4D Proteomics

4D Proteomics — Ion Mobility Enhanced DIA

Building on the three classical dimensions — retention time, m/z and ion intensity — 4D proteomics adds ion mobility (CCS) as a fourth separation dimension, markedly improving peptide selectivity and identification depth in complex samples. Centered on DIA acquisition with timsTOF platforms, it combines high throughput, high reproducibility and deep coverage, ideal for large-cohort proteomics and low-abundance samples.

Technical Specifications

TECHNICAL SPECIFICATIONS

Platform	timsTOF-series 4D MS (ion-mobility separation)
Acquisition mode	dia-PASEF data-independent acquisition
Analysis Content	Protein identification & quantification, differential analysis, functional enrichment, PPI networks
Best For	Large-cohort screening, low-input samples, deep-coverage needs

Sample Requirements

SAMPLE REQUIREMENTS

Cells

≥ 1 × 10⁶ cells

Tissue

≥ 50 mg

Serum / Plasma

≥ 50 μL

Replicates: ≥3–4 biological replicates per group; large cohorts are recommended to be processed in unified batches.

Shipping notes: store samples at -80°C and ship on dry ice; standardized blood collection and processing are recommended for serum samples.

Workflow

WORKFLOW

Consultation

Study goals / sample types

Proposal & Quote

Depth / timeline / agreement

Sample Intake

Pre-check / protein assay

Experiment

DIA acquisition / QC

Delivery

Quantification matrix + analysis report

FAQ

How long does a 4D Proteomics project take?

Standard proteomics projects take 3-5 weeks depending on sample number and analysis depth; key milestones (sample QC, LC-MS/MS completion) are proactively synced with you.

How should proteomics samples be stored and shipped?

Store at -80°C and ship on dry ice; avoid repeated freeze-thaw cycles. Protease inhibitors are recommended for protein samples. A tailored Sample Collection Guide is provided before shipping.

How can DIA proteomics results be validated?

We recommend PRM targeted proteomics for candidate validation (antibody-free, highly reproducible), or classic assays such as Western Blot and ELISA, forming a "discovery → validation" closed loop.

What samples do you need for 4D Proteomics?

Cells ≥1×10⁶, tissue ≥50 mg, serum/plasma ≥50 μL, FFPE ≥4 sections (5 μm). Protein samples tolerate freeze–thaw poorly — aliquot so each tube is thawed once; for PTM work include matched controls and avoid phosphate buffers. See Technical Resources → Sample Guide.