The practice of bottom‐up proteomics relies to a large extent on the separation performance that can be achieved with state‐of‐the art nano LC‐MS/MS equipment. Depending on the sample complexity or the instrument time that can be dedicated to a certain sample, different LC columns and corresponding LC‐MS/MS methods are required. When aiming for comprehensive proteome analysis with deep coverage, relatively long columns (lengths up to 75 cm) are typically operated with long and shallow solvent gradients, delivering the highest chromatographic performance. However, daily routine proteome analysis often deals with much less complex samples or demands increased sample throughput, making total analysis times above 120 min undesirable or even impossible. The LC columns typically used for this type of analyses do not exceed 25 cm in length, with a focus on workflow robustness and efficiency rather than on maximizing chromatographic performance or peak capacity (1).In the past few years, micro pillar array column (μPAC™) technology has evolved from a tool to perform fundamental LC research to a powerful alternative for classical nano LC columns. The inherent high permeability and low ‘on‐column’ dispersion obtained by the perfect order of the separation bed makes pillar array based chromatography unique in its kind. The peak dispersion originating from heterogeneous flow paths in the separation bed is drastically reduced and therefore components remain much more concentrated during separation (2). Apart from an improved efficiency, pillar array columns can also be designed with substantially lower flow resistances compared to packed bed columns. The distance between the pillars can be independently controlled from the pillar size, enabling the fabrication of columns over a range of external porosities.Using a 50 cm long reversed phase C18 μPAC™ nano LC column in combination with a Thermo Orbitrap Elite mass spectrometer for detection, we demonstrate extremely robust and high‐throughput proteome analysis at capillary flow rates up to 2 μl/min. At these flow rates, sample throughput can be increased to 20, 30, 60 and even 100 samples per day with corresponding peak capacity values (nC) of respectively 300, 250, 200 and 150. When comparing the chromatographic performance that could be obtained for single protein and cell lysate tryptic digest samples to state‐of‐the art packed bed nano LC columns (packed with sub 2 μm silica particles), average peptide peak widths could be reduced by a factor of 1.6. For complex HeLa cell digest samples, this resulted in an increase in peptide and protein group identifications of respectively 60 and 40%.
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