Fluorescence two-dimensional difference gel electrophoresis for biomaterial applications

Abstract

Fluorescence two-dimensional difference gel electrophoresis (DiGE) is rapidly becoming established as a powerful technique for the characterization of differences in protein expression levels between two or more conditions. In this review, we consider the application of DiGE-both minimal and saturation labelling-to biomaterials research, considering the challenges and rewards of this approach.

Differential Proteomics of Helicobacter pylori Associated with Autoimmune Atrophic Gastritis

“…In this study, we focused on the comparative proteome of HP associated with AAG versus those of HP associated with DU or GC by using the DIGE approach (35). Protein profiles of HP isolated from AAG patients (corpus or antrum) were compared with reference maps of HP associated with corpus or antrum protein maps of DU or GC patients (Supplementary Table S3).…”

Quantitative gel electrophoresis: New records in precision by elaborated staining and detection protocols

“…The most common method is the 1-D SDS-PAGE [1][2][3][4]. Although primarily used for qualitative analyses, quantitation in GE is essential as well, especially in the proteomic field, the discovery of diagnostic markers and for quality control of biopharmaceuticals [5][6][7]. In proteomics and diagnostics, the increase or decrease of a protein concentration will be very often the relevant signal.…”

Metabolomics: a valuable tool for stem cell monitoring in regenerative medicine

“…This could comprise, for example, testing metabolic extracts from stem cells cultured in different numbers of tissue culture plastic (TCP) culture wells (if material conservation is necessary, and culture on TCP represents a comparable proliferation rate to that when the cells are cultured on the material of interest), with cells seeded at the same density and for the length of culture period that will be used in the main experiment. We have previously highlighted the importance of using controls with the same surface chemistry as the topographically structured 'test' materials in metabolomics [5] and discussed the possibility of pooling substrates to generate more material in the context of proteomics [2]. For metabolomics studies, it is important that the samples remain sufficiently concentrated to detect the metabolites-this will be affected by the cell seeding density and the amount of extraction solvent used per sample, and should be tested prior to the main experiment.…”

“…In addition, typical extraction and sample processing protocols are less technically demanding than for high-sensitivity saturation labelled twodimensional difference gel electrophoresis (saturation DiGE; discussed in greater detail in McNamara et al [1] and in relation to biomaterials research in McNamara et al [2]), making the technique more accessible for researchers with access to high-sensitivity mass spectrometers. The techniques are complementary, however, and the combination of protein abundance data generated by a proteomic approach, such as saturation DiGE, and the metabolic data from a metabolomic study should both facilitate the global comprehension of changes in stem cell profiles during differentiation.…”