Immobilized enzyme reactors in proteomics

Ultrafast protein digestion using an immobilized enzyme reactor following high-resolution mass spectrometry analysis for rapid identification of abrin toxin

Abrin toxin, highly dangerous with an estimated human lethal dose of 0.1-1 μg per kg body weight, has attracted much attention regarding criminal and terroristic misuse over the past decade. Therefore, developing a rapid detection method for abrin toxin is of great significance in the field of biosecurity. In this study, based on the specific dissociation method of an immobilized enzyme reactor, the trypsin immobilized reactor Fe3O4@CTS-GA-Try was prepared to replace free trypsin, and the immobilized enzyme digestion process was systematically investigated and optimized by using bovine serum albumin as the simulant of abrin. After 5 min one-step denaturation and reduction, a satisfactory peptide number and coverage were yielded with only 15 s assisted by an ultrasound probe to identify model proteins. Subsequently, abrin was rapidly digested using the established method, resulting in a stable and highly reproducible characteristic peptide number of 39, which can be analyzed by nanoelectrospray ionization coupled with high-resolution mass spectrometry. With the acquisition mode of full MS scan coupled with PRM, not only MS spectroscopy of total abrin peptides but also the corresponding MS/MS spectroscopy of specific abrin peptides can achieve the characteristic detection of abrin toxin and its different isoforms in less than 10 minutes, with high repeatability. This assay provides a universal platform and has great potential for the development of on-site detection and rapid mass spectrometric analysis techniques for macromolecular protein toxins and can further be applied to the integrated detection of chemical and biological agents.

Online protein digestion in membranes between capillary electrophoresis and mass spectrometry

This research employs pepsin-containing membranes to digest proteins online after a capillary electrophoresis (CE) separation and prior to tandem mass spectrometry. Proteolysis after the separation allows the peptides from a given protein to enter the mass spectrometer in a single plug. Thus, migration time can serve as an additional criterion for confirming the identification of a peptide. The membrane resides in a sheath-flow electrospray ionization (ESI) source to enable digestion immediately before spray into the mass spectrometer, thus limiting separation of the digested peptides. Using the same membrane, digestion occurred reproducibly during 20 consecutive CE analyses performed over a 10 h period. Additionally, after separating a mixture of six unreduced proteins with CE, online digestion facilitated protein identification with at least 2 identifiable peptides for all the proteins. Sequence coverages were >75% for myoglobin and carbonic anhydrase II but much lower for proteins containing disulfide bonds. Development of methods for efficient separation of reduced proteins or identification of cross-linked peptides should enhance sequence coverages for proteins with disulfide bonds. Migration times for the peptides identified from a specific protein differed by <∼30 s, which allows for rejection of some spurious peptide identifications.

Bottom-Up Proteomics: Advancements in Sample Preparation

Liquid chromatography–tandem mass spectrometry (LC–MS/MS)-based proteomics is a powerful technique for profiling proteomes of cells, tissues, and body fluids. Typical bottom-up proteomic workflows consist of the following three major steps: sample preparation, LC–MS/MS analysis, and data analysis. LC–MS/MS and data analysis techniques have been intensively developed, whereas sample preparation, a laborious process, remains a difficult task and the main challenge in different applications. Sample preparation is a crucial stage that affects the overall efficiency of a proteomic study; however, it is prone to errors and has low reproducibility and throughput. In-solution digestion and filter-aided sample preparation are the typical and widely used methods. In the past decade, novel methods to improve and facilitate the entire sample preparation process or integrate sample preparation and fractionation have been reported to reduce time, increase throughput, and improve reproducibility. In this review, we have outlined the current methods used for sample preparation in proteomics, including on-membrane digestion, bead-based digestion, immobilized enzymatic digestion, and suspension trapping. Additionally, we have summarized and discussed current devices and methods for integrating different steps of sample preparation and peptide fractionation.

