Dual Matrix-Based Immobilized Trypsin for Complementary Proteolytic Digestion and Fast Proteomics Analysis with Higher Protein Sequence Coverage

Automated proteomic sample preparation: The key component for high throughput and quantitative mass spectrometry analysis

Sample preparation for mass spectrometry-based proteomics has many tedious and time-consuming steps that can introduce analytical errors. In particular, the steps around the proteolytic digestion of protein samples are prone to inconsistency. One route for reliable sample processing is the development and optimization of a workflow utilizing an automated liquid handling workstation. Diligent assessment of the sample type, protocol design, reagents, and incubation conditions can significantly improve the speed and consistency of preparation. When combining robust liquid chromatography-mass spectrometry with either discovery or targeted methods, automated sample preparation facilitates increased throughput and reproducible quantitation of biomarker candidates. These improvements in analysis are also essential to process the large patient cohorts necessary to validate a candidate biomarker for potential clinical use. This article reviews the steps in the workflow, optimization strategies, and known applications in clinical, pharmaceutical, and research fields that demonstrate the broad utility for improved automation of sample preparation in the proteomic field.

Industrial applications of immobilized nano-biocatalysts

Immobilized enzyme-based catalytic constructs could greatly improve various industrial processes due to their extraordinary catalytic activity and reaction specificity. In recent decades, nano-enzymes, defined as enzyme immobilized on nanomaterials, gained popularity for the enzymes' improved stability, reusability, and ease of separation from the biocatalytic process. Thus, enzymes can be strategically incorporated into nanostructured materials to engineer nano-enzymes, such as nanoporous particles, nanofibers, nanoflowers, nanogels, nanomembranes, metal-organic frameworks, multi-walled or single-walled carbon nanotubes, and nanoparticles with tuned shape and size. Surface-area-to-volume ratio, pore-volume, chemical compositions, electrical charge or conductivity of nanomaterials, protein charge, hydrophobicity, and amino acid composition on protein surface play fundamental roles in the nano-enzyme preparation and catalytic properties. With proper understanding, the optimization of the above-mentioned factors will lead to favorable micro-environments for biocatalysts of industrial relevance. Thus, the application of nano-enzymes promise to further strengthen the advances in catalysis, biotransformation, biosensing, and biomarker discovery. Herein, this review article spotlights recent progress in nano-enzyme development and their possible implementation in different areas, including biomedicine, biosensors, bioremediation of industrial pollutants, biofuel production, textile, leather, detergent, food industries and antifouling.

A Sensitive and Simple Enzyme-Linked Immunosorbent Assay Using Polymer as Carrier

In this study, a new and sensitive enzyme-linked immunosorbent assay (ELISA) was developed by introducing a polymer as a reaction carrier. The results suggest that the newly developed ELISA method is more convenient than the existing paper-based ELISA method and applicable to a wider range of environments. In addition, the sensitivity of the new method is much higher than that of the existing paper-based ELISA method and even higher than that of the traditional ELISA method.

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.

Kinase-loaded magnetic beads for sequentialin vitrophosphorylation of peptides and proteins

Kinases ERK2 and GSK-3β loaded magnetic beads for sequentialin vitrophosphorylation of peptides and proteins.

Fast on-Site Visual Detection of Active Ricin Using a Combination of Highly Efficient Dual-Recognition Affinity Magnetic Enrichment and a Specific Gold Nanoparticle Probe

