Separation efficiency kinetics of capillary flow micro-pillar array columns for liquid chromatography

Liquid phase detection in the miniature scale. Microfluidic and capillary scale measurement and separation systems. A tutorial review

Microfluidic and capillary devices are increasingly being used in analytical applications while their overall size keeps decreasing. Detection sensitivity for these microdevices gains more importance as device sizes and consequently, sample volumes, decrease. This paper reviews optical, electrochemical, electrical, and mass spectrometric detection methods that are applicable to capillary scale and microfluidic devices, with brief introduction to the principles in each case. Much of this is considered in the context of separations. We do consider theoretical aspects of separations by open tubular liquid chromatography, arguably the most potentially fertile area of separations that has been left fallow largely because of lack of scale-appropriate detection methods. We also examine the theoretical basis of zone electrophoretic separations. Optical detection methods discussed include UV/Vis absorbance, fluorescence, chemiluminescence and refractometry. Amperometry is essentially the only electrochemical detection method used in microsystems. Suppressed conductance and especially contactless conductivity (admittance) detection are in wide use for the detection of ionic analytes. Microfluidic devices, integrated to various mass spectrometers, including ESI-MS, APCI-MS, and MALDI-MS are discussed. We consider the advantages and disadvantages of each detection method and compare the best reported limits of detection in as uniform a format as the available information allows. While this review pays more attention to recent developments, our primary focus has been on the novelty and ingenuity of the approach, regardless of when it was first proposed, as long as it can be potentially relevant to miniature platforms.

Biological mass spectrometry enables spatiotemporal 'omics: From tissues to cells to organelles

Biological processes unfold across broad spatial and temporal dimensions, and measurement of the underlying molecular world is essential to their understanding. Interdisciplinary efforts advanced mass spectrometry (MS) into a tour de force for assessing virtually all levels of the molecular architecture, some in exquisite detection sensitivity and scalability in space-time. In this review, we offer vignettes of milestones in technology innovations that ushered sample collection and processing, chemical separation, ionization, and 'omics analyses to progressively finer resolutions in the realms of tissue biopsies and limited cell populations, single cells, and subcellular organelles. Also highlighted are methodologies that empowered the acquisition and analysis of multidimensional MS data sets to reveal proteomes, peptidomes, and metabolomes in ever-deepening coverage in these limited and dynamic specimens. In pursuit of richer knowledge of biological processes, we discuss efforts pioneering the integration of orthogonal approaches from molecular and functional studies, both within and beyond MS. With established and emerging community-wide efforts ensuring scientific rigor and reproducibility, spatiotemporal MS emerged as an exciting and powerful resource to study biological systems in space-time.

On-Chip Comparison of the Performance of First- and Second-Generation Micropillar Array Columns

Because of its dimensions, the recently introduced micropillar array columns are most suited for high-efficiency liquid chromatography separations in proteomics. Unlike the packed bed columns and capillary-based column formats, the micropillar array concept still has significant room to progress in terms of the reduction of its characteristic size (i.e., pillar diameter and interpillar distance) to open the road to even higher-efficiency separations and their applications. We report here on the on-chip comparison between first-generation (Gen 1) and second-generation (Gen 2) micropillar array columns wherein the pillar and interpillar size have been halved. Because of the on-chip measurements, the observed plate heights H represent the fundamental band broadening, devoid of any extra-column band-broadening effects. The observed reduction of H with a factor of 2 around the uopt-velocity and with a factor of 4 in the C-term dominated regime of the van Deemter-curve is in full agreement with the theoretically expected gain. This shows the pillar and interpillar size reduction could be effectuated without affecting the theoretical separation potential of the micropillar arrays. Compared to Gen 1, Gen 2 offers a 4-fold reduction of the required analysis time around the optimal velocity and about a 16-fold reduction in the C-term-dominated range.

