Achieving a Peak Capacity of 1800 Using an 8 m Long Pillar Array Column

Repurposed 3D Printer Allows Economical and Programmable Fraction Collection for Proteomics of Nanogram Scale Samples

In this work, we describe the construction and application of a repurposed 3D-printer as a fraction collector. We utilize a nano-LC to ensure minimal volumes and surfaces although any LC can be coupled. The setup operates as a high-pH fractionation system capable of effectively working with nanogram scales of lysate digests. The 2D RP-RP system demonstrated superior proteome coverage over single-shot data-dependent acquisition (DDA) analysis using only 5 ng of human cell lysate digest with performance increasing with increasing amounts of material. We found that the fractionation system allowed over 60% signal recovery at the peptide level and, more importantly, we observed improved protein level intensity coverage, which indicates the complexity reduction afforded by the system outweighs the sample losses endured. The application of data-independent acquisition (DIA) and wide window acquisition (WWA) to fractionated samples allowed nearly 8000 proteins to be identified from 50 ng of the material. The utility of the 2D system was further investigated for phosphoproteomics (>21 000 phosphosites from 50 μg starting material) and pull-down type experiments and showed substantial improvements over single-shot experiments. We show that the 2D RP-RP system is a highly versatile and powerful tool for many proteomics workflows.

The best structures of LC columns-A theoretical perspective

The largest peak capacity (n) that LC analysis can generate in isocratic or gradient elution analysis of a given sample in a given time at a given pressure is proportional to the quality factor (qmax) of its column structure. In this study, the multi-channel structures with open pseudo-planar channels (OPPC) and open circular channels (OCC) where compared with PC2 - a typical core-shell column packed with 2 μm particles. These columns have qmax of 1.27, 1.17 and 0.41, respectively. The former two qmax are the highest among all known column structures - about 3 times higher than qmax of PC2. This means that the OPPC and OCC can generate about 3 times higher n compared to what a PC2 can in the same analysis time (tanal) at the same pressure, or they require about 81 times shorter tanal (81 is the 4th power of 3) to generate the same n as a PC2 can at the same pressure. However, while PC2 is a commercially available column, there are substantial challenges in manufacturing the OPPC and OCC that can compete with PC2 in practical applications. In order to be competitive with PC2, the OPPC and OCC should have sub-1μm characteristic dimensions (e.g., the inter-pillar distance, g, in OPPC-based pillar array columns, internal diameters of OCC). Thus, in order to compete with PC2 in one scenario, an OPPC requires g ≤ 0.14 μm. Additionally, to be competitive with PC2, OPPC and OCC should be able to sustain the same high pressure. Highlighting the challenges of their design and manufacturing might help to develop the manufacturable columns substantially superior to the packed ones.

Rapid detection of glycosylated hemoglobin levels by a microchip liquid chromatography system in gradient elution mode

BACKGROUND

The determination of glycosylated hemoglobin (HbA1c) is crucial for diabetes diagnosis and can provide more substantial results than the simple measurement of glycemia. While there is a lack of simple methods for the determination of HbA1c using a point-of-care test (POCT) compared to glycemia measurement. In particular, high-performance liquid chromatography (HPLC) is considered the current gold standard for determining HbA1c levels. However, commercial HPLC systems usually have some sort of disadvantages such as bulky size, high-cost and need for qualified operators. Therefore, there is an urgent demand to develop a portable, and fast HbA1c detection system consuming fewer reagents.

RESULTS

We present a novel microchip that integrates a micromixer, passive injector, packed column and detection cell. The integrated microchip, in which all the microstructures were formed in the CNC machining center through micro-milling, is small in size (30 mm × 70 mm × 10 mm), and can withstand 1600 psi of liquid pressure. The integrated design is beneficial to reduce the band broadening caused by dead volume. Based on the microchip, a microchip liquid chromatography (LC) system was built and applied to the analysis of HbA1c. The separation conditions of HbA1c in blood calibrator samples were optimized using the microchip LC system. Samples containing four levels of HbA1c were completely separated within 2 min in optimal gradient conditions, with an inaccuracy (<3.2 %), a coefficient of variation (c.v. < 2.1 %) and a correlation coefficient (R2 = 0.993), indicating excellent separation efficiency and reproducibility.

SIGNIFICANCE

The POCT of HbA1c is critical for diabetes diagnosis. The microchip chromatography system was developed for HbA1c determination, which contains an integrated microchip and works under a gradient elution. It surpasses existing chip technology in terms of separation performance and detection speed, providing a competitive advantage for POCT of HbA1c. It is considered one important step for realizing efficient portable systems for timely and accurate diabetes diagnosis.

