Two-dimensional gel electrophoresis

Silver staining is 100x more sensitive than Coomassie brilliant blue with a 40-fold range of linearity.

[citation needed] A common technique is to use an Immobilized pH gradient (IPG) in the first dimension.

Typically IPG-DALT is not used for quantification of proteins due to the loss of low molecular weight components during the transfer to the SDS-PAGE gel.

Additionally, these tools match spots between gels of similar samples to show, for example, proteomic differences between early and advanced stages of an illness.

For example, while PDQuest and SameSpots tend to agree on the quantification and analysis of well-defined well-separated protein spots, they deliver different results and analysis tendencies with less-defined less-separated spots.

[5] Comparative studies have previously been published to guide researchers on the "best" software for their analysis.

2D-Gels (Coomassie stained)
Robots are used for the isolation of protein spots from 2D gels in modern laboratories.
Warping: Images of two 2D electrophoresis gels, overlaid with Delta2D. First image is colored in orange, second one colored in blue. Due to running differences, corresponding spots do not overlap.
Warping: Images of two 2D electrophoresis gels after warping. First image is colored in orange, second one colored in blue. Corresponding spots overlap after warping. Common spots are colored black, orange spots are only present (or much stronger) on the first image, blue spots are only present (or much stronger) on the second image.