Octadecylated Silica Monolith Capillary Column with Integrated Nanoelectrospray Ionization Emitter for Highly Efficient Proteome Analysis

A Microfluidic-Fabricated Rod Sprayer for Nanoelectrospray Mass Spectrometry

The nanoelectrosprayer is a key device in the hyphenation of nanoLC-ESI-MS, and its development plays a crucial role in pushing forward the mining depth of biological discovery and industrialization of omics science. In this work, a new type of nanoelectrospray emitter, a rod sprayer, was developed based on microfluidic manufacture. Due to its porous silica structure, the rod sprayer in effect worked as a multinozzle sprayer, which is composed of a bunch of micrometer sized spray channels. Without the need for sophisticated microfabrication equipment, a superclean environment, or a complicated assembling process, such sprayer rods can be facilely fabricated in a mass production style: 3,600 rods with excellent monodispersity have been fabricated in 1 h, and rod sprayers thus made have demonstrated excellent intraday, interday, and interbatch reproducibilities: RSD = 1.9, 4.9, and 6.1%, respectively. The rod sprayer can generate stable electrospray in a wide voltage range from 2.6 to 3.2 kV and flow rates from 50 to 1000 nL/min, covering typical flow rates of subnanoLC, nanoLC, to microLC, and work steadily even under complex matrix environments (e.g., Hank's balanced salt solution containing sodium, magnesium, and calcium ions) without clogging. Meanwhile, the rod sprayers exhibited 200-1800% ionization efficiency enhancement in comparison with commonly used tapered tip emitters, for small molecule drugs, peptides, and proteins, respectively, and provided a broadened linear dynamic range of 4 orders of magnitude. The excellent characteristics of the rod sprayer, together with its small size and mass production capacity, should provide a high quality, high durability, high consistency, and disposable use-supported nanoelectrospray solution for MS-based bioanalyses.

Growth of two-layer copolymer as the stationary phase with very high separation efficiency for separating peptides in capillary electrochromatography

Open tubular CEC (OT-CEC) column with a very high separation efficiency was prepared for peptides separation. A pretreated silica-fused capillary was reacted with 3-(methacryloxy) propyltrimethoxysilane followed by vinylbenzyl chloride and divinylbenzene to produce first thin monolithic monolayer. The second copolymer layer was formed on thin monolithic monolayer of the capillary by reversible addition-fragmentation transfer polymerization of N-phenylacrylamide and styrene. The key parameters including buffer pH value and organic modifier were systematically evaluated to provide the optimal chromatographic condition. The resultant OT-CEC columns were validated by separating a synthetic mixture of peptides and cytochrome C tryptic digest in capillary electrochromatography. The number of theoretical plates as high as 2.4 million per column was achieved for synthetic mixture peptides. In addition, the fabricated OT-CEC column also resolved more than 18 high-efficiency digestion peptides from a mixture containing tryptic digest of cytochrome C. The column to column and inter- to intraday repeatabilities of OT-CEC column through RSD% were found better than 3.0%, exhibiting satisfactory stability and repeatability of the two-layer deposited OT-CEC column. The results reveal that the open tubular capillary column modified with two-layer copolymer shows the great prospect for the separation of proteins in capillary electrochromatography.

Advancements in the preparation and application of monolithic silica columns for efficient separation in liquid chromatography

Fast and efficient separation remains a big challenge in high performance liquid chromatography (HPLC). The need for higher efficiency and resolution in separation is constantly in demand. To achieve that, columns developed are rapidly moving towards having smaller particle sizes and internal diameters (i.d.). However, these parameters will lead to high back-pressure in the system and will burden the pumps of the HPLC instrument. To address this limitation, monolithic columns, especially silica-based monolithic columns have been introduced. These columns are being widely investigated for fast and efficient separation of a wide range of molecules. The present article describes the current methods developed to enhance the column efficiency of particle packed columns and how silica monolithic columns can act as an alternative in overcoming the low permeability of particle packed columns. The fundamental processes behind the fabrication of the monolith including the starting materials and the silica sol-gel process will be discussed. Different monolith derivatization and end-capping processes will be further elaborated and followed by highlights of the performance such monolithic columns in key applications in different fields with various types of matrices.

