Review: Microfluidic applications in metabolomics and metabolic profiling.

Metabolomics is an emerging area of research focused on measuring small molecules in biological samples. There are a number of different types of metabolomics, ranging from global profiling of all metabolites in a single sample to measurement of a selected group of analytes. Microfluidics and related technologies have been used in this research area with good success. The aim of this review article is to summarize the use of microfluidics in metabolomics. Direct application of microfluidics to the determination of small molecules is covered first. Next, important sample preparation methods developed for microfluidics and applicable to metabolomics are covered. Finally, a summary of metabolomic work as it relates to analysis of cellular events using microfluidics is covered.

Electrode array detector for microchip capillary electrophoresis.

Selectivity and resolution for analyses conducted using microfluidic devices can be improved by increasing the total number of individual detection elements in the device. Here, a poly(dimethylsiloxane) capillary electrophoresis microchip was fabricated with an integrated electrode array for selective detection of small molecules. Eight individually addressable gold electrodes were incorporated in series after a palladium current decoupler in the separation channel of an electrophoresis microchip. The electrode array device was characterized using a mixture of biologically relevant analytes and xenobiotics: norepinephrine, 4-aminophenol, acetaminophen, uric acid, and 3,4-dihydroxyphenylacetic acid. Separation efficiencies as high as 9000 +/- 1000 plates (n = 3) for 3,4-dihydroxyphenylacetic acid and limits of detection as low as 2.6 +/- 1.2 microM (n = 3) for norepinephrine were obtained using this device. After characterizing the performance of the device, potential step detection was conducted at the array electrodes and selective detection achieved based upon differences in redox potentials for individual analytes. Utilization of potential step detection was particularly advantageous for resolving co-migrating species; resolution of 3,4-dihydroxy-l-phenylalanine from acetaminophen using potential control was demonstrated. Finally, a human urine sample was analyzed using potential step detection to demonstrate the applicability of this device for complex sample analysis.

Integrated membrane filters for minimizing hydrodynamic flow and filtering in microfluidic devices.

Microfluidic devices have gained significant scientific interest due to the potential to develop portable, inexpensive analytical tools capable of quick analyses with low sample consumption. These qualities make microfluidic devices attractive for point-of-use measurements where traditional techniques have limited functionality. Many samples of interest in biological and environmental analysis, however, contain insoluble particles that can block microchannels, and manual filtration prior to analysis is not desirable for point-of-use applications. Similarly, some situations involve limited control of the sample volume, potentially causing unwanted hydrodynamic flow due to differential fluid heads. Here, we present the successful inclusion of track-etched polycarbonate membrane filters into the reservoirs of poly(dimethylsiloxane) capillary electrophoresis microchips. The membranes were shown to filter insoluble particles with selectivity based on the membrane pore diameter. Electrophoretic separations with membrane-containing microchips were performed on cations, anions, and amino acids and monitored using conductivity and fluorescence detection. The dependence of peak areas on head pressure in gated injection was shown to be reduced by up to 92%. Results indicate that separation performance is not hindered by the addition of membranes. Incorporating membranes into the reservoirs of microfluidic devices will allow for improved analysis of complex solutions and samples with poorly controlled volume.

Instrumentation for medium-throughput two-dimensional capillary electrophoresis with laser-induced fluorescence detection.

