Multidimensional high performance liquid chromatography--capillary electrophoresis separation of a protein digest: an update

The trypsin digest of a mixture of two proteins, namely cytochrome c and myoglobin, was first separated in the first dimension by high-performance liquid chromatography (HPLC). Fractions from the HPLC were collected every 30s with the aid of a fraction collector into a 96-well microtiter plate. After concentration, all the collected fractions were analyzed simultaneaosly in the second dimension by a 96-array capillary electrophoresis system. The labeled peptides were detected by laser-induced fluorescence. An internal standard, allura red, was added to all the fractions, prior to capillary electrophoretic analysis. The internal standard serves two functions, migration time correction and signal intensity correction. The data are presented in two different formats, as an electropherogram of all the fractions and in a two-dimensional (2-D) format. The 2-D plot of the data shows the density of each spot, which corresponds to the concentration of the migrating peptides. The total experimental time for the HPLC and capillary electrophoretic analyses ist less than 1 h, which ist much faster than using 2-D slab-gel electrophoresis or single-capillary capillary electrophoresis.     

Quantitative analysis of the low molecular weight serum proteome using 18O stable isotope labeling in a lung tumor xenograft mouse model

With advancements in the analytical technologies and methodologies in proteomics, there is great interest in biomarker discovery in biofluids such as serum and plasma. Current hypotheses suggest that the low molecular weight (LMW) serum proteome possesses an archive of clipped and cleaved protein fragments that may provide insight into disease development. Though these biofluids represent attractive samples from which new and more accurate disease biomarkers may be found, the intrinsic person-to-person variability in these samples complicates their discovery. Mice are one of the most extensively used animal models for studying human disease because they represent a highly controllable experimental model system. In this study, the LMW serum proteome was compared between xenografted tumor-bearing mice and control mice by differential labeling utilizing trypsin-mediated incorporation of the stable isotope of oxygen, 18O. The digestates were combined, fractionated by strong cation exchange chromatography, and analyzed by nanoflow reversed-phase liquid chromatography coupled online with tandem mass spectrometry, resulting in the identification of 6003 proteins identified by at least a single, fully tryptic peptide. Almost 1650 proteins were identified and quantitated by two or more fully tryptic peptides. The methodology adopted in this work provides the means for future quantitative measurements in comparative animal models of disease and in human disease cohorts.     

Capillary electrophoresis separation of heterocyclic nitrosoamino acid-conformers at sub-ambient temperatures

The separation of a selected group of naturally occurring, heterocyclic nitrosoamino acids was achieved by capillary zone electrophoresis and the resolution of the syn and anti conformers improved as the temperature was lowered to 5 °C. The double peaks observed for each nitrosoamino acid are probably caused by the slow kinetics of conformational isomerism. The experimental setup consisted of a P/ACE 5510 electrophoresis system, a 57 cm polyacrylamidecoated capillary, and a 10 mM phosphate buffer, pH 7.2, containing 2 mM of 3-(N-N-dimethylmyristylammonio)propanesulfonate (DMMAPS) and 0.1% Tween 20. Our study shows that (a) the lower the temperature, the greater the resolution and the longer the migration times; and (b) different nitrosoamino acid conformers were resolved at different temperatures because of differences in the rate of isomerization. For example, the conformers of N-nitrosothiazolidine-4-carboxylic acid were partially resolved at 30 °C while those of N-nitrosoproline were well resolved at the same temperature.     

Two dimensional mapping of cancer cell extracts by liquid chromatography-capillary electrophoresis with ultraviolet absorbance detection

A two-dimensional liquid chromatography/capillary electrophoresis technique was developed for rapid and comprehensive mapping of cell extracts. The cell extracts were first separated by reversed-phase HPLC based on hydrophobicity. Fractions of the effluent from the HPLC system were collected into 96-well microtiter plates and dried under vacuum. The fractions were reconstituted with deionized water, separated by capillary array electrophoresis based on charge-to-size ratio, and detected by UV absorption at 214 nm. Prior to analysis by multiplexed capillary electrophoresis, the reconstituted fractions were concentrated on-column using large volume sample stacking with polarity switching. In this way, high-resolution analysis of even the minor components in the complicated mixture was possible.