A novel one-pot strategy of preparation of N-phenylacrylamide-styrene co-polymer open tubular capillary column for peptides separation

An open tubular capillary column (100 μm internal diameter and 120 cm length) was first fabricated with N-phenylacrylamide and styrene copolymer layer on the inner surface by in situ one-pot strategy, while ethylene dimethacrylate was used as the cross-linker. The pretreated silica-fused capillary was reacted with 3-trimethoxysilyl propyl methacrylate to attach a double-bond ligand onto the inner surface of the capillary. Further, a thick and stabile copolymer layer was generated on the inner surface of the capillary by the novel method in situ one-pot reaction of styrene-N-phenylacrylamide. The effects of reaction temperature and composition of the polymerization mixture on the morphology and permeability of the copolymer were investigated. The separation performance of the fabricated polymer columns were validated by separation of five synthetic peptides. The excellent efficiency (188 500 plates/m) of 100 μm internal diameter open tubular column with the separation media prepared by mixed one-pot copolymerization has not been achieved via the isocratic elution mode. The column to column, intraday, and interday repeatabilities evaluated from the relative standard deviation were found better than 4%, exhibiting considerable repeatability of the column.

Improved Sensitivity of Ultralow Flow LC-MS-Based Proteomic Profiling of Limited Samples Using Monolithic Capillary Columns and FAIMS Technology

In this work, we pioneered a combination of ultralow flow (ULF) high-efficiency ultranarrow bore monolithic LC columns coupled to MS via a high-field asymmetric waveform ion mobility spectrometry (FAIMS) interface to evaluate the potential applicability for high sensitivity, robust, and reproducible proteomic profiling of low nanogram-level complex biological samples. As a result, ULF LC-FAIMS-MS brought unprecedented sensitivity levels and high reproducibility in bottom-up proteomic profiling. In addition, FAIMS improved the dynamic range, signal-to-noise ratios, and detection limits in ULF LC-MS-based measurements by significantly reducing chemical noise in comparison to the conventional nanoESI interface used with the same ULF LC-MS setup. Two, three, or four compensation voltages separated by at least 15 V were tested within a single LC-MS run using the FAIMS interface. The optimized ULF LC-ESI-FAIMS-MS/MS conditions resulted in identification of 2,348 ± 42 protein groups, 10,062 ± 285 peptide groups, and 15,734 ± 350 peptide-spectrum matches for 1 ng of a HeLa digest, using a 1 h gradient at the flow rate of 12 nL/min, which represents an increase by 38%, 91%, and 131% in respective identifications, as compared to the control experiment (without FAIMS). To evaluate the practical utility of the ULF LC-ESI-FAIMS-MS platform in proteomic profiling of limited samples, approximately 100, 1,000, and 10,000 U937 myeloid leukemia cells were processed, and a one-tenth of each sample was analyzed. Using the optimized conditions, we were able to reliably identify 251 ± 54, 1,135 ± 80, and 2,234 ± 25 protein groups from injected aliquots corresponding to ∼10, 100, and 1,000 processed cells.

Integrated Microstructured Photonic Fiber as a Bifunctional Robust Frit and Efficient Electrospray Emitter of a Packed Column for Capillary Liquid Chromatography-Tandem Mass Spectrometry Analysis of Complex Biological Samples

