A poly(dimethylsiloxane) (PDMS) microfluidic chip-based cartridge was fabricated by sandwiching commercial dialysis membrane and inserting fused-silica capillary into the end of channel according to the principle and structure of a commercial fused-silicon capillary-based cartridge, which can adapt to an IEF analyzer for isoelectric focusing with whole channel imaging detection (IEF-WCID). The novel design of sandwiching membrane in this chip not only eliminated the unfavorable hydrodynamic pressure, leading to poor IEF reproducibility, but made the sample injection much easy. Thus the reproducibility of analysis was very good. The prepared microfluidic chips were applied for qualitative and quantitative analysis of proteins. The six pI markers in the range of 3–10 were separated by IEF under the optimized conditions. The pH gradients exhibited good linear by plotting the pI versus peak position, and the correlation coefficient reached to 0.9994 and 0.9995. The separation of more complicated human hemoglobin control and myoglobin sample could be achieved. By comparison with the separation efficiency obtained on the microfluidic chip and commercial cartridge, the results were similar, which indicates the capillary cartridge may be replaced with the cost-efficient PDMS microfluidic chip. It is anticipated the high throughput analysis can be easily performed on this microfluidic chip patterned multi-channels. The techniques of capillary electrophoresis (CE) have been extensively explored for the chip-based separation. Isoelectric focusing (IEF) as one of high-resolution CE techniques has been widely applied for the separation of zwitterionic biomolecules, such as proteins and peptides. After the samples were focused at their corresponding pIs, the focused zones were mobilized to pass through the detection point for obtaining an electropherogram. This single-point detection imposes extensive restriction for chip-based IEF because a mobilization process requires additional time and lowers resolution and reproducibility of the separation [1]. An alternative is whole-column imaging detection developed by Pawliszyn et al [2] is an ideal detection method for IEF because no mobilization is required, which avoids the disadvantages as mentioned previously. Most microfluidic systems could be fabricated in glass/silicon or polymers in which the channels are defined using photolithography and micromachining. Mao and Pawliszyn [3] have developed a method for IEF on an etched quartz chip following whole-channel imaging detection (WCID). Ren et al [4] presented an integrated WCID system on glass microfluidic chip. However, these materials have some disadvantages such as expensive and fragile and so on. An attractive alternative for fabrication of microfluidic devices is using poly(dimethylsiloxane) (PDMS) as material, which has unique properties such as nontoxic, optical transparent down to 280 nm, elastomeric, hydrophobic surface chemistry Yao et al. [5] designed the glass/PDMS microchip integrated whole-column fluorescence imaging detection for IEF of R-phycoerythrin. Our preliminary studies have successfully developed a PDMS chip-based cartridge for IEF-WCID. It is due to hydrodynamic flow between two reservoirs that the focused zones were mobilized, thus gave poor reproducibility and difficulty in sample infusion. As membranes have been integrated into microchips for microdialysis, protein digestion, solid-phase extraction, desalting, pumping and so on, it could minimize hydrodynamic flow by using membranes as a filter. Although a simple PDMS chip-based cartridge has been successfully fabricated in our labs according to the principle of commercial capillary-based cartridge, it is difficult to introduce the sample into channel for IEF-WCID. As the vacuum was applied in one end of channel for infusing of solution into channel, the lifetime of this chip-based cartridge is shortened. Additionally, the hydrodynamic flow is occurred due to the different heights of anolyte and catholyte in two reservoirs, respectively. The IEF separation was deteriorated by the infusion of anolyte or catholyte, thus leading to poor reproducibility of IEF-WCID analysis. Similar to the hollow fiber in the commercial capillary-based cartridge in which it is aimed to separate the sample in the capillary and electrolytes in the reservoirs, porous membrane was integrated into PDMS chips for decrease of hydrodynamic flow [6]. As a result, integration of dialysis membrane is considered into the design of our new chip-based cartridge. Up to now, many approaches have been described to integrate membranes into glass/quartz or polymeric microfluidic chips. A simple method is direct incorporation by gluing or clamping commercial flat membranes. A major problem of this method is sealing, otherwise, a phenomenon of leakage around the membranes is always occurred due to the capillary force. A novel approach of sandwiching dialysis membrane was developed as schematically indicated in Figure 1. After optimizing IEF conditions, the separation of pI markers was performed on the obtained PDMS microfluidic chip. As exhibited in Figure 2a, six pI markers could be well separated on the PDMS chips patterned the channel of 100 μm deep, 100 μm wide by IEF-WCID. All the peaks were sharp and symmetric, indicating that both EOF and analytes adsorption were completely suppressed by the dynamic coating of PVP. The plots of peak position versus pI of these pI markers suggested good linearity of pH gradient (as shown in Figure 2b). The linear correlation coefficient was 0.9995 (n = 6). As expected to the capillary-based cartridge, the PDMS microfluidic chips could be applied for qualitative and quantitative analysis of proteins. Figure 3a exhibited that human hemoglobin control AFSC contains four known isoforms (HbA, HbF, HbS and HbC) mixed with two pI marker 6.14 and 8.18 were well separated on the PDMS chip by IEF-WCID, indicating the strong separation ability of chip similar to the commercial capillary-based cartridge. According to the linearity of pH gradient, these four isoforms with the pIs of 7.0, 7.1, 7.3 and 7.5, respectively, could be detected. An unknown isoform in human hemoglobin control marked asterisk in Figure 3A observed besides the definite four isoforms A, F, S and C. The myoglobin from horse heart contains two isoforms, whose pIs are 6.8 and 7.2, respectively. It can be seen from Figure 3b that these two isoforms were separated on PDMS chip by IEF-WCID. The peak 1 and 2 could be assigned to the two isoforms according to their pI. The pI of unknown peak marked asterisk could be measured to 6.25.