Ultrasensitive assay of O-GlcNAc transferase using capillary electrophoresis-laser induced fluorescence

O-linked N-acetylglucosamine (O-GlcNAc) transferase (OGT) is directly associated with the level of O-GlcNAc glycosylation of biomolecules and various diseases, and it is expected to be a promising potential new therapeutic target. Here, we develop a robust and sensitive method for OGT assay based on capillary electrophoresis-laser induced fluorescence (CE-LIF) method. AF-488-modified peptide containing serine active group is designed as substrate for OGT-catalyzed reaction, and nonradioactive UDP-GlcNAc is employed as sugar donor to perform O-GlcNAc glycosylation modification. The enzyme activity of OGT is measured by quantitative determination of glycosylated peptide produced by the reaction. Large volume sample stacking technique for sample injection and a unique fluorescence collection system for LIF detection are adopted to greatly enhance the detection sensitivity, thus a low limit of detection down to 0.23 pM for OGT detection is achieved. The method is successfully applied to detect OGT activity in clinical blood samples with satisfactory accuracy. Our study provides a simple, accurate, and sensitive method with great potential application in clinical diagnosis of O-GlcNAc-related diseases.

Peptide mapping of proteins by capillary electromigration methods

This review article provides a wide overview of important developments and applications of capillary electromigration methods in the area of peptide mapping of proteins in the period 1997-mid-2022, including review articles on this topic. It deals with all major aspects of peptide mapping by capillary electromigration methods: i) precleavage sample preparation involving purification, preconcentration, denaturation, reduction and alkylation of protein(s) to be analyzed, ii) generation of peptide fragments by off-line or on-line enzymatic and/or chemical cleavage of protein(s), iii) postcleavage preparation of the generated peptide mixture for capillary electromigration separation, iv) separation of the complex peptide mixtures by one-, two- and multidimensional capillary electromigration methods coupled with mass spectrometry detection, and v) a large application of peptide mapping for variable purposes, such as qualitative analysis of monoclonal antibodies and other protein biopharmaceuticals, monitoring of posttranslational modifications, determination of primary structure and investigation of function of proteins in biochemical and clinical research, characterization of proteins of variable origin as well as for protein and peptide identification in proteomic and peptidomic studies.

3D-Printed High-Pressure-Resistant Immobilized Enzyme Microreactor (μIMER) for Protein Analysis

Additive manufacturing (3D printing) has greatly revolutionized the way researchers approach certain technical challenges. Despite its outstanding print quality and resolution, stereolithography (SLA) printing is cost-effective and relatively accessible. However, applications involving mass spectrometry (MS) are few due to residual oligomers and additives leaching from SLA-printed devices that interfere with MS analyses. We identified the crosslinking agent urethane dimethacrylate as the main contaminant derived from SLA prints. A stringent washing and post-curing protocol mitigated sample contamination and rendered SLA prints suitable for MS hyphenation. Thereafter, SLA printing was used to produce 360 μm I.D. microcolumn chips with excellent structural properties. By packing the column with polystyrene microspheres and covalently immobilizing pepsin, an exceptionally effective microscale immobilized enzyme reactor (μIMER) was created. Implemented in an online liquid chromatography-MS/MS setup, the protease microcolumn enabled reproducible protein digestion and peptide mapping with 100% sequence coverage obtained for three different recombinant proteins. Additionally, when assessing the μIMER digestion efficiency for complex proteome samples, it delivered a 144-fold faster and significantly more efficient protein digestion compared to 24 h for bulk digestion. The 3D-printed μIMER withstands remarkably high pressures above 130 bar and retains its activity for several weeks. This versatile platform will enable researchers to produce tailored polymer-based enzyme reactors for various applications in analytical chemistry and beyond.