Two-dimensional liquid chromatography-mass spectrometry for lipidomics using off-line coupling of hydrophilic interaction liquid chromatography with 50 cm long reversed phase capillary columns

Comprehensive characterization of the lipidome remains a challenge requiring development of new analytical approaches to expand lipid coverage in complex samples. In this work, offline two-dimensional liquid chromatography-mass spectrometry was investigated for lipidomics from human plasma. Hydrophilic interaction liquid chromatography was implemented in the first dimension to fractionate lipid classes. Nine fractions were collected and subjected to a second-dimension separation utilizing 50 cm capillary columns packed with 1.7 µm C18 particles operated on custom-built instrumentation at 35 kpsi. Online coupling with time-of-flight mass spectrometry allowed putative lipid identification from precursor-mass based library searching. The method had good orthogonality (fractional coverage of ∼40%), achieved a peak capacity of approximately 1900 in 600 min, and detected over 1000 lipids from a 5 µL injection of a human plasma extract while consuming less than 3 mL of solvent. The results demonstrate the expected gains in peak capacity when employing long columns and two-dimensional separations and illustrate practical approaches for improving lipidome coverage from complex biological samples.

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.

Deep Single-Shot NanoLC-MS Proteome Profiling with a 1500 Bar UHPLC System, Long Fully Porous Columns, and HRAM MS

This study demonstrates how the latest ultrahigh-performance liquid chromatography (UHPLC) technology can be combined with high-resolution accurate-mass (HRAM) mass spectrometry (MS) and long columns packed with fully porous particles to improve bottom-up proteomics analysis with nanoflow liquid chromatography–mass spectrometry (nanoLC-MS) methods. The increased back pressures from the UHPLC system enabled the use of 75 μm I.D. × 75 cm columns packed with 2 μm particles at a typical 300 nL/min flow rate as well as elevated and reduced flow rates. The constant pressure pump operation at 1500 bar reduced sample loading and column washing/equilibration stages and overall overhead time, which maximizes MS utilization time. The versatility of flow rate optimization to balance the sensitivity, throughput with sample loading amount, and capability of using longer gradients contributes to a greater number of peptide and protein identifications for single-shot bottom-up proteomics experiments. The routine proteome profiling and precise quantification of >7000 proteins with single-shot nanoLC-MS analysis open possibilities for large-scale discovery studies with a deep dive into the protein level alterations. Data are available via ProteomeXchange with identifier PXD035665.

Nanoscale Solid-Phase Isobaric Labeling for Multiplexed Quantitative Phosphoproteomics

We established a workflow for highly sensitive multiplexed quantitative phosphoproteomics using a nanoscale solid-phase tandem mass tag (TMT) labeling reactor. Phosphopeptides were first enriched by titanium oxide chromatography and then labeled with isobaric TMT reagents in a StageTip packed with hydrophobic polymer-based sorbents. We found that TMT-labeled singly phosphorylated peptides tend to flow through the titanium oxide column. Therefore, TMT labeling should be performed after the enrichment step from tryptic peptides, resulting in the need for microscale reactions with small amounts of phosphopeptides. Using an optimized protocol for tens to hundreds of nanograms of phosphopeptides, we obtained a nearly 10-fold increase in sensitivity compared to the conventional solution-based TMT protocol. We demonstrate that this nanoscale phosphoproteomics protocol works for 50 μg of HeLa proteins treated with selumetinib, and we successfully quantified the selumetinib-regulated phosphorylated sites on a proteome scale. The MS raw data files have been deposited with the ProteomeXchange Consortium via the jPOST partner repository (https://jpostdb.org) with the data set identifier PXD025536.

Three-dimensional graphing representing six variables for speed and separation performance in liquid chromatography

The two variables, flow rate and column length, enable naive determination of the number of theoretical plates (N) in isocratic elution; this, in turn, enables the formation of a three-dimensional graph with N as the z-axis. An alternate three-dimensional graph with N as the z-axis can be drawn, then, with the alternate basal plane illustrating the pressure drop and hold-up time. In this article, the pressure drop and hold-up time are formulated so as to be represented unitarily in the former graph, because the flow rate and column length interact simultaneously as operational variables. This formulation manipulates both the pressure drop and the hold-up time as logarithmic axes, to evaluate the landscape. Also of use is the representation, in the same graph, of the height equivalent to a theoretical plate, as the fundamental property of the packing supports. For this purpose, the number of theoretical plates per unit length are here introduced as the sixth variable, instead of the height equivalent to a theoretical plate. Representing the six variables in three-dimensional graphs enables a clear understanding both of the separation condition optimization methods and the relation among variables for the speed and separation performance. The linear velocity, column length, N, velocity-length product, hold-up time, and number of theoretical plates per unit length, are here selected as the six elementary variables for the three-dimensional graphs; and, based on the packing supports of 2, 3, and 5-μm particle and monolithic columns. Finally, the usage of logarithmic three-dimensional graph is illustrated for understanding the speed and separation performance.

