Due to its unique structure, core-shell material has presented significantly improved chromatographic performance in comparison with conventional totally porous material. This has been well demonstrated in the analytical column format, e.g. 4.6 mm i.d. columns. In the proteomics field, there is always a demand for high resolution microseparation tools. In order to explore core-shell material\'s potential in proteomics-oriented microseparations, we investigated chromatographic performance of core-shell material in a nanoLC format, as well as its resolving power for protein digests. The results show core-shell nanoLC columns have similar van Deemter curves to the totally porous particle-packed nanoLC columns. For 100 µm i.d. capillary columns, the core-shell material does not have significantly better dynamics. However, both core-shell and totally porous particle-packed nanoLC columns have shown high efficiencies: plate heights of ~11 µm, equivalent to 90000 plates per meter, have been achieved with 5 µm particles. Using a 60 cm long core-shell nanoLC column, 72000 plates were realized in an isocratic separation of neutral compounds. For a 15 cm long nanoLC column, a maximum peak capacity of 220 has been achieved in a 5 hour gradient separation of protein digests, indicating the high resolving power of core-shell nanoLC columns. With a standard HeLa cell lysate as the sample, 2546 proteins were identified by using the core-shell nanoLC column, while 2916 proteins were identified by using the totally porous particle-packed nanoLC column. Comparing the two sets of proteomics data, it was found that 1830 proteins were identified by both columns, while 1086 and 716 proteins were uniquely identified by using totally porous and core-shell particle-packed nanoLC columns, respectively, suggesting their complementarity in nanoLC-MS based proteomics.

Column heating strategy is often applied in nano-high-performance liquid chromatography-mass spectrometer (nanoHPLC-MS) platform for enhancing the analytical efficiency of peptides or proteins. Nonetheless, the influence effects of column heating in peptides or proteins identification still lack of deep understanding. In this study, a systematic comparison of room temperature (RT) and column heating of nanoHPLC was done. Based on the data, under column heating condition, the backpressure of nanoHPLC can be decreased. Due to the increase of resolution, the peak widths of precursor ion were narrowed. As a result, in MS/MS data acquisition part, more time was spared for MS1 detecting and MS2 fragmenting, which eventually resulted in increased identification of peptides and proteins. Moreover, we also proposed the application scope of column heating by evaluating its influence on sample detection. On one hand, column heating significantly increased the identification of membrane proteins due to more efficient elution of highly hydrophobic peptides compared with RT. On the other hand, heating was not suitable for analyzing short or/and hydrophilic peptides with low retention time, which would be eluted out during sample loading process under high temperature and missed by mass spectrometric detection. In conclusion, our study provides a reference for rational application of column heating in proteomics research.

Hydrophilic interaction liquid chromatography, HILIC, is a relatively new HPLC mode. Compared with other HPLC modes, HILIC is a high resolution chromatographic mode with high peak capacity for separations of complex mixtures. Although the separation mechanism is still not completely clear, HILIC has been widely used for analysis of hydrophilic compounds which are difficult for reversed phase chromatography to retain and separate. In this study, we fabricated and investigated nanoHILIC columns in terms of separation efficiency, van Deemter curves and more importantly, we focused on long packed capillary columns, and studied their extreme resolution for protein digests. Using meter long nanoHILIC columns packed with 5 μm particles, we realized a high peak capacity of 130. Based on nanoLC-MS, we compared the resolution and protein identification capabilities of nanoHILIC and nanoRPLC. The results indicate both nanoHILIC and nanoRPLC can provide high resolution for protein sequencing but neither mode is significantly better than the other. Among the 99 digest peptides identified, 17 were uniquely identified by nanoHILIC-MS and 20 were uniquely identified by nanoRPLC-MS and 62 were identified by both methods. Although at this moment in time, nanoRPLC is the most popular microseparation tool in proteomics, the excellent complementarity of nanoHILIC and nanoRPLC suggests their combined use in achieving deep-coverage in MS-based proteomics.

High-performance nanoflow liquid-phase separation techniques such as nanoflow liquid chromatography (nanoLC), capillary electrophoresis (CE), and microchip chromatography and electrophoresis (chip-ICP-MS) have been hyphenated with inductively coupled plasma mass spectrometry (ICP-MS) extensively. This hyphenation combines the excellent characteristics of the front-end separation technology, such as high selectivity, sensitivity, and speed, and low sample consumption, and the advantages of back-end ICP-MS, such as high resolution, wide dynamic range, and absolute quantification capability. Thus, such hyphenation is becoming an increasingly important analytical tool. Herein we systematically introduce the recent development of hyphenated nanoLC, CE, and chip-ICP-MS, review its application in chemical and biochemical analysis, and discuss potential future developments of hyphenating these technologies.