Coupling suspension trapping-based sample preparation and data-independent acquisition mass spectrometry for sensitive exosomal proteomic analysis

It has been a challenge to analyze minute amounts of proteomic samples in a facile and robust manner. Herein, we developed a quantitative proteomics workflow by integrating suspension trapping (S-Trap)-based sample preparation and label-free data-independent acquisition (DIA) mass spectrometry and then applied it for the analysis of microgram and even nanogram amounts of exosome samples. S-Trap-based sample preparation outperformed the traditional in-solution digestion-based approach and the commonly used filter-aided sample preparation (FASP)-based approach with regard to the number of proteins and peptides identified. Moreover, S-Trap-based sample preparation coupled with DIA mass spectrometry also showed the highest reproducibility for protein quantification. In addition, this approach allowed for identification and quantification of exosome proteins with low starting amounts (down to 50 ~ 200 ng). Finally, the proposed method was successfully applied to label-free quantification of exosomal proteins extracted from MDA-MB-231 breast cancer cells and MCF-10A non-tumorigenic epithelial breast cells. Prospectively, we envision the integrated S-Trap sample preparation coupled with DIA quantification strategy as a promising alternative for highly efficient and sensitive analysis of trace amounts of proteomic samples (e.g., exosomal samples).

Evaluation of Fast and Sensitive Proteome Profiling of FF and FFPE Kidney Patient Tissues

The application of proteomics to fresh frozen (FF) and formalin-fixed paraffin-embedded (FFPE) human tissues is an important development spurred on by requests from stakeholder groups in clinical fields. One objective is to complement current diagnostic methods with new specific molecular information. An important goal is to achieve adequate and consistent protein recovery across and within large-scale studies. Here, we describe development of several protocols incorporating mass spectrometry compatible detergents, including Rapigest, PPS, and ProteaseMax. Methods were applied on 4 and 15 μm thick FF tissues, and 4 μm thick FFPE tissues. We evaluated sensitivity and repeatability of the methods and found that the protocol containing Rapigest enabled detection of 630 proteins from FF tissue of 1 mm² and 15 μm thick, whereas 498 and 297 proteins were detected with the protocols containing ProteaseMax and PPS, respectively. Surprisingly, PPS-containing buffer showed good extraction of the proteins from 4 μm thick FFPE tissue with the average of 270 protein identifications (1 mm²), similar to the results on 4 μm thick FF. Moreover, we found that temperature increases during incubation with urea on 4 μm thick FF tissue revealed a decrease in the number of identified proteins and increase in the number of the carbamylated peptides.

Hydrogen/Deuterium Exchange Mass Spectrometry with Integrated Electrochemical Reduction and Microchip-Enabled Deglycosylation for Epitope Mapping of Heavily Glycosylated and Disulfide-Bonded Proteins

Hydrogen/deuterium exchange mass spectrometry (HDX-MS) is a recognized method to study protein conformational dynamics and interactions. Proteins encompassing post-translational modifications (PTMs), such as disulfide bonds and glycosylations, present challenges to HDX-MS, as disulfide bond reduction and deglycosylation is often required to extract HDX information from regions containing these PTMs. In-solution deglycosylation with peptide-N4-(N-acetyl-β-d-glucosaminyl)-asparagine amidase A (PNGase A) or PNGase H⁺ combined with chemical reduction using tris-(2-carboxyethyl)phosphine (TCEP) has previously been used for HDX-MS analysis of disulfide-linked glycoproteins. However, this workflow requires extensive manual sample preparation and consumes large amounts of enzyme. Furthermore, large amounts of TCEP and glycosidases often result in suboptimal liquid chromatography-mass spectrometry (LC-MS) performance. Here, we compare the in-solution activity of PNGase A, PNGase H⁺, and the newly discovered PNGase Dj under quench conditions and immobilize them onto thiol-ene microfluidic chips to create HDX-MS-compatible immobilized microfluidic enzyme reactors (IMERs). The IMERS retain deglycosylation activity, also following repeated use and long-term storage. Furthermore, we combine a PNGase Dj IMER, a pepsin IMER, and an electrochemical cell to develop an HDX-MS setup capable of efficient online disulfide-bond reduction, deglycosylation, and proteolysis. We demonstrate the applicability of this setup by mapping the epitope of a monoclonal antibody (mAb) on the heavily disulfide-bonded and glycosylated sema-domain of the tyrosine-protein kinase Met (SD c-Met). We achieve near-complete sequence coverage and extract HDX data to identify regions of SD c-Met involved in mAb binding. The described methodology thus presents an integrated and online workflow for improved HDX-MS analysis of challenging PTM-rich proteins.

