Analyte concentration, effect zone electrophoresis

We therefore sought to evaluate reproducibility of shotgun proteomics in studies of archival FFPE tissue. Because FFPE samples are more complex than non-cross-linked samples, we evaluated FFPE human liver for analytical reproducibility and confidence in protein assignments.20 This complexity strengthens the argument for using high-resolution separations to maximize analyte concentration and minimize matrix effects. In this case, we used transient capillary isotachophoresis/capillary zone electrophoresis (cITP/cZE) in place of IEF to help address this effect. cITP/cZE has a resolution superior even to cIEF (90% of identified peptides in 1 fraction, 95% in 2 fractions or less for cITP/cZE, vs. 75% and 80%, respectively, for cIEF). 

Micellar electrokinetic capillary chromatography (MECC), in contrast to capillary electrophoresis (CE) and capillary zone electrophoresis (CZE), is useful for the separation of neutral and partially charged species [266,267]. In MECC, a surfactant, usually sodium dodecyl sulfate (SDS), is added to the buffer solution above its critical micellar concentration to form micelles. Although SDS is certainly the most popular anionic surfactant in MECC, other surfactants such as bile salts have proved to be very effective in separating nonpolar analytes that could not be resolved using SDS [268]. 

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