4D Post-translational Modifications Proteomics Service

Proteomics analysis is mostly based on liquid chromatography–tandem mass spectrometry (LC-MS/MS). Although it enables the identification of proteins and modifications in complex samples, there are still certain limitations in sensitivity, resolution, and coverage. With the development of mass spectrometry technology, 4D proteomics (4D Proteomics) has emerged. Its core is the introduction of ion mobility separation (Ion Mobility, IM), which, combined with liquid chromatography (LC), mass-to-charge ratio (m/z), signal intensity (Intensity), and ion mobility (IM), achieves higher resolution and deeper analysis of complex biological samples.

MtoZ Biolabs, relying on an advanced 4D proteomics platform (timsTOF Pro system, combined with TIMS and PASEF technologies), can efficiently and accurately detect and quantify multiple post-translational modifications. Our 4D Post-translational Modifications Proteomics Service not only helps researchers gain deeper insights into the roles of PTMs in physiological and pathological processes but also provides solid data support for drug development, biomarker discovery, and personalized medicine.

Services at MtoZ Biolabs

The 4D post-translational modifications proteomics service provided by MtoZ Biolabs covers the entire analysis process from sample preparation to data delivery, including:

1. Post-translational modification detection

Capable of detecting multiple modifications including phosphorylation, acetylation, methylation, ubiquitination, SUMOylation, carboxylation, hydroxylation, and glycosylation. For low-abundance and highly dynamic modifications, we can combine enrichment strategies to achieve high-sensitivity detection.

 

2. Qualitative and quantitative analysis

Based on the high resolution and high sensitivity of the 4D mass spectrometry platform, we can precisely identify modified proteins and modification sites, and support relative quantification and multi-sample comparison.

3. Functional annotation and pathway analysis

Through bioinformatics analysis, the detection results are compared with public databases to provide annotation of modified proteins in signaling pathways, metabolic networks, and functional modules, helping clients understand the biological significance.

4. Customized research solutions

According to client research goals, flexible experimental designs are provided, including detection combinations of different modification types, multi-omics integrated analysis, and customized schemes for specific target proteins.

Analysis Workflow

1. Sample pretreatment: protein extraction, digestion, and necessary enrichment steps.

2. Liquid chromatography separation: efficient separation of peptides.

3. 4D mass spectrometry detection: LC-TIMS-MS/MS analysis for four-dimensional detection.

4. Data processing and database search: identification of modified proteins and modification sites.

5. Bioinformatics analysis: functional annotation, pathway enrichment, and quantitative comparison.

6. Result delivery: standardized reports and data files.

Figure 1. Workflow of 4D Post-translational Modifications Proteomics 

 

Service Advantages

1. High resolution and high coverage

MtoZ Biolabs, through its 4D proteomics platform powered by the timsTOF Pro system, utilizes TIMS ion mobility separation in combination with the PASEF acquisition mode to achieve high-resolution and high-sensitivity protein and post-translational modification analysis. Our 4D post-translational modifications proteomics service enables the identification of more peptides and modification sites within the same detection time, effectively improving the detection rate of low-abundance proteins and rare modifications.

2. Multiple enrichment methods

MtoZ Biolabs has established and optimized multiple enrichment strategies for different types of post-translational modifications. For example, in phosphorylation analysis, we combine IMAC and TiO₂ dual-mode enrichment, which significantly reduces non-specific binding and improves the recovery rate and specificity of modified peptides; in acetylation and methylation lysine modification detection, we use optimized modification-specific antibody enrichment to enhance the detection of low-abundance modification sites; in ubiquitination and chain-type analysis, we introduce the K-ε-GG (diglycine) motif enrichment scheme, which enables high-sensitivity capture of ubiquitinated residues. Through these technology combinations and optimizations, we can still obtain a more complete modification profile under complex sample backgrounds and provide a solid experimental foundation for differential quantification and functional studies.

3. Flexible customization

According to research goals, personalized experimental designs and analysis schemes are provided, adapting to different sample types and research needs. At the same time, complete technical support and follow-up consultation are offered to facilitate smooth progress of research projects.

4. One-Time Charge

Our pricing is transparent, with no hidden fees or additional costs.

Applications

• Disease mechanism research: Explore the roles of PTMs in cancer, neurodegenerative diseases, autoimmune diseases, etc.

• Drug development: Reveal drug targets and mechanisms of action, supporting new drug development and efficacy evaluation.

• Biomarker discovery: Identify modification-related proteins associated with diseases, promoting clinical diagnosis and prognosis evaluation.

• Basic biological research: Analyze the regulatory roles of PTMs in signaling pathway regulation, metabolic network dynamics, and cellular stress responses.

Sample Submission Suggestions

Sample Type	Minimum Amount	Notes
Co-IP sample	2–5 μg protein	Suitable for immunoprecipitation products
Protein sample	≥50 μg total protein	Tissue or cell lysates can be used for protein extraction
Cell sample	≥1×10⁷ cells	Cell status should be good, avoid excessive dead cells
Animal tissue	≥200 mg	Fresh or frozen tissue
Plant tissue	≥1 g	Fresh or frozen tissue
Blood	≥1 mL	Collect using anticoagulant tubes
Urine	≥2 mL	Freeze immediately
Serum	≥0.2–0.5 mL	Avoid repeated freeze-thaw
Microbial sample	≥200 mg (dry weight)	Measure dry weight and freeze for storage

Transportation and Storage Requirements

• Use sufficient dry ice for transportation to avoid sample degradation.

• Choose express delivery to reduce transport time.

• Avoid repeated freeze-thaw cycles.

• If there are any questions about sample preparation, MtoZ Biolabs can provide detailed submission guidelines.

Deliverables

• Experimental report (including experimental conditions and quality control information)

• Identification list of proteins and modification sites

• Quantitative results of modification abundance

• Data visualization results (distribution plots, heatmaps, pathway enrichment plots, etc.)

• Raw mass spectrometry data files

Post-translational modification research is an important approach to revealing life activities and disease mechanisms, and 4D proteomics brings higher resolution and stronger data depth to PTM research. MtoZ Biolabs, with an advanced 4D mass spectrometry platform and rich experimental experience, provides you with systematic, accurate, and reliable 4D Post-translational Modifications Proteomics Service. Contact us to explore how customized analysis solutions can support your research and development projects.