Development of an immobilized-trypsin reactor coupled to liquid chromatography and tandem mass spectrometry for the analysis of human hemoglobin adducts with sulfur mustard

Sulfur mustard reacts with blood proteins, such as hemoglobin, to form stable adducts that can be used as long-lived biomarkers of exposure. These adducts can be analyzed by liquid chromatography coupled to tandem mass-spectrometry (LC-MS/MS) after an enzymatic digestion step. The objective of this study was to develop trypsin-based immobilized enzyme reactors (IMERs) in order to obtain a faster digestion of hemoglobin than the conventional in-solution digestion. Trypsin IMERs were synthetized by grafting the enzyme on a CNBr-Sepharose gel and the influence of several parameters on the digestion yields, such as the transfer volume between the injection loop and the IMER, the temperature and the digestion time was studied. The repeatability of the digestion on three laboratory-made IMERs was demonstrated for pure hemoglobin and hemoglobin previously exposed to different concentrations of sulfur mustard (RSD inferior to 13% and 21% respectively) and was better than that obtained for in-solution digestions (RSD inferior to 28% and up to 53% respectively). A preferential adduction of sulfur mustard on the histidine residues of hemoglobin was confirmed, for both in-solution and IMER digestion results. On a quantitative point of view, the performances of in-solution and IMER digestions were similar, with the theoretical possibility to detect peptides resulting from the in vitro incubation of hemoglobin in pure water with sulfur mustard at 7.5 ng⋅mL^-1. However, digestion on IMER proved to be more repeatable and 32 times faster than in-solution digestion, and a given IMER could be reused at least 60 times.

Controllable Synthesis of Hollow Microtubular Covalent Organic Frameworks as an Enzyme-Immobilized Platform for Enhancing Catalytic Activity

Despite great achievement that has been made in the synthesis of covalent organic frameworks (COFs), precise construction of COFs with well-defined nano/microstructures poses a rigorous challenge. Herein, we introduce a simple template-free strategy for controllable synthesis of hollow microtubular COFs. The obtained COFs show a spontaneous morphology transformation from a microfiber to a hollow microtubular structure when the concentrations of catalytic acid are regulated elaborately. Furthermore, the as-prepared COFs exhibit high crystallinity, well-defined hollow tubular morphology, and high surface areas (∼2600 m2/g). Taking the advantages of the unique morphological structure, the hollow microtubular COFs can serve as an ideal host material for enzymes. The resultant biocomposites show high catalytic performance and can be successfully applied to rapid and high-efficiency proteolysis of proteins. This work blazes a trail for controllable synthesis of the hollow microtubular COFs through a template-free process and expands the application of COFs as a promising platform for enzyme immobilization.

Development of an All-in-One Protein Digestion Platform Using Sorbent-Attached Membrane Funnel-Based Spray Ionization Mass Spectrometry

In this work, the sorbent-attached microfunnels used in funnel-based spray ionization mass spectrometry were evaluated for the all-in-one digestion of proteins. Sorbent materials, including C₁₈ and TiO₂ powders, were used as substrates to support in-funnel digestion and subsequent solid-phase extraction and purification of the digested products. In-funnel digestion protocols with and without reductive alkylation were developed for the analysis of proteins with and without disulfide linkages. Compared with in-solution digestion of the same loadings, the sequence coverage of in-funnel digestion of ovalbumin (with one disulfide bond) and ovocystatin (with two disulfide bonds) increased from 36% to 65% and from 21% to 81%, respectively. Loading 100 fmol of ovalbumin was sufficient to generate detectable tryptic fragments on C₁₈-attached funnels. Notably, some phosphorylated digestion fragments were solely detected on C₁₈-attached funnels and some nonphosphorylated digestion fragments were detected only on TiO₂-attached funnels. Complex biological protein mixtures (i.e., bovine milk) and mouse liver protein extract could also be digested on C₁₈- and TiO₂-attached funnels. Using this platform, 30 samples were digested at the same time with enhanced digestion efficiency and were analyzed by funnel-based spray ionization mass spectrometry. This approach is potentially useful for sensitive and high-throughput bottom-up proteomic studies of complex biological samples.