[Recent advances in microchip liquid chromatography]

Miniaturization is an important trend in modern analytical instrument development, including miniaturized gas chromatography and liquid chromatography, as well as micro bore columns and capillary-to-microfluidics-based platforms. Apart from the miniaturization of the separation column, which is the core part of a chromatographic system, other parts of the system, including the sampler, pumping system, gradient generation, and detection systems, have been miniaturized. Miniaturized liquid chromatography significantly reduces solvent and sample consumption while providing comparable or even better separation efficiency. When liquid chromatography is coupled with mass spectroscopy, a low flow rate can increase the ionization efficiency, leading to enhanced sensitivity of the mass spectrometer. In contrast, normal-scale liquid chromatography suffers from its relatively high volumetric flow rate, which challenges the scanning frequency of the mass spectrometer. On the other hand because of the small sample size, other detection strategies such as spectrometric methods cannot provide sufficient sensitivity and limits of detection. In this sense, mass spectrometry has become the detection method of choice for micro-scale liquid-phase chromatography. Miniaturized liquid chromatography can diminish sample dilution efficiently when extremely small amounts of samples are used. The main driving force for this miniaturization trend, especially in liquid-phase separations, is the desperate need for microscale analyses of biological and clinical samples, given these samples are precious and the sample size is usually very small. At present, microscale liquid-phase chromatography is the only method of choice for such small, precious, and highly informative samples. The miniaturization of liquid chromatography systems, especially chromatographic columns, would be advantageous to the modularization and integration of liquid chromatography instrumental systems. Chip liquid chromatography is an integration of chromatography columns, liquid control systems, and detection methods on a single microfluidic chip. Chip liquid chromatography is an excellent format for the miniaturization of liquid chromatography systems, and it has already attracted significant attention from academia and industry. However, this attempt is challenging, and great effort is required on fundamental techniques, such as the substrate material of the microfluidic chip, structure of the micro-chromatography column, fluid control method, and detection methods, in order to make the chips suitable for liquid chromatography. Currently, the major problem in chip liquid chromatography is that the properties of the chip substrate materials cannot meet the requirements for further miniaturization and integration of chip liquid chromatography. The strength of the existing chip substrate materials is generally below 60 MPa, and the material properties limit further advances in the miniaturization and integration of chromatographic chips. Therefore, new chip substrate materials and the standard of chip channel design such as channel size and channel structure should be the key for further development of chip liquid chromatography. Mainstream instrumentation companies as well as new start-up innovation companies are now undertaking efforts toward the development of microchip liquid chromatographic products. Agilent, the first instrumentation company that introduced commercial microchip liquid chromatographic columns to the market, has led this field. Apart from microchip-based columns, Agilent introduced trap columns for different kinds of biological molecules as well as gradient generation systems for microchip-based liquid phase chromatography. Recently, another start-up company introduced microchip columns based on the in situ microfabrication of the column bed rather than packing the column with a particulate material. Such developments in microfabrication may further propel the advancement of micro-scale liquid-phase chromatography to an unprecedented level, which is beyond the conventional components and materials employed in normal-scale liquid chromatography. This review introduces the recent research progress in microchip liquid chromatography technologies, and briefly discusses the current state of commercialization of microchips for liquid chromatography by major instrumentation companies.

