Pillar array columns for peptide separations in nanoscale reversed-phase chromatography

On the contribution of the top and bottom walls in micro-pillar array columns and related high-aspect ratio chromatography systems

We report on a steady-state based, and hence highly accurate numerical modelling study of the effect of the top and bottom wall in the current generation of micro-pillar array columns. These have a mesoporous retention layer that not only covers the pillar walls but also the bottom wall. Our results show that the performance of these columns can in general not be improved by also covering the top wall with the same layer, despite the increased column symmetry this approach would offer. The reason for this is that the local species retardation caused by a retentive layer is much stronger than the pure flow arresting effect of an uncovered wall. At least, this has a crucial impact in high aspect-ratio systems such as micro-pillar array columns because these require a small inter-pillar distance to promote mass transfer together with a large channel depth to enable a sufficiently high flow rate. On the other hand, a notable improvement could be made if micro-pillar array would be produced without having a retentive layer at the bottom. At Péclet number Pe = 50 and aspect ratio AR = 5 for flow-channels, this gain amounts up to about 4.5 h-units at a zone retention factor k'' = 2 and 1.75 h-units at k'' = 16 (gain scales almost linearly with Pe). To verify these results, we also considered another high aspect-ratio system with a simplified geometry: the open-tubular channel with a flat-rectangular cross-section. This led to very similar observations, thus confirming the findings for the micro-pillar array. The results produced in the present study also allow us to conclude that the classic modelling paradigm adopted in chromatography, which is based on the independency and hence additivity of the hCm- and hCs-contributions, can lead to large modelling errors in chromatographic systems with a high aspect-ratio, even when their geometry is so simple as that of a straight open-tubular channel with constant cross-section. Indeed, when both zones are treated independently, the analysis misses how the vertical diffusion through the retentive layer helps suppressing the vertical gradients in the mobile zone. The diffusion through this layer occurs in a ratio of k''Ds/Dm (Dm being the diffusion coefficient in mobile phase zone and Ds being the diffusion coefficient in stationary phase zone), such that at high retention factors this diffusion contribution even becomes the dominant one.

Theoretical computation of the band broadening in micro-pillar array columns

We have investigated the possibility to establish a theoretical plate height expression for the band broadening in the most widely used micro-pillar array column format, i.e., a cylindrical pillar array wherein the pillar walls and the channel bottom are coated with a thin layer of meso‑porous material. Assuming isotropic diffusion in the shell-layer, it was found that the vertical diffusive transport along the porous shell-layer covering the pillar walls significantly suppresses the band broadening originating from the vertical migration velocity gradients. As the vertical transport in the shell-layer increases linearly with the retention equilibrium constant K, this leads to an anomalous dependency on the retention factor. Indeed, instead of increasing with k'' and following the classic (1+ak''+bk''2)/(1 + k'')2-dependency governing a classic Taylor-Aris system, the variation of the mobile zone mass transfer resistance term hCm in a 3D pillar array with bottom-wall retention goes through a maximum (resp. factor 1.5 (k''=4) and 2 (k''=16) difference between observed and classic Taylor-Aris behaviour). This effect increases with increasing pillar heights and increasing reduced velocities. Because of this complex k''-dependency, it proves very cumbersome to establish a general plate height equation covering all conditions. Instead, a plate height expression was established that is limited up to k''=4, but remains accurate for higher k''-values for cases where the ratio of pillar height over inter-pillar distance remains below 5. It can however be anticipated the proposed analytical model is only valid in a rather limited range around the presently considered external porosity of ε=0.5.

