Commercial chromatographic instrumentation for bottom-up proteomics is often inadequate to resolve the number of peptides in many samples. This has inspired a number of complex approaches to increase peak capacity, including various multidimensional approaches, and reliance on advancements in mass spectrometry. One-dimensional reversed phase separations are limited by the pressure capabilities of commercial instruments and prevent the realization of greater separation power in terms of speed and resolution inherent to smaller sorbents and ultrahigh pressure liquid chromatography. Many applications with complex samples could benefit from the increased separation performance of long capillary columns packed with sub-2 µm sorbents. Here, we introduce a system that operates at a constant pressure and is capable of separations at pressures up to 45 kpsi. The system consists of a commercially available capillary liquid chromatography instrument, for sample management and gradient creation, and is modified with a storage loop and isolated pneumatic amplifier pump for elevated separation pressure. The system’s performance is assessed with a complex peptide mixture and a range of microcapillary columns packed with sub-2 µm C18 particles.

The need for multidimensional separations for bottom-up proteomic analyses has been well demonstrated by many over the past decade. The vast majority of reported approaches has focused primarily on improving the separation once the sample has already been digested. The work presented in this study shows an improvement in multidimensional approaches by prefractionation of intact proteins prior to digestion and separation of the peptides. Two modes of intact protein separation were compared, anion-exchange and reversed-phase, to assess the utility of each mode for the purpose of fractionation. Each of the samples was then enzymatically digested and analyzed by RP-UPLC-MS(E). To assess the validity of each approach, baker's yeast (Saccharomyces cerevisiae) was grown on two different carbon sources, glycerol and dextrose. More proteins were identified by the reversed-phase prefractionation approach (546) than were found by the anion-exchange method (262). As a result, there was much greater coverage of the metabolic pathways of interest for the reversed-phase method than for the anion-exchange method.

In recent years protein therapeutics have seen increasing use in the therapeutic arena. As with traditional small molecule drug substances, one is obligated to ensure purity and stability of the various dosage forms. With these higher molecular weight therapeutics a common approach for analytical characterization is enzymatic digestion followed by gradient elution liquid chromatography with mass spectrometry detection to create a peptide map (bottom-up protein analysis). Due to the difficult to separate mixtures frequently encountered, there is the need for advanced chromatographic systems featuring increased resolution and/or peak capacity that can be operated in the gradient elution format. Presently we describe an extreme ultra-pressure liquid chromatography (XUPLC) system that has been implemented as an in-house add-on to a commercial ultra-pressure chromatography system. This add-on allows operation at the 38 Kspi range, accommodates the use of capillary columns in excess of one meter packed with sub-2 μm particles and can be operated in the gradient elution format. To evaluate the utility of this system, rat growth hormone was used as a model protein and was exposed to light (λ 254 nm) to create a stress environment. When enzymatic digests of control and stressed protein were analyzed with the XUPLC system using MS detection, greater than 92% peptide coverage was achieved, including the identification some peptides where pre-oxidation of Met residues had occurred, as well as chemistry specifically related to the photolysis of protein disulfide linkages. When the same samples were analyzed by commercial UPLC and compared to the XUPLC results, the utility of the increased peak capacity available with the XUPLC was apparent as previously co-eluting peaks were now well resolved. In particular one specific degradation route was identified where a pair of isobaric cis/trans diastereomerically related peptides were well resolved by XUPLC while they were unresolved by UPLC. Clearly the use of this system operating at the higher pressure regime with long capillary columns is and will be useful in continued investigations of protein stability, especially in cases where only subtle differences in the amino acid residues have occurred during degradation.