Fast analysis using pillar array columns: Quantification of branched-chain α-keto acids in human plasma samples

Branched-chain α-keto acids (BCKAs, namely, α-ketoisovaleric acid (KIV), α-ketoisocaproic acid (KIC), and α-keto-β-methylvaleric acid (KMV)) are related to many diseases such as myeloid leukemia, liver cancer, and diabetes mellitus. A rapid quantitative analytical method for BCKAs using pillar array columns was developed. α-Keto acids were labeled with 1,2-diamino-4,5-methylenedioxybenzene (DMB), followed by their separation on octadecylsilane-treated pillar array columns with MeOH/H₂O as the mobile phase. Five DMB-labelled α-keto acids including the internal standard were separated in 160 s. The lower limits of quantification for DMB-α-keto acids were 2-5 μM. The intra- and interday precisions were 2.9-6.6 % and 5.2-10.7 %, respectively. The developed method was applied to BCKA quantification in human plasma samples; KIV, KIC, and KMV concentrations were determined to be 13.8, 24.2, and 15.2 μM, respectively. The method realized rapid, sensitive, and precise analysis of BCKAs and can be applied for clinical diagnosis.

An overview of open tubular liquid chromatography with a focus on the coupling with mass spectrometry for the analysis of small molecules

Open tubular liquid chromatography (OT-LC) can provide superior chromatographic performance and more favorable mass spectrometry (MS) detection conditions. These features could provide enhanced sensitivity when coupled with electrospray ionization sources (ESI-) and lead to unprecedented detection capabilities if interfaced with a highly structural informative electron ionization (EI) source. In the past, the exploitation of OT columns in liquid chromatography evolved slowly. However, the recent instrumental developments in capillary/nanoLC-MS created new opportunities in developing and applying OT-LC-MS. Currently, the analytical advantages of OT-LC-MS are mainly exploited in the fields of proteomics and biosciences analysis. Nevertheless, under the right conditions, OT-LC-MS can also offer superior chromatographic performance and enhanced sensitivity in analyzing small molecules. This review will provide an overview of the latest developments in OT-LC-MS, focusing on the wide variety of employed separation mechanisms, innovative stationary phases, emerging column fabrication technologies, and new OT formats. In the same way, the OT-LC's opportunities and shortcomings coupled to both ESI and EI will be discussed, highlighting the complementary character of those two ionization modes to expand the LC's detection boundaries in the performance of targeted and untargeted studies.

History, advancement, bottlenecks, and future of chiral capillary electrochromatography

Capillary electrochromatography (CEC) represents a technique with less than 30 years of intense development and in this period this technique has seen huge promise, fast development, stagnation, and significant decline of innovative activity. The major goal of the present overview is not to present an extensive review of the literature on chiral CEC but to analyze the reasons for this dramatic development and attempting to answer questions such as: 1) Was the potential of CEC reasonably evaluated in 1990s before starting the explosive development in this field? 2) Did the development of this technique take the right track? 3) What other developments and competitive trends led to stagnation in the advancement of CEC? 4) Why is the activity in this field currently decreasing? 5) What are the current challenges and promises and what is the future of chiral CEC?

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.

Reduction of Taylor-Aris dispersion by lateral mixing for chromatographic applications

Chromatographic columns are suffering from Taylor-Aris dispersion, especially for slowly diffusing molecules such as proteins. Since downscaling the channel size to reduce Taylor-Aris dispersion meets fundamental pressure limitations, new strategies are needed to further improve chromatography beyond its current limits. In this work we demonstrate a method to reduce Taylor-Aris dispersion by lateral mixing in a newly designed silicon AC-electroosmotic flow mixer. We obtained a reduction in κ_aris by a factor of three in a 40 μm × 20 μm microchannel, corresponding to a plate height gain of 2 to 3 under unretained conditions at low to high Pe values. We also demonstrate an improvement of a reverse-phase chromatographic separation of coumarins.

Practical limits to column performance in liquid chromatography - Optimal operations

Columns of different structures have different potential kinetic performance - the trade-off between separation, time, and pressure. However, the full potential of a structure cannot always be realized in practically existing columns. Each combination of column efficiency, time, and pressure requires certain cross-sectional dimensions of the column flow-through channels. However, there are limits to the narrowest flow-through channels that can be manufactured with current technology. As a result, columns of some structures cannot be optimized for providing the required efficiency in the shortest time. Additionally, the full potential of its structure can be realized only if a column can operate at the highest pressure available from liquid chromatography (LC) equipment, has sufficient loadability, and satisfies other practical requirements. Equations tailored for a systematic approach to evaluation of factors affecting performance of optimized LC columns (effects of column structure, column dimensions, operational conditions, etc.) were developed. Parameters quantifying the performance of a specific column at and below its largest acceptable pressure were identified. New objective performance parameters of columns and their structures were introduced. Among them are the apparent structural quality factor accounting for the effect of insufficiently high pressure acceptable for the column, the dimensionless plate duration - the parameter of a column structure affecting its performance when the pressure is not limited, - and others. Applying the theory developed herein to published data, the performance of several differently structured columns is evaluated, and the factors affecting their comparative performance are discussed. In the final count, not the quality of a column structure, but practical factors such as the narrowest manufacturable flow-through channels can dominate the choice of the kinetically most suitable column for a practical LC analysis.

