2D DIGE vs LC-MS/MS
What are the differences between 2D DIGE and LC-MS/MS?
Applied Biomics offers both 2D DIGE-MS (gel based) and LC-MS/MS (liquid based) services. These are both powerful techniques for proteomics analysis, but they differ in their workflows and applications.
It is obvious that the separation of proteins by both Mw and pI is of higher resolution than that of large number of small peptides by hydrophobicity only. Of course, LCMSMS will achieve better resolutions if coupled with removing abundant proteins or fractionation, at an extra cost. LCMSMS is also less labor-intensive than 2D DIGE, with a single run capable of identifying thousands of proteins. On the other hand, 2D DIGE allows visualization of intact proteins, degradations and PTM forms, which no other platform can achieve. This makes 2D DIGE ideal for HCP antibody coverage and HCP profiling studies.
The following is a quick guide to help you decide which platform is more suitable for your project:
| Application | 2D DIGE – MS | LC – MS/MS | Preferred |
|---|---|---|---|
| Global Proteome Profiling | Good | Comprehensive | LC-MS/MS |
| Differential Expression | Good | Excellent | LC-MS/MS |
| PTM Site Identification | No | Yes | LC-MS/MS |
| Protein Isoforms | Excellent | Limited | 2D DIGE-MS |
| Protein Degradation | Excellent | Limited | 2D DIGE-MS |
| Visualize Intact Proteins | Yes | No | 2D DIGE-MS |
| Serum Proteomics | Excellent | Good, needsextra sample prep | 2D DIGE-MS |
| Large Scale Studies | Low-Med throughput | High throughput | LC-MS/MS |
| Quantitative Accuracy | High | High | LC-MS/MS |
| HCP Antibody Coverage | Excellent | Limited, needs AAE | 2D DIGE-MS |
| HCP Profile Visualization | Excellent | No | 2D DIGE-MS |