In two-dimensional capillary electrophoresis, a sample undergoes separation in the first dimension capillary by sieving electrophoresis. Fractions are periodically transferred across an interface into a second dimension capillary, where components are further resolved by micellar electrokinetic capillary electrophoresis. Previous instruments employed one pair of capillaries to analyze a single sample. We now report a multiplexed system that allows separation of five samples in parallel. Samples are injected into five first-dimension capillaries, fractions are transferred across an interface to 5 second-dimension capillaries, and analyte is detected by laser-induced fluorescence in a five-capillary sheath-flow cuvette. The instrument produces detection limits of 940 +/- 350 yoctomoles for 3-(2-furoyl)quinoline-2-carboxaldehyde labeled trypsin inhibitor in one-dimensional separation; detection limits degrade by a factor of 3.8 for two-dimensional separations. Two-dimensional capillary electrophoresis expression fingerprints were obtained from homogenates prepared from a lung cancer (A549) cell line, on the basis of capillary sieving electrophoresis (CSE) and micellar electrophoresis capillary chromatography (MECC). An average of 131 spots is resolved with signal-to-noise greater than 10. A Gaussian surface was fit to a set of 20 spots in each electropherogram. The mean spot width, expressed as standard deviation of the Gaussian function, was 2.3 +/- 0.7 transfers in the CSE dimension and 0.46 +/- 0.25 s in the MECC dimension. The standard deviation in spot position was 1.8 +/- 1.2 transfers in the CSE dimension and 0.88 +/- 0.55 s in the MECC dimension. Spot capacity was 300.

Reproducible two-dimensional capillary electrophoresis analysis of Barrett's esophagus tissues.

We have constructed a high-speed, two-dimensional capillary electrophoresis system with a compact and high-sensitivity fluorescence detector. This instrument is used for the rapid and reproducible separations of Barrett's esophagus tissue homogenates. Proteins and biogenic amines are labeled with the fluorogenic reagent 3-(2-furoyl)quinoline-2-carboxaldehyde. Labeled biomolecules are separated sequentially in two capillaries. The first capillary employs capillary sieving electrophoresis using a replaceable sieving matrix. Fractions are successively transferred to a second capillary where they undergo additional separation by micellar electrokinetic capillary chromatography. The comprehensive two-dimensional separation requires 60 min. Within-day migration time reproducibility is better than 1% in both dimensions for the 50 most intense features. Between-day migration time precision is 1.3% for CSE and better than 0.6% for MECC. Biopsies were obtained from the squamous epithelium in the proximal tubular esophagus, Barrett's epithelium from the distal esophagus, and fundus region of the stomach from each of three Barrett's esophagus patients with informed consent. We identified 18 features from the homogenate profiles as biogenic amines and amino acids. For each of the patients, Barrett's biopsies had more than 5 times the levels of phenylalanine and alanine as compared to squamous tissues. The patient with high-grade dysplasia shows the highest concentrations for 13 of the amino acids across all tissue types. Concentrations of glycine are 40 times higher in squamous biopsies compared to Barrett's and fundal biopsies from the patient with high-grade dysplasia. These results suggest that two-dimensional capillary electrophoresis may be of value for the rapid characterization of endoscopic and surgical biopsies.

Identification of proteins in single-cell capillary electrophoresis fingerprints based on comigration with standard proteins.

In the previous paper in this Journal, we reported the use of capillary sieving electrophoresis to characterize proteins expressed by single cancer cells at specific phases in the cell cycle. Analysis of the data revealed one component with cell cycle-dependent changes in expression at the 99% confidence limit. However, the amount of protein present in a single cell is far too small to allow its direct identification by mass spectrometry. In this paper, we report a method by which such proteins can be tentatively identified. We perform standard SDS-PAGE electrophoresis of the proteins contained within a homogenate prepared from an HT29 cell culture. Proteins extracted from bands in the gel are identified by mass spectrometry. The proteins also provide a set of standards that can be used to spike the sample before capillary sieving electrophoresis (CSE) separation; comigration is taken as evidence for the identity of the target protein. In a proof-of-principle experiment, a single band migrating at approximately 47 kDa was isolated from the SDS-PAGE gel generated from the HT29 cell line. Proteins extracted from this band were used to spike a CSE separation of the same extract. This band comigrated with a cell cycle-dependent component identified from single-cell analysis. In-gel digestion and LC/MS/MS were used to identify five proteins, including cytokeratin 18, which is the product of the most highly expressed gene in this cell line.