One-pot synthesis of trypsin-based magnetic metal-organic frameworks for highly efficient proteolysis

Immobilization of enzymes onto metal-organic frameworks (MOFs) through a biomimetic mineralization approach can preserve biological functionality in harsh environments. Despite the success of this approach, the alkaline environment of the reaction system, which is caused by the organic monomers of MOFs, makes it unsuitable for some pH-sensitive enzymes, especially for trypsin. Herein, we reported a facile approach for the one-pot synthesis of trypsin-immobilized magnetic zeolite imidazolate framework-8 (iron oxide@ZIF-8@trypsin), where the growth of ZIF-8 around the citric acid-modified iron oxide and immobilization of trypsin occurred simultaneously when the pH of the reaction system was changed to some extent. With a large specific surface area and a high enzyme loading capacity, the resultant iron oxide@ZIF-8@trypsin exhibited 2.6 times higher enzymatic activity than free trypsin. Moreover, it showed a favourable magnetic response (43 emu g^-1) which made the operation and recycling easy and convenient. In addition, iron oxide@ZIF-8@trypsin could be applied as an immobilized enzyme microreactor (IMER) to rapidly and efficiently digest proteins and complex human serum samples with satisfactory results, showing great promise for application in proteomic analysis.

Challenges and Advances in the Fabrication of Monolithic Bioseparation Materials and their Applications in Proteomics Research

High-performance liquid chromatography integrated with tandem mass spectrometry (HPLC-MS/MS) has become a powerful technique for proteomics research. Its performance heavily depends on the separation efficiency of HPLC, which in turn depends on the chromatographic material. As the "heart" of the HPLC system, the chromatographic material is required to achieve excellent column efficiency and fast analysis. Monolithic materials, fabricated as continuous supports with interconnected skeletal structure and flow-through pores, are regarded as an alternative to particle-packed columns. Such materials are featured with easy preparation, fast mass transfer, high porosity, low back pressure, and miniaturization, and are next-generation separation materials for high-throughput proteins and peptides analysis. Herein, the recent progress regarding the fabrication of various monolithic materials is reviewed. Special emphasis is placed on studies of the fabrication of monolithic capillary columns and their applications in separation of biomolecules by capillary liquid chromatography (cLC). The applications of monolithic materials in the digestion, enrichment, and separation of phosphopeptides and glycopeptides from biological samples are also considered. Finally, advances in comprehensive 2D HPLC separations using monolithic columns are also shown.

Application of Capillary Electrophoresis with Laser-Induced Fluorescence to Immunoassays and Enzyme Assays

Capillary electrophoresis using laser-induced fluorescence detection (CE-LIF) is one of the most sensitive separation tools among electrical separation methods. The use of CE-LIF in immunoassays and enzyme assays has gained a reputation in recent years for its high detection sensitivity, short analysis time, and accurate quantification. Immunoassays are bioassay platforms that rely on binding reactions between an antigen (analyte) and a specific antibody. Enzyme assays measure enzymatic activity through quantitative analysis of substrates and products by the reaction of enzymes in purified enzyme or cell systems. These two category analyses play an important role in the context of biopharmaceutical analysis, clinical therapy, drug discovery, and diagnosis analysis. This review discusses the expanding portfolio of immune and enzyme assays using CE-LIF and focuses on the advantages and disadvantages of these methods over the ten years of existing technology since 2008.

Enzyme-containing spin membranes for rapid digestion and characterization of single proteins

Proteolytic digestion is an important step in characterizing protein sequences and post-translational modifications (PTMs) using mass spectrometry (MS). This study uses pepsin- or trypsin-containing spin membranes for rapid digestion of single proteins or simple protein mixtures prior to ultrahigh-resolution Orbitrap MS analysis. Centrifugation of 100 μL of pretreated protein solutions through the functionalized membranes requires less than 1 min and conveniently digests proteins into large peptides that aid in confirming specific protein sequence variations and PTMs. Peptic and tryptic peptides from spin digestion of apomyoglobin and four commercial monoclonal antibodies (mAbs) typically cover 100% of the protein sequences in direct infusion MS analysis. Increasing the spin rate leads to a higher fraction of large peptic peptides for apomyoglobin, and MS analysis of peptic and tryptic peptides reveals mAb PTMs such as N-terminal pyroglutamate formation, C-terminal lysine clipping and glycosylation. Relative to overnight in-solution digestion of mAbs, spin digestion yields higher sequence coverages. Spin-membrane digestion followed by infusion MS readily differentiates a mAb to the Ebola virus from a related antibody that differs by addition of a single amino acid.

