Quantitative proteomics measures protein abundance in complex samples using high-resolution Orbitrap and 4D timsTOF mass spectrometers in our laboratory and at partner platforms. It is well suited to biomarker discovery, proof-of-concept studies for drug candidates and signalling-network analysis.
Data analysis is carried out by our bioinformatics team and reviewed by senior bioinformatics experts before delivery; see proteomics and metabolomics data analysis for details.
Typical turnaround (assay + standard analysis): 20–30 working days, as stated in the written plan.
1. DIA (data-independent acquisition): good quantitative reproducibility and fewer missing values than DDA; suited to large sample sets.
2. TMT (tandem mass tag) / iTRAQ quantification: up to 16 samples are labelled and measured together in a single LC-MS run.
3. Post-translational modifications (PTMs): antibody- or affinity-based enrichment, followed by quantification of phosphorylation, acetylation, ubiquitination and glycosylation.
Deliverables include protein expression matrices, volcano plots, clustered heatmaps and functional enrichment results.
| Item | Details |
|---|---|
| Instruments | High-resolution Orbitrap / 4D timsTOF mass spectrometers (our laboratory and partner platforms) |
| Proteome depth | The number of proteins identified depends on sample type and is stated in the written plan |
| Low-input samples | Protein extraction from small samples such as needle biopsies is supported |
| Downstream analysis | Volcano plots, pathway heatmaps, protein–protein interaction (PPI) networks, multi-omics pathway enrichment |
Protein extraction and sample preparation depend on sample quality. Please make sure samples meet the following requirements:
| Sample type | Amount | Preparation | Shipping |
|---|---|---|---|
| Fresh animal or plant tissue | Animal tissue > 50 mg; plant tissue > 100 mg | Snap-freeze in liquid nitrogen; avoid repeated freeze–thaw cycles | Sealed, on dry ice |
| Cell pellet | ≥ 1 × 10^7 cells | Remove medium, wash with PBS, pellet, remove the supernatant and snap-freeze in liquid nitrogen | Sealed, on dry ice |
| Serum / plasma | ≥ 200 µL/sample | Centrifuge to remove blood cells; avoid haemolysis | Sealed, on dry ice |
| Needle biopsy (low input) | 3–5 needle cores | Snap-freeze in cryotubes | Sealed, on dry ice |
As downstream products of cellular processes, metabolites reflect how environmental stimuli or genetic changes affect phenotype. We use liquid chromatography–mass spectrometry (LC-MS) to profile hundreds to thousands of metabolites.
Data analysis is carried out by our bioinformatics team and reviewed by senior bioinformatics experts before delivery; see proteomics and metabolomics data analysis for details.
Typical turnaround (assay + standard analysis): 20–30 working days, as stated in the written plan.
1. Untargeted metabolomics: broad profiling of metabolite changes across samples, suited to exploratory studies and candidate marker discovery.
2. Targeted quantification: absolute quantification against calibration standards for key metabolite classes such as bile acids, amino acids and short-chain fatty acids.
3. Lipidomics and metabolic flux: coverage of lipid classes such as triglycerides and phospholipids, with stable-isotope tracing available.
Deliverables include identification and quantification tables, multivariate statistics (PCA, OPLS-DA), VIP plots and pathway enrichment results.
| Analysis | Deliverables | Purpose |
|---|---|---|
| Metabolite identification | MS/MS spectral match scores, high-resolution accurate mass | Identify endogenous and exogenous small-molecule metabolites |
| Multivariate statistics | PCA score plots, PLS-DA/OPLS-DA | Assess overall variation and separation between groups |
| Candidate markers | VIP plots, volcano plots | Find the differential metabolites that contribute most to group separation |
| Pathway mapping | KEGG pathway bubble plots, pathway networks | Link differential metabolites to upstream genes and proteins |
Metabolites degrade easily and are prone to contamination. Please follow these sample requirements closely:
| Sample type | Amount | Preparation | Shipping |
|---|---|---|---|
| Plasma / serum | ≥ 100 µL/sample | Centrifuge immediately after collection to remove cells; avoid haemolysis; snap-freeze | Sealed, on dry ice |
| Urine / cerebrospinal fluid | ≥ 200 µL/sample | Centrifuge to remove cells and debris; freeze promptly | Sealed, on dry ice |
| Animal or plant tissue | ≥ 100 mg | Dissect quickly on ice, rinse with PBS and snap-freeze in liquid nitrogen | Sealed, on dry ice |
| Faeces / intestinal contents | ≥ 100 mg | Collect in sterile cryovials and transfer promptly to liquid nitrogen or −80°C | Sealed, on dry ice |