Although capillary liquid chromatography married with tandem mass spectrometry (cLC-MS/MS) has become a powerful technique for proteomics and metabolomics research, it is still a great challenge to fabricate durable capillary-based analytical columns coupling continuous nanoflow (<1 000 nL/min) electrospray ionization (ESI) with MS, owing to the issue of clogging and fragile of emitters. Here, we proposed a simple approach to integrate microstructured photonic fibers (MPFs) into wide bore capillaries with 150 μm i.d., serving as an integral bifunctional frit or/and ESI emitter of packed columns. Two kinds of MPFs containing 126 homogeneous microchannels with different inner diameter, 3.2 μm for MPF-1 and 2.6 μm for MPF-2, were explored for preparation. The octadecylsilicate (ODS) silica-packed column using MPF-1 as a frit exhibited the lowest plate heights of 14.2-19.7 μm for five alkylbenzenes at the velocity of 1.5 mm/s, which were slightly lower than those of packed column with porous polymer monolith (PPM)-based frit by cLC coupling with ultraviolet (UV) detection. Additionally, the packed columns with integral MPF frit-emitters were further applied in analysis of a complex biological sample of digest of Hela cells by cLC-MS. An average of 7109 unique peptides could be identified in a single analysis by using MPF-1 emitter, and 7110 unique peptides were identified by using the MPF-2 emitter, which were superior to the identified result of packed column with an integral tapered tip emitter (6894 peptides). It is obvious that this novel integral MPF-based frit-emitter does not easily suffer from the issues of cracking owing to the silica cladding around independent microchannels (>100), which always encumbers both independent and integral tapered tip emitters for cLC-MS.

Advances in microscale separations towards nanoproteomics applications

Microscale separation (e.g., liquid chromatography or capillary electrophoresis) coupled with mass spectrometry (MS) has become the primary tool for advanced proteomics, an indispensable technology for gaining understanding of complex biological processes. In recent decades significant advances have been achieved in MS-based proteomics. However, the current proteomics platforms still face an analytical challenge in overall sensitivity towards nanoproteomics applications for starting materials of less than 1μg total proteins (e.g., cellular heterogeneity in tissue pathologies). Herein, we review recent advances in microscale separation techniques and integrated sample processing strategies that improve the overall sensitivity and proteome coverage of the proteomics workflow, and their contributions towards nanoproteomics applications.

Facile preparation of multi-functionalized hybrid monoliths via two-step photo-initiated reactions for two-dimensional liquid chromatography-mass spectrometry

A facile approach was developed to prepare hybrid monoliths with different functions via two-step photo-initiated reactions. Firstly, acrylopropyl polyhedral oligomertic silsesquioxane (acryl-POSS) and propargyl acrylate (PA) were used as precursors to synthesize alkynyl-functionalized hybrid monoliths via photo-initiated free radical polymerization. Secondly, the hybrid monoliths were modified with 1-octadecanethiol (ODT) and sodium 3-mercapto-1-propanesulfonate (SMPS) via photo-initiated thiol-yne click reaction to prepare reversed-phase (RP) and strong cation-exchange (SCX) hybrid monoliths, respectively. The results of chromatographic characterization indicated that the column efficiencies for alkylbenzenes on ODT-modified hybrid monolith reached 84,000-87,700 plates per meter at the velocity of 0.58mm/s, and also revealed a retention-independent efficient performance of small molecules in isocratic elution. The SMPS-modified hybrid monolith exhibited both hydrophobicity and ion-exchange mechanisms, and the dynamic binding capacity was calculated to be 1.4×10^-4μmol/cm. Human Hela cells tryptic digest was well separated on ODT-modified hybrid monolith in one-dimensional RPLC-MS/MS, and 2786 unique peptides and 685 proteins were identified. Furthermore, the SMPS-modified monolith coupled with ODT-modified monolith was used for two-dimensional separation of human Hela cells tryptic digest in SCX-RPLC-MS/MS, and the results showed that 9744 unique peptides and 2749 proteins were identified. Compared to those identified in one-dimensional RP system, the total numbers of unique peptides and proteins identified in SCX-RP system increased by 249.7% and 301.3%, respectively.

Monoliths in capillary electrochromatography and capillary liquid chromatography in conjunction with mass spectrometry

Here, we have reviewed separation studies utilizing monolithic capillary columns for separation of compounds preceding MS analysis. The review is divided in two parts according to the used separation method, namely CEC and capillary LC (cLC). Based on our overview, monolithic CEC-MS technique have been more focused on the syntheses of highly specialized and selective separation phase materials for fast and efficient separation of specific types of analytes. In contrast, monolithic cLC-MS is more widely used and is often employed, for instance, in the analysis of oligonucleotides, metabolites, and peptides and proteins in proteomic studies. While poly(styrene-divinylbenzene)-based and silica-based monolithic capillaries found their place in proteomic analyses, the other laboratory-synthesized monoliths still wait for their wider utilization in routine analyses. The development of new monolithic materials will most likely continue due to the demand of more efficient and rapid separation of increasingly complex samples.