Mixed-mode ion exchange-based integrated proteomics technology for fast and deep plasma proteome profiling

Plasma proteome profiling by LC-MS based proteomics has drawn great attention recently for biomarker discovery from blood liquid biopsy. Due to standard multi-step sample preparation could potentially cause plasma protein degradation and analysis variation, integrated proteomics sample preparation technologies became promising solution towards this end. Here, we developed a fully integrated proteomics sample preparation technology for both fast and deep plasma proteome profiling under its native pH. All the sample preparation steps, including protein digestion and two-dimensional fractionation by both mixed-mode ion exchange and high-pH reversed phase mechanism were integrated into one spintip device for the first time. The mixed-mode ion exchange beads design achieved the sample loading at neutral pH and protein digestion within 30 min. Potential sample loss and protein degradation by pH changing could be voided. 1 μL of plasma sample with depletion of high abundant proteins was processed by the developed technology with 12 equally distributed fractions and analyzed with 12 h of LC-MS gradient time, resulting in the identification of 862 proteins. The combination of the Mixed-mode-SISPROT and data-independent MS method achieved fast plasma proteome profiling in 2 h with high identification overlap and quantification precision for a proof-of-concept study of plasma samples from 5 healthy donors. We expect that the Mixed-mode-SISPROT become a generally applicable sample preparation technology for clinical oriented plasma proteome profiling.

Systematic Evaluation of Immobilized Trypsin-Based Fast Protein Digestion for Deep and High-Throughput Bottom-Up Proteomics

Immobilized trypsin (IM) has been recognized as an alternative to free trypsin (FT) for accelerating protein digestion 30 years ago. However, some questions of IM still need to be answered. How does the solid matrix of IM influence its preference for protein cleavage and how well can IM perform for deep bottom-up proteomics compared to FT? By analyzing Escherichia coli proteome samples digested with amine or carboxyl functionalized magnetic bead-based IM (IM-N or IM-C) or FT, it is observed that IM-N with the nearly neutral solid matrix, IM-C with the negatively charged solid matrix, and FT have similar cleavage preference considering the microenvironment surrounding the cleavage sites. IM-N (15 min) and FT (12 h) both approach 9000 protein identifications (IDs) from a mouse brain proteome. Compared to FT, IM-N has no bias in the digestion of proteins that are involved in various biological processes, are located in different components of cells, have diverse functions, and are expressed in varying abundance. A high-throughput bottom-up proteomics workflow comprising IM-N-based rapid protein cleavage and fast CZE-MS/MS enables the completion of protein sample preparation, CZE-MS/MS analysis, and data analysis in only 3 h, resulting in 1000 protein IDs from the mouse brain proteome.

Recent advances in biomolecule immobilization based on self-assembly: organic-inorganic hybrid nanoflowers and metal-organic frameworks as novel substrates

In the past few years, the immobilization of biomolecules on hybrid nanoflowers and metal-organic frameworks (MOFs) via self-assembly synthesis has received much attention due to its simplicity, high efficiency, and a bright prospect of enhancing the stability, activity and even selectivity of biomolecules compared to conventional immobilization methods. In the synthesis of organic-inorganic hybrid nanoflowers, biomolecules used as organic components are simply mixed with metal ions which act as inorganic components to form flower-like nanocomposites, while in the self-assembly process of encapsulating biomolecules in MOFs (biomolecule@MOF composites), the biomolecules just need to be added to the precursor mixtures of MOFs, in which the biomolecules are therefore embedded in MOF crystals with small pores. In this review, we focus on the recent advances of these composites, especially in the synthesis strategies, mechanism and applications in biosensors, biomedicine, pollutant disposal, and industrial biocatalysis, and future perspectives are discussed as well.