Ultrasensitive detection of nonlabelled bovine serum albumin using photothermal optical phase shift detection with UV excitation

Ultrasensitive detection of nonlabelled bovine serum albumin is performed in micro/nanofluidic chips using a photothermal optical phase shift (POPS) detection system. Currently, micro- and nanofluidics allow the analysis of various single cells, and their targets of interest are shifting from nucleic acids to proteins. Previously, our group developed photothermal detection techniques for the sensitive detection of nonfluorescent molecules. For example, we developed a thermal lens microscope (TLM) with ultrahigh sensitivity at the single-molecule level and a POPS detector that is applicable to nanochannels smaller than the wavelength of light. The POPS detector also realized the detection of nonlabelled proteins in nanochannels, although its detection sensitivity is less than that of the TLM in microchannels due to insufficient background light reduction. To overcome this problem, we developed a new POPS detector using relay optics for further reduction of the background light. In addition, heat transfer from the sample solution to the nanochannel wall was thoroughly investigated to achieve ultrahigh sensitivity. The limit of detection (LOD) obtained with the new POPS detector is 30 molecules in 1.0 fL. Considering this LOD, the performance of the new POPS detector is comparable with that of the TLM. Owing to the applicability of the POPS detector for sensitive detection even in nanochannels or single-μm channels, which cannot be realized with the TLM, combinations of the POPS detector and separation techniques employing unique nanochannel properties will contribute to advances in single-cell proteomics in the future.

Mass Spectrometry Advances and Perspectives for the Characterization of Emerging Adoptive Cell Therapies

Adoptive cell therapy is an emerging anti-cancer modality, whereby the patient's own immune cells are engineered to express T-cell receptor (TCR) or chimeric antigen receptor (CAR). CAR-T cell therapies have advanced the furthest, with recent approvals of two treatments by the Food and Drug Administration of Kymriah (trisagenlecleucel) and Yescarta (axicabtagene ciloleucel). Recent developments in proteomic analysis by mass spectrometry (MS) make this technology uniquely suited to enable the comprehensive identification and quantification of the relevant biochemical architecture of CAR-T cell therapies and fulfill current unmet needs for CAR-T product knowledge. These advances include improved sample preparation methods, enhanced separation technologies, and extension of MS-based proteomic to single cells. Innovative technologies such as proteomic analysis of raw material quality attributes (MQA) and final product quality attributes (PQA) may provide insights that could ultimately fuel development strategies and lead to broad implementation.

Liquid chromatography above 20,000 PSI

Continued improvements in HPLC have led to faster and more efficient separations than previously possible. One important aspect of these improvements has been the increase in instrument operating pressure and the advent of ultrahigh pressure LC (UHPLC). Commercial instrumentation is now capable of up to ~20 kpsi, allowing fast and efficient separations with 5-15 cm columns packed with sub-2 μm particles. Home-built instruments have demonstrated the benefits of even further increases in instrument pressure. The focus of this review is on recent advancements and applications in liquid chromatography above 20 kpsi. We outline the theory and advantages of higher pressure and discuss instrument hardware and design capable of withstanding 20 kpsi or greater. We also overview column packing procedures and stationary phase considerations for HPLC above 20 kpsi, and lastly highlight a few recent applicatioob pressure instruments for the analysis of complex mixtures.

Simultaneous enantioseparation of nonsteroidal anti-inflammatory drugs by a one-dimensional liquid chromatography technique using a dynamically coated chiral porous silicon pillar array column

The preparation of a highly efficient chiral liquid chromatography (LC) column is explored by dynamically coating a reversed-phase porous silicon pillar array column with hydroxypropyl-β-cyclodextrin (Hp-β-CD) as the chiral selector. Analyte mixtures composed of non-steroidal anti-inflammatory drugs were tested to reveal the enantioseparation potential of the column. The mechanism of chiral discrimination was investigated. The adsorbed Hp-β-CDs on the column surface experience different interaction with enantiomers. The chiral stationary phase showed satisfying stability and could be easily restored by recovering the selector with sufficient flushing and repeating the loading procedure. The peak capacity of the column was evaluated, and it was found high enough to separate three enantiomer couples using a one-dimensional LC technique.