Three-dimensional hydrodynamic focusing microfluidic emitter: a strategy to inhibit sample ion expansion in nanoelectrospray ionization

A proposed 3D HFNE was used to generate a wrapped electrospray to achieve the inhibition of sample ion expansion, thus restraining injection loss in electrospray ionization.

Nano-LC in proteomics: recent advances and approaches

In proteomics, nano-LC is arguably the most common tool for separating peptides/proteins prior to MS. The main advantage of nano-LC is enhanced sensitivity, as compounds enter the MS in more concentrated bands. This is particularly relevant for determining low abundant compounds in limited samples. Nano-LC columns can produce peak capacities of 1000 or more, and very narrow columns can be used to perform proteomics of 1000 cells or less. Also, nano-LC can be coupled with online add-ons such as selective trap columns or enzymatic reactors, for faster and more automated analysis. Nano-LC is today an established tool for research laboratories; but can nano-LC-based systems soon be ready for more routine settings, such as in clinics?

Efficient selection of glycoprotein-binding DNA aptamers via boronate affinity monolithic capillary

Systematic evolution of ligands by exponential enrichment (SELEX) is the workhorse method for selecting aptamers that are capable of binding target molecules from a random oligonucleic acid library. However, conventional SELEX methods are associated with apparent drawbacks including labor-intensive, time-consuming, large reagent consumption and strong nonspecific binding with separation media. Herein, we report a boronate affinity monolithic capillary-based SELEX approach for rapid selection of high-specificity glycoprotein-binding DNA aptamers. Boronate affinity monolithic capillary is an advanced functional material appeared in recent years, which allows for facile capture/release of glycoproteins in a pH-switchable fashion. By using boronate affinity monolithic capillary as a platform for target immobilization and aptamer isolation, the proposed SELEX method allowed for efficient selection of glycoprotein-binding aptamers by 6 rounds and the dissociation constants were at 10(-8) M level. Because of the employment of boronate affinity monolithic capillary, the new SELEX approach overcame the above-mentioned drawbacks and provided several significant advantages, including rapid selection speed (only 2 days were needed), high specificity toward the target molecules, and minute reagent consumption.

Proteomic analysis of gingival tissue and alveolar bone during alveolar bone healing

Bone tissue regeneration is orchestrated by the surrounding supporting tissues and involves the build-up of osteogenic cells, which orchestrate remodeling/healing through the expression of numerous mediators and signaling molecules. Periodontal regeneration models have proven useful for studying the interaction and communication between alveolar bone and supporting soft tissue. We applied a quantitative proteomic approach to analyze and compare proteins with altered expression in gingival soft tissue and alveolar bone following tooth extraction. For target identification and validation, hard and soft tissue were extracted from mini-pigs at the indicated times after tooth extraction. From triplicate experiments, 56 proteins in soft tissue and 27 proteins in alveolar bone were found to be differentially expressed before and after tooth extraction. The expression of 21 of those proteins was altered in both soft tissue and bone. Comparison of the activated networks in soft tissue and alveolar bone highlighted their distinct responsibilities in bone and tissue healing. Moreover, we found that there is crosstalk between identified proteins in soft tissue and alveolar bone with respect to cellular assembly, organization, and communication. Among these proteins, we examined in detail the expression patterns and associated networks of ATP5B and fibronectin 1. ATP5B is involved in nucleic acid metabolism, small molecule biochemistry, and neurological disease, and fibronectin 1 is involved in cellular assembly, organization, and maintenance. Collectively, our findings indicate that bone regeneration is accompanied by a profound interaction among networks regulating cellular resources, and they provide novel insight into the molecular mechanisms involved in the healing of periodontal tissue after tooth extraction.