Thiol-ene Monolithic Pepsin Microreactor with a 3D-Printed Interface for Efficient UPLC-MS Peptide Mapping Analyses

To improve the sample handling, and reduce cost and preparation time, of peptide mapping LC-MS workflows in protein analytical research, we here investigate the possibility of replacing conventional enzymatic digestion methods with a polymer microfluidic chip based enzyme reactor. Off-stoichiometric thiol-ene is utilized as both bulk material and as a monolithic stationary phase for immobilization of the proteolytic enzyme pepsin. The digestion efficiency of the, thiol-ene based, immobilized enzyme reactor (IMER) is compared to that of a conventional, agarose packed bed, pepsin IMER column commonly used in LC-MS based protein analyses. The chip IMER is found to rival the conventional column in terms of digestion efficiency at comparable residence time and, using a 3D-printed interface, be directly interfaceable with LC-MS.

Characterization of an immobilized enzyme reactor for on-line protein digestion

Despite the developments for faster liquid chromatographic and mass spectral detection techniques, the standard in-solution protein digestion for proteomic analyses has remained relatively unchanged. The typical in-solution trypsin protein digestion is usually the slowest part of the workflow, albeit one of the most important. The development of a highly efficient immobilized enzyme reactor (IMER) with rapid performance for on-line protein digestion would greatly decrease the analysis time involved in a proteomic workflow. Presented here is the development of a silica based IMER for on-line protein digestion, which produced rapid digestions in the presence of organic mobile phase for both model proteins and a complex sample consisting of the insoluble portion of a yeast cell lysate. Protein sequence coverage and identifications evaluated between the IMER and in-solution digestions were comparable. Overall, for a yeast cell lysate with only a 10s volumetric residence time on-column, the IMER identified 507 proteins while the in-solution digestion identified 490. There were no significant differences observed based on identified protein's molecular weight or isoelectric point between the two digestion methods. Implementation of the IMER into the proteomic workflow provided similar protein identification results, automation for sample analysis, and reduced the analysis time by 15h.

A novel protocol for enzymatic digestion based on covalent binding by protein immobilization

The process of protein digestion is a critical step for successful protein identification in proteomic analysis. Many efforts have been dedicated to enhancing the digestion efficiency for sufficient digestion. Among these approaches, protein complete denaturation with denaturants is a common process for better digestion. However, the removal of denaturants was tedious or would cause protein loss and other problems. In this work, a feasible digestion approach, immobilized protein digestion (IPD), based on covalent binding has been developed. Proteins can be completely denatured and immobilized on the surface of functional materials by covalent binding to form a monolayer. Subsequently, varieties of denaturants or contaminants would be removed thoroughly by washing. To achieve fast immobilization and high digestion efficiency, different functional materials and denaturants were selected. Compared with traditional in-solution digestion, the method achieved a prominent increase in identified peptides numbers and sequence coverage of proteins. Data analysis also showed that covalent binding could evidently decrease enzymatic missed cleavage for various protein sequences. Furthermore, possible peptide losses due to covalent binding were also investigated. Also, it has been proved to be efficient for complex biological sample digestion. Graphical abstract Workflow of the IPD method, including protein denaturation, immobilization, digestion, and identification.

Simple and Integrated Spintip-Based Technology Applied for Deep Proteome Profiling

Great efforts have been taken for developing high-sensitive mass spectrometry (MS)-based proteomic technologies, among which sample preparation is one of the major focus. Here, a simple and integrated spintip-based proteomics technology (SISPROT) consisting of strong cation exchange beads and C18 disk in one pipet tip was developed. Both proteomics sample preparation steps, including protein preconcentration, reduction, alkylation, and digestion, and reversed phase (RP)-based desalting and high-pH RP-based peptide fractionation can be achieved in a fully integrated manner for the first time. This easy-to-use technology achieved high sensitivity with negligible sample loss. Proteomic analysis of 2000 HEK 293 cells readily identified 1270 proteins within 1.4 h of MS time, while 7826 proteins were identified when 100000 cells were processed and analyzed within only 22 h of MS time. More importantly, the SISPROT can be easily multiplexed on a standard centrifuge with good reproducibility (Pearson correlation coefficient > 0.98) for both single-shot analysis and deep proteome profiling with five-step high-pH RP fractionation. The SISPROT was exemplified by the triplicate analysis of 100000 stem cells from human exfoliated deciduous teeth (SHED). This led to the identification of 9078 proteins containing 3771 annotated membrane proteins, which was the largest proteome data set for dental stem cells reported to date. We expect that the SISPROT will be well suited for deep proteome profiling for fewer than 100000 cells and applied for translational studies where multiplexed technology with good label-free quantification precision is required.