Universal method for the isolation of microvessels from frozen brain tissue: A proof-of-concept multiomic investigation of the neurovasculature

The neurovascular unit, comprised of vascular cell types that collectively regulate cerebral blood flow to meet the needs of coupled neurons, is paramount for the proper function of the central nervous system. The neurovascular unit gatekeeps blood-brain barrier properties, which experiences impairment in several central nervous system diseases associated with neuroinflammation and contributes to pathogenesis. To better understand function and dysfunction at the neurovascular unit and how it may confer inflammatory processes within the brain, isolation and characterization of the neurovascular unit is needed. Here, we describe a singular, standardized protocol to enrich and isolate microvessels from archived snap-frozen human and frozen mouse cerebral cortex using mechanical homogenization and centrifugation-separation that preserves the structural integrity and multicellular composition of microvessel fragments. For the first time, microvessels are isolated from postmortem ventromedial prefrontal cortex tissue and are comprehensively investigated as a structural unit using both RNA sequencing and Liquid Chromatography with tandem mass spectrometry (LC-MS/MS). Both the transcriptome and proteome are obtained and compared, demonstrating that the isolated brain microvessel is a robust model for the NVU and can be used to generate highly informative datasets in both physiological and disease contexts.

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.

Structured microgroove columns as a potential solution to obtain perfectly ordered particle beds

We report on a novel concept to produce ordered beds of spherical particles in a suitable format for liquid chromatography. In this concept, spherical particles are either positioned individually (single-layer column) or stacked (multi-layer column) in micromachined pockets that form an interconnected array of micro-grooves acting as a perfectly ordered chromatographic column. As a first step towards realizing this concept, we report on the breakthrough we realized by obtaining a solution to uniformly fill the micro-groove arrays with spherical particles. We show this can be achieved in a few sweeps using a dedicated rubbing approach wherein a particle suspension is manually rubbed over a silicon chip. In addition, numerical calculations of the dispersion in the newly introduced column format have been carried out and demonstrate the combined advantage of order and reduced flow resistance the newly proposed concept has over the conventional packed bed. For fully-porous particles and a zone retention factor of k'' = 2, the h_min decreases from h_min = 1.9 for the best possible packed bed column to around h_min = 1.0 for the microgroove array, while the interstitial velocity-based separation impedance E_i (a direct measure for the required analysis time) decreases from 1450 to 200. The next steps will focus on the removal of occasional particles remaining on the sides of the micro-pockets, the addition of a cover substrate to seal the column and the subsequent conduction of actual chromatographic separations.

A Practical and Analytical Comparative Study of Gel-Based Top-Down and Gel-Free Bottom-Up Proteomics Including Unbiased Proteoform Detection

Proteomics is an indispensable analytical technique to study the dynamic functioning of biological systems via different proteins and their proteoforms. In recent years, bottom-up shotgun has become more popular than gel-based top-down proteomics. The current study examined the qualitative and quantitative performance of these two fundamentally different methodologies by the parallel measurement of six technical and three biological replicates of the human prostate carcinoma cell line DU145 using its two most common standard techniques, label-free shotgun and two-dimensional differential gel electrophoresis (2D-DIGE). The analytical strengths and limitations were explored, finally focusing on the unbiased detection of proteoforms, exemplified by discovering a prostate cancer-related cleavage product of pyruvate kinase M2. Label-free shotgun proteomics quickly yields an annotated proteome but with reduced robustness, as determined by three times higher technical variation compared to 2D-DIGE. At a glance, only 2D-DIGE top-down analysis provided valuable, direct stoichiometric qualitative and quantitative information from proteins to their proteoforms, even with unexpected post-translational modifications, such as proteolytic cleavage and phosphorylation. However, the 2D-DIGE technology required almost 20 times as much time per protein/proteoform characterization with more manual work. Ultimately, this work should expose both techniques' orthogonality with their different contents of data output to elucidate biological questions.