Nano-flow multidimensional liquid chromatography platform integrated with combination of protein and peptide separation for proteome analysis

An integrated multidimensional nano-flow liquid chromatography platform with the combination of protein and peptide separation via online digestion by an immobilized enzymatic reactor was established, and successfully applied for proteome analysis. By this platform, proteins were first separated by a weak anion and weak cation mixed-bed microcolumn under a series of salt steps, online digested by a trypsin immobilized enzymatic reactor, digests trapped and desalted by a C18 precolumn, separated by nano-reversed phase liquid chromatography, and finally identified by electrospray ionization-MS/MS. To evaluate the performance of such a platform, Escherichia coli whole cell lysate proteins were analyzed. Compared with the results obtained by shotgun approach, the identified protein number was increased by 6%, with the consumed time decreased from 38 to 14 h. We also compared with integrate platform based on micro-HPLC, and the required sample amount was decreased to 8 μg. These results demonstrated that such an integrated approach would be an attractive alternative to commonly applied approaches for proteome research.

Recent advances on multidimensional liquid chromatography-mass spectrometry for proteomics: from qualitative to quantitative analysis--a review

With the acceleration of proteome research, increasing attention has been paid to multidimensional liquid chromatography-mass spectrometry (MDLC-MS) due to its high peak capacity and separation efficiency. Recently, many efforts have been put to improve MDLC-based strategies including "top-down" and "bottom-up" to enable highly sensitive qualitative and quantitative analysis of proteins, as well as accelerate the whole analytical procedure. Integrated platforms with combination of sample pretreatment, multidimensional separations and identification were also developed to achieve high throughput and sensitive detection of proteomes, facilitating highly accurate and reproducible quantification. This review summarized the recent advances of such techniques and their applications in qualitative and quantitative analysis of proteomes.

High efficiency, high temperature separations on silica based monolithic columns

The effect of temperature on separation using reversed-phase monolithic columns has been investigated using a nano-LC pumping system for gradient separation of tryptic peptides with MS detection. A goal of this study was to find optimal conditions for high-speed separations. The chromatographic performance of the columns was evaluated by peak capacity and peak capacity per time unit. Column lengths ranging from 20 to 100 cm and intermediate gradient times from 10 to 30 min were investigated to assess the potential of these columns in a final step separation, e.g. after fractionation or specific sample preparation. Flow rates from 250 to 2000 nL/min and temperatures from 20 to 120°C were investigated. Temperature had a significant effect on fast separations, and a flow rate of 2000 nL/min and a temperature of 80°C gave the highest peak capacity per time unit. These settings produced 70% more protein identifications in a biological sample compared to a conventional packed column. Alternatively, an equal amount of protein identifications was obtained with a 40% reduction in run time compared to the conventional packed column.

Silica-based and organic monolithic capillary columns for LC: recent trends in proteomics

The use of monolithic liquid chromatography (LC) columns for proteomics, covering the scientific literature from 2004 to the beginning of 2011, is reviewed. Attention is paid to recent developments in column technology and materials, focusing on silica-based and organic (polystyrene and methacrylate) monolithic capillary columns for proteomics. The applicability of these columns is illustrated by examples of the analysis of (complex) protein digests and proteins conveniently summarized in tables. Furthermore, characteristics of column materials are compared and future trends and prospects are presented.

The development of flow-through bio-catalyst microreactors from silica micro structured fibers for lipid transformations

This study demonstrates the utility of a flow-through enzyme immobilized silica microreactor for lipid transformations. A silica micro structured fiber (MSF) consisting of 168 channels of internal diameter 4-5 μm provided a large surface area for the covalent immobilization of Candida antartica lipase. The specific activity of the immobilized lipase was determined by hydrolysis of p-nitrophenyl butyrate and calculated to be 0.81 U/mg. The catalytic performance of the lipase microreactor was demonstrated by the efficient ethanolysis of canola oil. The parameters affecting the performance of the MSF microreactor, including temperature and reaction flow rate, were investigated. Characterization of the lipid products exiting the microreactor was performed by non-aqueous reversed-phased liquid chromatography (NARP-LC) with evaporative light scattering detector (ELSD) and by comprehensive two-dimensional gas chromatography (GC x GC). Under optimized conditions of 1 μL/min flow rate of 5 mg/mL trioleoylglycerol (TO) in ethanol and 50 °C reaction temperature, 2-monooleoylglycerol was the main product at > 90% reaction yield. The regioselectivity of the Candida antartica lipase immobilized MSF microreactor in the presence of ethanol was found to be comparable to that obtained under conventional conditions. The ability of these reusable flow-through microreactors to regioselectively form monoacylglycerides in high yield from triacylglycerides demonstrate their potential use in small-scale lipid transformations or analytical lipids profiling.