Hyphenation of a Deoxyribonuclease I immobilized enzyme reactor with liquid chromatography for the online stability evaluation of oligonucleotides

The stability of antisense oligonucleotides (ONs) toward nucleases is a key aspect for their possible implementation as therapeutic agents. Typically, ON stability studies are performed off-line, where the ONs are incubated with nucleases in solution, followed by their analysis. The problematics of off-line processing render the detailed comparison of relative ON stability quite challenging. Therefore, the development of an online platform based on an immobilized enzyme reactor (IMER) coupled to liquid chromatography (LC) was developed as an alternative for improved ON stability testing. More in detail, Deoxyribonuclease I (DNase I) was immobilized on epoxy-silica particles of different pore sizes and packed into a column for the construction of an IMER. Subsequently, the hyphenation of the IMER with ion-pair chromatography (IPC) and ion-exchange chromatography (IEC) was evaluated, leading to the successful development of two online methodologies: IMER-IPC and IMER-IEC. More specifically, natural and modified DNA and RNA oligonucleotides were used for testing the performance of the methodologies. Both methodologies proved to be simple, automatable, fast and highly reproducible for the quantitative and qualitative evaluation of ON degradation. In addition, the extended IMER life time in combination with a more straightforward control of the reaction kinetics substantiate the applicability of the IMER-LC platform for ON stability tests and its implementation in routine and research laboratories.

Uncovering immobilized trypsin digestion features from large-scale proteome data generated by high-resolution mass spectrometry

Immobilized trypsin produces very fast protein digestion, which is attractive for application to high throughput bottom-up proteomics. While there is a rich literature on the preparation of immobilized trypsin, there are very few studies that investigate its application to complex proteomic samples. In this work, we compared solution-phase trypsin with trypsin immobilized on magnetic microspheres for digestion of two complex proteomes, Escherichia coli and the MCF7 cell line. The digests were separated by HPLC, and detected with a Q-Exactive mass spectrometer, which generated high resolution and high quality parent- and fragment-ion mass spectra. The data were analyzed using MaxQuant. We make several conclusions about the features of immobilized trypsin digestion of complex proteomes. First, both immobilized and solution-phase trypsin generate peptides that sample the same protein pool. Second, immobilized trypsin can digest complex proteomes two orders of magnitude faster than solution-phase trypsin while retaining similar numbers of protein identifications and proteome depth. Digestion using immobilized trypsin for 5-min produces a similar number of missed cleavages as solution-based trypsin digestion for 4-h; digestion using immobilized trypsin for 20-min produces a similar number of missed cleavages as solution-based trypsin digestion for 12-h. Third, immobilized trypsin produces quantitatively reproducible digestion of complex proteomes. Finally, there is small but measurable loss of peptide due to non-specific adsorption to the immobilization matrix. This adsorption generates a bias against detection of basic peptides.

A mesofluidic platform integrating on-chip probe ultrasonication for multiple sample pretreatment involving denaturation, reduction, and digestion in protein identification assays by mass spectrometry

A novel mesofluidic platform integrating on-chip probe ultrasonication for automated high-throughput shotgun proteomic assays.

A capillary electrophoresis-based immobilized enzyme reactor using graphene oxide as a support via layer by layer electrostatic assembly

Using graphene oxide as an enzyme support, we developed a novel CE-based microreactor via layer-by-layer electrostatic assembly, which can be used for accurate on-line analysis and characterization of peptides and proteins.