Potential of Single Pulse and Multiplexed Drift-Tube Ion Mobility Spectrometry Coupled to Micropillar Array Column for Proteomics Studies

Proteomics is one of the most significant methodologies to better understand the molecular pathways involved in diseases and to improve their diagnosis, treatment and follow-up. The investigation of the proteome of complex organisms is challenging from an analytical point of view, because of the large number of proteins present in a wide range of concentrations. In this study, nanofluidic chromatography, using a micropillar array column, was coupled to drift-tube ion mobility and time-of-flight mass spectrometry to identify as many proteins as possible in a protein digest standard of HeLa cells. Several chromatographic parameters were optimized. The high interest of drift-tube ion mobility to increase the number of identifications and to separate isobaric coeluting peptides was demonstrated. Multiplexed drift-tube ion mobility spectrometry was also investigated, to increase the sensitivity in proteomics studies. This innovative proteomics platform will be useful for analyzing patient samples to better understand unresolved disorders.

A Practical Guide to Small Protein Discovery and Characterization Using Mass Spectrometry

Small proteins of up to ∼50 amino acids are an abundant class of biomolecules across all domains of life. Yet due to the challenges inherent in their size, they are often missed in genome annotations, and are difficult to identify and characterize using standard experimental approaches. Consequently, we still know few small proteins even in well-studied prokaryotic model organisms. Mass spectrometry (MS) has great potential for the discovery, validation, and functional characterization of small proteins. However, standard MS approaches are poorly suited to the identification of both known and novel small proteins due to limitations at each step of a typical proteomics workflow, i.e., sample preparation, protease digestion, liquid chromatography, MS data acquisition, and data analysis. Here, we outline the major MS-based workflows and bioinformatic pipelines used for small protein discovery and validation. Special emphasis is placed on highlighting the adjustments required to improve detection and data quality for small proteins. We discuss both the unbiased detection of small proteins and the targeted analysis of small proteins of interest. Finally, we provide guidelines to prioritize novel small proteins, and an outlook on methods with particular potential to further improve comprehensive discovery and characterization of small proteins.

Behavior of micro pillar array column in high pressure gas chromatography

Micro pillar array column with interpillar distance of 2.5 µm for pillars diameter of 5 µm has been introduced in high pressure gas chromatographic systems for online industrial analysis. Separation of gas mixtures have been performed under carrier gas pressure as high as 60 bar using rotating valve for gas injection without sample decompression stage prior to injection. A very low intrinsic height equivalent to a theoretical plate value of 14 µm has been obtained in few seconds. Instead of conventional gas chromatography, carrier gas nature such as helium, argon and carbon dioxide and pressure can be used to tune the selectivity. Liquid hydrocarbon samples have been successfully introduced in the column using a septum based split/splitless injector modified to work up to 40 bar. Separations of VOCs and gasoline samples have been successfully performed.

Liquid chromatography, a key tool for the advancement of single-cell omics analysis

Single-cell analysis can allow for an in-depth understanding of diseases, diagnostics, and aid the development of therapeutics. However, single-cell analysis is challenging, as samples are both extremely limited in size and complex. But the concept is gaining promise, much due to novel sample preparation approaches and the ever-improving field of mass spectrometry. The mass spectrometer's output is often linked to the preceding compound separation step, typically being liquid chromatography (LC). In this review, we focus on LC's role in single-cell omics. Particle-packed nano LC columns (typically 50-100 μm inner diameter) have traditionally been the tool of choice for limited samples, and are also used for single cells. Several commercial products and systems are emerging with single cells in mind, featuring particle-packed columns or miniaturized pillar array systems. In addition, columns with inner diameters as narrow as 2 μm are being explored to maximize sensitivity. Hence, LC column down-scaling is a key focus in single-cell analysis. But narrow columns are associated with considerable technical challenges, while single cell analysis may be expected to become a "routine" service, requiring higher degrees of robustness and throughput. These challenges and expectations will increase the need and attention for the development (and even the reinvention) of alternative nano LC column formats. Therefore, monolith columns and even open tubular columns may finally find their "killer-application" in single cell analysis.

