 4D-PTMomics, 4D Glycoproteomics and Glycoform Profiling
These modules focus on high-resolution, site-specific identification of regulatory modifications that control protein function and signaling.
- 4D-PTMomics supports in-depth mapping of phosphorylation (pSer/pThr/pTyr), acetylation, ubiquitination, and other PTMs, with enhanced isomer separation and modification site localization.
- 4D Glycoproteomics allows simultaneous identification of glycosylation sites and glycoform heterogeneity, capturing both occupancy and structural diversity at individual modification
3. Microbial Community Proteomics
Module: 4D Metaproteomics
Tailored for complex biological mixtures, this module enables species- and function-level protein identification from microbiomes and multispecies samples.
The enhanced separation capacity of 4D proteomics allows accurate detection of microbial proteins in challenging matrices such as stool, soil, fermentation broth, or biofilms—without the need for extensive sample cleanup.
Sample Types and Requirements
MtoZ Biolabs accommodates a wide range of biological matrices to support diverse research scenarios, from clinical trials to basic discovery projects. Our 4D proteomics service is optimized
for high sensitivity and low input volumes, making it ideal for projects involving precious or limited samples.
Supported Sample Types:
Transport Instructions: All samples should be shipped on dry ice with proper insulation. We recommend using an express courier to reduce freeze-thaw cycles and degradation risk. Samples with high SDS or salt concentrations may require buffer exchange prior to processing—please consult our technical support team for guidance.
Comprehensive 4D Proteomics Data Analysis & Reporting
A critical strength of MtoZ Biolabs’ 4D proteomics service lies not only in high-performance mass spectrometry, but also in our advanced data analysis and transparent reporting. Every 4D proteomics analysis project is processed by a dedicated team of bioinformatics specialists who translate complex spectral data into meaningful biological insights tailored to your research objectives.
1. Core Data Analysis Features
- Protein Quantification & Statistics: Normalized abundance metrics (LFQ, DIA, iBAQ), fold-change calculations, and FDR-adjusted significance testing.
- Exploratory Visualization: Principal Component Analysis (PCA), hierarchical clustering, volcano plots.
- Functional Annotation: GO classification (Biological Process, Molecular Function, Cellular Component), KEGG pathway enrichment, COG domain annotation.
- Post-Translational Modification Mapping: Accurate identification of site-specific modifications, including phosphorylation, acetylation, ubiquitination, glycosylation.
- Network & Systems Biology: Protein–protein interaction (PPI) network modeling; optional modules include WGCNA, time-course clustering, survival curve and ROC analysis.
All results are consolidated into a publication-ready report designed for maximum usability in both academic and industrial settings.
2. What’s Included in Your Report
- Experimental Protocols and Sample Processing Details
- LC-MS/MS Acquisition Parameters and Instrumentation
- Total Ion Chromatogram (TIC) & Quality Control Metrics
- Data Preprocessing and Statistical Summary
- Functional Enrichment Analysis & Pathway Mapping
- Customized Visualizations (PCA, PPI, trend clusters)
- Raw and Processed Data Files (vendor-native formats + Excel/CSV exports)
By combining deep analytical power with full documentation, our 4D proteomics service empowers researchers to move seamlessly from mass spectrometry to manuscript.
Why Choose MtoZ Biolabs?
MtoZ Biolabs is more than a CRO—we are your scientific partner. Our services go beyond technical execution to offer collaborative project support, consultative experimental design, and tailored data interpretation for researchers aiming to publish, patent, or apply their findings.
1. Advanced Analysis Platform
MtoZ Biolabs’ advanced proteomics platform, powered by the next-generation timsTOF Pro mass spectrometer, guarantees reliable, fast, and highly accurate analytical performance across a wide range of biological systems. Whether you’re pursuing exploratory discovery or targeted validation, our integrated 4D proteomics service enables researchers to achieve deeper proteome coverage with minimal sample consumption—making it ideal for scarce or valuable samples. We support applications from drug mechanism studies and biomarker profiling to PTM mapping and microbial ecology.
2. One-Time-Charge Pricing
Our pricing is fully transparent, with no hidden fees or incremental costs. Each 4D proteomics analysis project is offered as a clearly defined package, covering all steps—from consultation and sample processing to mass spectrometry and bioinformatics reporting. This all-in-one model helps researchers manage budgets with confidence while eliminating unexpected expenses. Whether you’re conducting a small pilot study or a large-scale cohort analysis, we ensure that every cost is known upfront.
3. High Data Quality with Integrated Intelligence
We maintain deep data coverage with strict data quality control at every stage—from sample preparation and MS acquisition to statistical and biological validation. Our AI-powered bioinformatics platform integrates all proteomic and metadata inputs, delivering clients a comprehensive, publication-ready data report that is both scientifically robust and visually clear. Multi-layered outputs (from raw data to annotated results) ensure downstream usability in publications, grant reports, or regulatory submissions.
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.
Whether you’re investigating subtle post-translational modifications, validating novel drug targets, or working with low-yield clinical or environmental samples, high-resolution proteomic data is crucial to driving biological insight and scientific impact. MtoZ Biolabs’ 4D proteomics service empowers researchers to go beyond traditional boundaries—enabling high-throughput, ultra-sensitive, and modification-aware protein analysis with confidence.
Our team of mass spectrometry and bioinformatics experts works closely with you from project design to data interpretation, ensuring that your research is not only completed on time, but also ready for publication, presentation, or regulatory submission.
Start your next proteomics project with precision and peace of mind!
Contact MtoZ Biolabs for a Free Scientific Consultation
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
Website: https://www.mtoz-biolabs.com
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Website: https://www.mtoz-biolabs.com
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Address: 155 Federal Street, Suite 700
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