Ricin, a highly toxic protein, is a controlled substance by both the Chemical Weapons Convention (CWC) and the Biological Weapons Convention (BWC). Therefore, fast precaution of potential ricin toxin plays an important role in national security and public safety. Herein, a simple, sensitive, and accurate visual detection of active ricin in complex samples is presented by combining magnetic affinity enrichment with a specific gold nanoparticle (AuNP) probe. In the first step, a dual-recognition magnetic absorbent was fabricated by simultaneously incorporating two different affinity ligands (concanavalin A and galactosamine) on low-foul polymer brushes grafted magnetic beads, which showed remarkable multivalent synergy binding capacity for ricin even under complex interfering environments. Subsequently, a homoadenine-constituted oligodeoxynucleotide named poly(21dA) was conjugated to AuNPs (the poly(21dA)-AuNPs), which served as a specific depurination substrate of active ricin. Coralyne can trigger the intact poly(21dA)-AuNPs aggregate by forming a non-Watson-Crick homoadenine/coralyne complex, but the poly(21dA)-AuNPs after reacting with active ricin failed to form this complex due to the loss of adenines. Based on these facts, active ricin can be detected as low as 12.5 ng mL^-1 with the naked eyes. This detection strategy could be well-applied in various ricin-spiked complex matrices. The features such as ready operation, facile readout, and easy accessibility make the assay a better choice for fast on-site active ricin detection.

Achieving efficient digestion faster with Flash Digest: potential alternative to multi-step detergent assisted in-solution digestion in quantitative proteomics experiments

RATIONALE

In quantitative analysis of protein biomarkers and therapeutic proteins by liquid chromatography/mass spectrometry (LC/MS), it is a preferred and well-established approach to digest with proteolytic enzymes to produce smaller peptide fragments which are more suitable for LC/MS analysis than the intact protein. In-solution digestion is one widely used method for protein digestion. Proteolytically resistant proteins often require digestion times that extend beyond normal working hours and prohibit same day analysis. We evaluated the performance of an immobilized enzyme reactor (IMER) to determine if this technology could reduce method development time, digestion time and increase throughput.

METHODS

We digested human plasma samples using a commercially available IMER, Flash Digest, and compared it to an in-solution digestion method for analysis of three different apolipoprotein biomarkers APOE, APOC2, and APOC3. The plasma digests were analyzed via LC/MS using electrospray ionization (ESI) and multiple reaction monitoring (MRM). Value assigned calibrators were selected over a relevant physiological concentration range for each protein of interest. Quality control samples (QCs) and 'unknown' human plasma samples were analyzed with both methods.

RESULTS

Flash Digest significantly reduced digestion time for APOC3, the most proteolytically resistant of the three proteins, to 30 min compared with overnight used with in-solution digestion. The Flash Digest achieved comparable digestion efficiency with minimal method development and reduced sample preparation time. Both methods showed linearity over a physiologically relevant concentration range. Precision was evaluated and a percentage coefficient of variance (% CV) less than 8% was obtained during intra-day reproducibility evaluation for all three apolipoproteins with Flash Digest. Concentrations observed for QCs and unknown samples using Flash Digest were comparable to the in-solution method.

CONCLUSIONS

An IMER such as Flash Digest may be a potential alternative to in-solution digestion to accelerate digestion of proteolytically resistant proteins in a quantitative proteomics experiments, reduce method development time and increase throughput. Copyright © 2016 John Wiley & Sons, Ltd.

Mass spectrometry methods for predicting antibiotic resistance

Developing elaborate techniques for clinical applications can be a complicated process. Whole-cell MALDI-TOF MS revolutionized reliable microorganism identification in clinical microbiology laboratories and is now replacing phenotypic microbial identification. This technique is a generic, accurate, rapid, and cost-effective growth-based method. Antibiotic resistance keeps emerging in environmental and clinical microorganisms, leading to clinical therapeutic challenges, especially for Gram-negative bacteria. Antimicrobial susceptibility testing is used to reliably predict antimicrobial success in treating infection, but it is inherently limited by the need to isolate and grow cultures, delaying the application of appropriate therapies. Antibiotic resistance prediction by growth-independent methods is expected to reduce the turnaround time. Recently, the potential of next-generation sequencing and microarrays in predicting microbial resistance has been demonstrated, and this review evaluates the potential of MS in this field. First, technological advances are described, and the possibility of predicting antibiotic resistance by MS is then illustrated for three prototypical human pathogens: Staphylococcus aureus, Escherichia coli, and Pseudomonas aeruginosa. Clearly, MS methods can identify antimicrobial resistance mediated by horizontal gene transfers or by mutations that affect the quantity of a gene product, whereas antimicrobial resistance mediated by target mutations remains difficult to detect.

