We report on the possibility to achieve ultra high efficiencies (order of 1 million theoretical plates) in liquid chromatography in a relatively short time of 20 min (elution time of unretained marker). This was achieved using a micropillar array column with optimized pillar diameter (5 μm) and interpillar distance (2.5 μm) to operate close to the Knox and Saleem limit of micropillar array columns in the region of the 1 million theoretical plate mark under the prevailing pressure restriction (350 bar in the present study). The obtained efficiency was slightly affected (some 15 to 20% around the optimal flow rate) by the turns that were inevitably needed to arrange a 3 m long column on a 4 in. silicon wafer.

Capitalizing on the massive increase in sample concentrations which are produced by extremely low elution volumes, nanoliquid chromatography–electrospray ionization-tandem mass spectrometry (nano-LC–ESI-MS/MS) is currently one of the most sensitive analytical technologies for the comprehensive characterization of complex protein samples. However, despite tremendous technological improvements made in the production and the packing of monodisperse spherical particles for nanoflow high-pressure liquid chromatography (HPLC), current state-of-the-art systems still suffer from limits in operation at the maximum potential of the technology. With the recent introduction of the μPAC system, which provides perfectly ordered micropillar array based chromatographic support materials, completely new chromatographic concepts for optimization toward the needs of ultrasensitive proteomics become available. Here we report on a series of benchmarking experiments comparing the performance of a commercially available 50 cm micropillar array column to a widely used nanoflow HPLC column for the proteomics analysis of 10 ng of tryptic HeLa cell digest. Comparative analysis of LC–MS/MS-data corroborated that micropillar array cartridges provide outstanding chromatographic performance, excellent retention time stability, and increased sensitivity in the analysis of low-input proteomics samples and thus repeatedly yielded almost twice as many unique peptide and unique protein group identifications when compared to conventional nanoflow HPLC columns.

In the light of the ongoing single-cell revolution, scientific disciplines are combining forces to retrieve as much relevant data as possible from trace amounts of biological material. For single-cell proteomics, this implies optimizing the entire workflow from initial cell isolation down to sample preparation, liquid chromatography (LC) separation, mass spectrometer (MS) data acquisition, and data analysis. To demonstrate the potential for single-cell and limited sample proteomics, we report on a series of benchmarking experiments where we combine LC separation on a new generation of micropillar array columns with state-of-the-art Orbitrap MS/MS detection and high-field asymmetric waveform ion mobility spectrometry (FAIMS). This dedicated limited sample column has a reduced cross section and micropillar dimensions that have been further downscaled (interpillar distance and pillar diameter by a factor of 2), resulting in improved chromatography at reduced void times. A dilution series of a HeLa tryptic digest (5–0.05 ng/μL) was used to explore the sensitivity that can be achieved. Comparative processing of the MS/MS data with Sequest HT, MS Amanda, Mascot, and SpectroMine pointed out the benefits of using Sequest HT together with INFERYS when analyzing sample amounts below 1 ng. Here, 2855 protein groups were identified from just 1 ng of HeLa tryptic digest hereby increasing detection sensitivity as compared to a previous contribution by a factor well above 10. By successfully identifying 1486 protein groups from as little as 250 pg of HeLa tryptic digest, we demonstrate outstanding sensitivity with great promise for use in limited sample proteomics workflows.

We report on the possibility to realize submicrometer plate heights using chromatographic pillar array columns filled with radially elongated diamond-shaped pillars, even when using a relatively large interpillar distance (2.5 μm) and axial pillar width (5 μm). It is demonstrated that the use of high aspect ratio radially elongated pillars which are 15 times wider in the radial than in the axial direction can lead to a fivefold reduction of the minimal plate height compared to beds filled with pillars with a similar interpillar distance but with an aspect ratio around unity (cylinders and diamonds).This increase in performance can be attributed to a decrease in longitudinal dispersion, reflected by a reduction of the B-term by a factor of about 25. Experiments were conducted at room temperature, as well as at elevated temperature (70 °C), where the B-term band broadening is known to be more critical. The main advantage of radially elongated pillar beds is that they enable a drastic reduction of the footprint of pillar array columns, allowing design of very long channels with a minimum of turns. Under retained conditions, a four-component laser dye mixture could be separated over a distance of only 1.5 mm.

Five different flow distributors have been compared as a function of the flow rate for their ability to distribute small sample volumes over the entire width of flat rectangular microfabricated pillar array columns. The investigated designs can be divided in two major categories: (1) bifurcating, radially non-interconnecting distributors and (2) radially interconnecting distributors consisting of diamond-shaped pillars, elongated in the direction perpendicular to the flow, providing a high ratio of radial permeability over axial permeability. The quality of the flow distribution was evaluated experimentally by injecting equal volumes of fluorescent tracer into each of the tested designs and calculating the obtained peak variances using the method of moments. Purely bifurcating distributors perform less well than the best possible radially interconnected distributors, because the former inevitably require the use of wide open channels (d > 10 microm), wherein a lot of band broadening can occur. By doubling the aspect ratio of the radially stretched pillars from 5 to 10, the measured peak variance drops to 1/8 of the original value. The best results were obtained with a distributor in which the flow is distributed by a bed of anisotropic pillars with an aspect ratio of 10, but our results indicate that a substantial improvement can still be made by increasing the aspect ratio and adding gradually diverging sidewalls to the inlet.

Electrochemical anodization has been applied to grow porous shell layers of 300 nm (30 nm pores) in 5 μm diameter pillar array columns (PACs) with a spacing of 2.5 μm. Using turn structures preceded and followed by the flow distributor structures recently introduced by our group and filled with radially elongated pillars, columns with quasi unlimited channel lengths could be conceived. The uniformity of the porous PAC was assessed by determining local plate heights along the channel, which appeared to be constant. Minimal (absolute) plate heights (H) between 4 and 6 μm were obtained at optimal flow rates when imposing increasing retention factors. Upon measuring the surface area involved in chromatographic retention as an indicator of the available surface area, an increase in the surface area by a factor of about 30 compared to that of non-anodized pillars was found. On reconfiguring a commercial HPLC instrument to enable on-chip injections, 90% of the performance (expressed in theoretical plates) could be maintained for a 1 m column, while for a 25 cm column severe losses were still observed. As the corresponding pressure drop for optimal operation of retained components is on the order of 10 bar per m only, portable and cheaper HPLC devices with high efficiencies become realistically conceivable.

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We report on a series of hydrodynamic chromatography separations conducted in micropillar array columns with an interpillar distance spacing of, respectively, 1.00, 0.70, and 0.47 μm. The columns have been produced using state-of-the-art deep-UV lithography and deep reactive ion etching techniques. Despite the fact that the efficiency was smaller than theoretically possible (due to fabrication limitations and significant injection and detection band broadening), it was nevertheless possible to separate mixtures of fluorescein isothiocyanate (used as the t(0) -marker) and 20- and 40-nm polystyrene beads. With the smallest interpillar distance, a resolution of R(s) = 0.5 between the 20- and 40-nm particles could be obtained in 90s over a column length of 4 cm. The selectivity obtained in the pillar array columns was found to be very similar to that observed in packed-bed columns. By detecting the fluorescent signals in a 90-μm-deep detection groove at the end of the column, the signal-to-noise ratio could be enhanced up to 150 times.