Open tubular liquid chromatography: Recent advances and future trends

Nano-liquid chromatography (nanoLC) is gaining significant attention as a primary analytical technique across various scientific domains. Unlike conventional high-performance LC, nanoLC utilizes columns with inner diameters (i.ds.) usually ranging from 10 to 150 μm and operates at mobile phase flow rates between 10 and 1000 nl/min, offering improved chromatographic performance and detectability. Currently, most exploration of nanoLC has focused on particle-packed columns. Although open tubular LC (OTLC) can provide superior performance, optimized OTLC columns require very narrow i.ds. (< 10 μm) and demand challenging instrumentation. At the moment, these challenges have limited the success of OTLC. Nevertheless, remarkable progress has been made in developing and utilizing OTLC systems featuring narrow columns (< 2 μm). Additionally, significant efforts have been made to explore larger columns (10-75 μm i.d), demonstrating practical applicability in many situations. Due to their perceived advantages, interest in OTLC has resurged in the last two decades. This review provides an updated outlook on the latest developments in OTLC, focusing on instrumental challenges, achievements, and advancements in column technology. Moreover, it outlines selected applications that illustrate the potential of OTLC for performing targeted and untargeted studies.

Mass spectrometry-based high-throughput proteomics and its role in biomedical studies and systems biology

There are multiple reasons why the next generation of biological and medical studies require increasing numbers of samples. Biological systems are dynamic, and the effect of a perturbation depends on the genetic background and environment. As a consequence, many conditions need to be considered to reach generalizable conclusions. Moreover, human population and clinical studies only reach sufficient statistical power if conducted at scale and with precise measurement methods. Finally, many proteins remain without sufficient functional annotations, because they have not been systematically studied under a broad range of conditions. In this review, we discuss the latest technical developments in mass spectrometry (MS)-based proteomics that facilitate large-scale studies by fast and efficient chromatography, fast scanning mass spectrometers, data-independent acquisition (DIA), and new software. We further highlight recent studies which demonstrate how high-throughput (HT) proteomics can be applied to capture biological diversity, to annotate gene functions or to generate predictive and prognostic models for human diseases.

Reversed-Phase Liquid Chromatography of Peptides for Bottom-Up Proteomics: A Tutorial

The performance of the current bottom-up liquid chromatography hyphenated with mass spectrometry (LC-MS) analyses has undoubtedly been fueled by spectacular progress in mass spectrometry. It is thus not surprising that the MS instrument attracts the most attention during LC-MS method development, whereas optimizing conditions for peptide separation using reversed-phase liquid chromatography (RPLC) remains somewhat in its shadow. Consequently, the wisdom of the fundaments of chromatography is slowly vanishing from some laboratories. However, the full potential of advanced MS instruments cannot be achieved without highly efficient RPLC. This is impossible to attain without understanding fundamental processes in the chromatographic system and the properties of peptides important for their chromatographic behavior. We wrote this tutorial intending to give practitioners an overview of critical aspects of peptide separation using RPLC to facilitate setting the LC parameters so that they can leverage the full capabilities of their MS instruments. After briefly introducing the gradient separation of peptides, we discuss their properties that affect the quality of LC-MS chromatograms the most. Next, we address the in-column and extra-column broadening. The last section is devoted to key parameters of LC-MS methods. We also extracted trends in practice from recent bottom-up proteomics studies and correlated them with the current knowledge on peptide RPLC separation.

Mass Fabrication of Capillary Columns Based on Centrifugal Packing

Packed capillary columns have become the standard front-end separation device for mass spectrometry-based proteomics. The development of simple, fast, and robust capillary column technology, especially that with mass-fabrication capacity, can greatly improve analytical throughput and reproducibility in omics research. In this technical note, we report a centrifugal packing technology, which has the capability to mass fabricate high quality capillary columns with a 2886 columns/day fabrication throughput. The centrifugally packed columns presented significantly improved efficiency (reduced plate height h_min = 1.6, 37%-40% improvement compared with slurry packed columns), advanced kinetic performance limit, and excellent column-to-column reproducibility (2.0% RSD for retention time, 50 columns). Such columns enabled ∼5300 HeLa proteins identified in single-shot proteomic analysis, displaying both intercolumn and inter-run retention time stability (retention time RSD = 0.94% between nine replicates on three columns for probing peptide sequence). The mass-fabrication technology reported in this technical note may support disposable use of high quality chromatographic columns in large-scale bioanalysis.