Identification of 7 000-9 000 Proteins from Cell Lines and Tissues by Single-Shot Microflow LC-MS/MS

A current trend in proteomics is to acquire data in a "single-shot" by LC-MS/MS because it simplifies workflows and promises better throughput and quantitative accuracy than schemes that involve extensive sample fractionation. However, single-shot approaches can suffer from limited proteome coverage when performed by data dependent acquisition (ssDDA) on nanoflow LC systems. For applications where sample quantities are not scarce, this study shows that high proteome coverage can be obtained using a microflow LC-MS/MS system operating a 1 mm i.d. × 150 mm column, at a flow-rate of 50 μL/min and coupled to an Orbitrap HF-X mass spectrometer. The results demonstrate the identification of ∼9 000 proteins from 50 μg of protein digest from Arabidopsis roots, 7 500 from mouse thymus, and 7 300 from human breast cancer cells in 3 h of analysis time in a single run. The dynamic range of protein quantification measured by the iBAQ approach spanned 5 orders of magnitude and replicate analysis showed that the median coefficient of variation was below 20%. Together, this study shows that ssDDA by μLC-MS/MS is a robust method for comprehensive and large-scale proteome analysis and which may be further extended to more rapid chromatography and data independent acquisition approaches in the future.̀.

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.

Proteomic Analysis of Porcine-Derived Collagen Membrane and Matrix

Collagen membranes and matrices being widely used in guided bone regeneration and soft tissue augmentation have characteristic properties based on their composition. The respective proteomic signatures have not been identified. Here, we performed a high-resolution shotgun proteomic analysis on two porcine collagen-based biomaterials designed for guided bone regeneration and soft tissue augmentation. Three lots each of a porcine-derived collagen membrane and a matrix derived from peritoneum and/or skin were digested and separated by nano-reverse-phase high-performance liquid chromatography. The peptides were subjected to mass spectrometric detection and analysis. A total of 37 proteins identified by two peptides were present in all collagen membranes and matrices, with 11 and 16 proteins being exclusively present in the membrane and matrix, respectively. The common extracellular matrix proteins include fibrillar collagens (COL1A1, COL1A2, COL2A1, COL3A1, COL5A1, COL5A2, COL5A3, COL11A2), non-fibrillar collagens (COL4A2, COL6A1, COL6A2, COL6A3, COL7A1, COL16A1, COL22A1), and leucine-rich repeat proteoglycans (DCN, LUM, BGN, PRELP, OGN). The structural proteins vimentin, actin-based microfilaments (ACTB), annexins (ANXA1, ANXA5), tubulins (TUBA1B, TUBB), and histones (H2A, H2B, H4) were also identified. Examples of membrane-only proteins are COL12A1 and COL14A1, and, of matrix only proteins, elastin (ELN). The proteomic signature thus revealed the similarities between but also some individual proteins of collagen membrane and matrix.

Robust, reproducible and quantitative analysis of thousands of proteomes by micro-flow LC-MS/MS

Nano-flow liquid chromatography tandem mass spectrometry (nano-flow LC–MS/MS) is the mainstay in proteome research because of its excellent sensitivity but often comes at the expense of robustness. Here we show that micro-flow LC–MS/MS using a 1 × 150 mm column shows excellent reproducibility of chromatographic retention time (<0.3% coefficient of variation, CV) and protein quantification (<7.5% CV) using data from >2000 samples of human cell lines, tissues and body fluids. Deep proteome analysis identifies >9000 proteins and >120,000 peptides in 16 h and sample multiplexing using tandem mass tags increases throughput to 11 proteomes in 16 h. The system identifies >30,000 phosphopeptides in 12 h and protein-protein or protein-drug interaction experiments can be analyzed in 20 min per sample. We show that the same column can be used to analyze >7500 samples without apparent loss of performance. This study demonstrates that micro-flow LC–MS/MS is suitable for a broad range of proteomic applications.

Mass spectrometry-based proteomics typically relies on highly sensitive nano-flow liquid chromatography (LC) but this can reduce robustness and reproducibility. Here, the authors show that micro-flow LC enables robust and reproducible high-throughput proteomics experiments at a very moderate loss of sensitivity.