Recent advances in micro-scale and nano-scale high-performance liquid-phase chromatography for proteome research

High-performance liquid chromatography-electrospray ionization tandem mass spectrometry (HPLC-ESI-MS-MS) is regarded as one of the most powerful techniques for separation and identification of proteins. Recently, much effort has been made to improve the separation capacity, detection sensitivity, and analysis throughput of micro- and nano-HPLC, by increasing column length, reducing column internal diameter, and using integrated techniques. Development of HPLC columns has also been rapid, as a result of the use of submicrometer packing materials and monolithic columns. All these innovations result in clearly improved performance of micro- and nano-HPLC for proteome research.

Label-free quantitative proteome analysis of skeletal tissues under mechanical load

Skeletal tissue has the capability to adapt its mass and structure in response to mechanical stress. However, the molecular mechanism of bone and cartilage to respond to mechanical stress are not fully understood. A label-free quantitative proteome approach was used for the first time to obtain a global perspective of the response of skeletal tissue to mechanical stress. Label-free quantitative analysis of 1D-PAGE-LC/MS/MS based proteomics was applied to identify differentially expressed proteins. Differential expression analysis in the experimental groups and control group showed significant changes for 248 proteins including proteins related to proliferation, differentiation, regulation of signal transduction and energy metabolic pathways. Fluorescence labeling by incorporation of alizarin/calcein in newly formed bone minerals qualitatively demonstrated new bone formation. Skeletal tissues under mechanical load evoked marked new bone formation in comparison with the control group. Bone material apposition was evident. Our data suggest that 39 proteins were assigned a role in anabolic process. Comparisons of anabolic versus catabolic features of the proteomes show that 42 proteins were related to catabolic. In addition, some proteins were related to regulation of signal transduction and energy pathways, such as tropomyosin 4, fibronectin 1, and laminin, might be new molecular targets that are responsive to mechanical force. Differentially expressed proteins identified in this model may offer a useful starting point for elucidating novel aspects of the effects of mechanical force on skeletal tissue.

Synthesis of hydrophilic boronate affinity monolithic capillary for specific capture of glycoproteins by capillary liquid chromatography

Boronate affinity chromatography is an important tool for specific isolation of cis-diol-containing compounds such as glycoproteins, RNA and carbohydrates. Boronate functionalized monolithic capillaries have been recently developed for specific capture of cis-diol-containing small biomolecules, but the apparent hydrophobicity of the columns prevents them from specific capture of glycoproteins. In this paper, a hydrophilic boronate affinity monolithic capillary was prepared by in situ free radical polymerization, using 4-vinylphenylboronic acid (VPBA) and N, N'-methylenebisacrylamide (MBAA) as functional monomer and cross-linker, respectively. The prepared poly(VPBA-co-MBAA) monolithic capillary exhibited uniform open channel network and high density of accessible boronic acid. Due to the utilization of hydrophilic cross-linker, the prepared column was hydrophilic, allowing for specific capture of glycoproteins.

Integration of monolithic frit into the particulate capillary (IMFPC) column in shotgun proteome analysis

Capillary column plays an important role in nano-flow liquid chromatography coupled with tandem mass spectrometry for dealing with the high dynamic range and complexity of protein samples in shotgun proteome analysis. In this study, the integrated monolithic frit into the particulate capillary (IMFPC) column was prepared. By comparing the prepared IMFPC column with conventionally fritless capillary column, smaller size of packing materials could be easily packed into the capillary to achieve higher average peak capacity and proteome coverage. As the monolithic emitter was integrated onto this type of column, the void volume between packing particles and electrospray emitter was eliminated and the electrospray quality was improved. The prepared IMFPC column was applied to proteome analysis of mouse liver extracts, and it was observed that the number of identified proteins and peptides increased 14.9 and 12.9% as well as the peak capacity increased 11.6% by using IMFPC column over conventionally fritless capillary column.