On the potential of micro-flow LC-MS/MS in proteomics

INTRODUCTION

Due to its excellent sensitivity, nano-flow liquid chromatography tandem mass spectrometry (LC-MS/MS) is the mainstay in proteome research; however, this comes at the expense of limited throughput and robustness. In contrast, micro-flow LC-MS/MS enables high-throughput, robustness, quantitative reproducibility, and precision while retaining a moderate degree of sensitivity. Such features make it an attractive technology for a wide range of proteomic applications. In particular, large-scale projects involving the analysis of hundreds to thousands of samples.

AREAS COVERED

This review summarizes the history of chromatographic separation in discovery proteomics with a focus on micro-flow LC-MS/MS, discusses the current state-of-the-art, highlights advances in column development and instrumentation, and provides guidance on which LC flow best supports different types of proteomic applications.

EXPERT OPINION

Micro-flow LC-MS/MS will replace nano-flow LC-MS/MS in many proteomic applications, particularly when sample quantities are not limited and sample cohorts are large. Examples include clinical analyses of body fluids, tissues, drug discovery and chemical biology investigations, plus systems biology projects across all kingdoms of life. When combined with rapid and sensitive MS, intelligent data acquisition, and informatics approaches, it will soon become possible to analyze large cohorts of more than 10,000 samples in a comprehensive and fully quantitative fashion.

3D printed device for epitachophoresis

Polyacrylamide or agarose gels are the most frequently used sieving and stabilizing media in slab gel electrophoresis. Recently, we have introduced a new electrophoretic technique for concentration/separation of milliliter sample volumes. In this technique, the gel is used primarily as an anticonvection media eliminating liquid flow during the electromigration. While serving well for the liquid stabilization, the gels can undergo deformation when exposed to a discontinuous electrolyte buffer system used in epitachophoresis. In this work, we have explored 3D printing to form rigid stabilizing manifolds to minimize liquid flow during the epitachophoresis run. The whole device was printed using the stereolithography technique from a low water-absorbing resin. The stabilizing manifold, serving as the gel substitute, was printed as a replaceable composite structure preventing electrolyte mixing during the separation. Different geometries of the 3D printed stabilizing manifolds were tested for use in concentrating ionic sample components without spatial separation. The presented device can focus analytes from 3 or 4 mL of the sample to 150 μL or less, depending on the collection cup size. With the 150 μL collection cup, this represents the enrichment factor from 20 to 27. The time of concentration was from 15 to 25 min, depending on stabilization media and power used.

Capillary ultrahigh-pressure liquid chromatography-mass spectrometry for fast and high resolution metabolomics separations

LC-MS is an important tool for metabolomics due its high sensitivity and broad metabolite coverage. The goal of improving resolution and decreasing analysis time in HPLC has led to the use of 5 - 15 cm long columns packed with 1.7 - 1.9 µm particles requiring pressures of 8 - 12 kpsi. We report on the potential for capillary LC-MS based metabolomics utilizing porous C18 particles down to 1.1 µm diameter and columns up to 50 cm long with an operating pressure of 35 kpsi. Our experiments show that it is possible to pack columns with 1.1 µm porous particles to provide predicted improvements in separation time and efficiency. Using kinetic plots to guide the choice of column length and particle size, we packed 50 cm long columns with 1.7 µm particles and 20 cm long columns with 1.1 µm particles, which should produce equivalent performance in shorter times. Columns were tested by performing isocratic and gradient LC-MS analyses of small molecule metabolites and extracts from plasma. These columns provided approximately 100,000 theoretical plates for metabolite standards and peak capacities over 500 in 100 min for a complex plasma extract with robust interfacing to MS. To generate a given peak capacity, the 1.1 µm particles in 20 cm columns required roughly 75% of the time as 1.7 µm particles in 50 cm columns with both operated at 35 kpsi. The 1.1 µm particle packed columns generated a given peak capacity nearly 3 times faster than 1.7 µm particles in 15 cm columns operated at ~10 kpsi. This latter condition represents commercial state of the art for capillary LC. To consider practical benefits for metabolomics, the effect of different LC-MS variables on mass spectral feature detection was evaluated. Lower flow rates (down to 700 nL/min) and larger injection volumes (up to 1 µL) increased the features detected with modest loss in separation performance. The results demonstrate the potential for fast and high resolution separations for metabolomics using 1.1 µm particles operated at 35 kpsi for capillary LC-MS.