Hollow silica bubble based immobilized trypsin for highly efficient proteome digestion and buoyant separation

Tryptic digestion before identification and quantification by mass spectrometry is an indispensable process for most proteomics studies.

Trypsin immobilization in ordered porous polymer membranes for effective protein digestion

Fast and effective protein digestion is a vital process for mass spectrometry (MS) based protein analysis. This study introduces a porous polymer membrane enzyme reactor (PPMER) coupled to nanoflow liquid chromatography-tandem MS (nLC-ESI-MS/MS) for on-line digestion and analysis of proteins. Poly (styrene-co-maleic anhydride) (PS-co-MAn) was fabricated by the breath figure method to make a porous polymer membrane in which the MAn group was covalently bound to enzyme. Based on this strategy, microscale PPMER (μPPMER) was constructed for on-line connection with the nLC-ESI-MS/MS system. Its capability for enzymatic digestion with bovine serum albumin (BSA) was evaluated with varied digestion periods. The on-line proteolysis of BSA and subsequent analysis with μPPMER-nLC-ESI-MS/MS revealed that peptide sequence coverage increased from 10.3% (digestion time 10 min) to 89.1% (digestion time 30 min). μPPMER can efficiently digest proteins due to the microscopic confinement effect, showing its potential application in fast protein identification and protease immobilization. Applications of on-line digestion using μPPMER with human plasma and urinary proteome samples showed that the developed on-line method yielded equivalent or better performance in protein coverage and identified more membrane proteins than the in-solution method. This may be due to easy accommodation of hydrophobic membrane proteins within membrane pores.

A new sample preparation method for the absolute quantitation of a target proteome using 18O labeling combined with multiple reaction monitoring mass spectrometry

A new sample preparation method for target proteome absolute quantitation using ¹⁸O labeling-MRM MS.

Ultrasensitive proteome analysis using paramagnetic bead technology

In order to obtain a systems-level understanding of a complex biological system, detailed proteome information is essential. Despite great progress in proteomics technologies, thorough interrogation of the proteome from quantity-limited biological samples is hampered by inefficiencies during processing. To address these challenges, here we introduce a novel protocol using paramagnetic beads, termed Single-Pot Solid-Phase-enhanced Sample Preparation (SP3). SP3 provides a rapid and unbiased means of proteomic sample preparation in a single tube that facilitates ultrasensitive analysis by outperforming existing protocols in terms of efficiency, scalability, speed, throughput, and flexibility. To illustrate these benefits, characterization of 1,000 HeLa cells and single Drosophila embryos is used to establish that SP3 provides an enhanced platform for profiling proteomes derived from sub-microgram amounts of material. These data present a first view of developmental stage-specific proteome dynamics in Drosophila at a single-embryo resolution, permitting characterization of inter-individual expression variation. Together, the findings of this work position SP3 as a superior protocol that facilitates exciting new directions in multiple areas of proteomics ranging from developmental biology to clinical applications.

Accelerating trypsin digestion: the immobilized enzyme reactor

Sample preparation has lagged far behind the evolution of instrumentation used in mass-linked protein analysis. Trypsin digestion, for example, still takes a day, as it did 50 years ago, while mass spectral analyses are achieved in seconds. Higher order structure of proteins is frequently modified by varying digestion conditions: shifting the initial points of trypsin cleavage, changing digestion pathways, accelerating peptide bond demasking and altering the distribution of miscleaved products at the completion of proteolysis. Reduction and alkylation are even circumvented in many cases. This review focuses on immobilized enzyme reactor technology as a means to achieve accelerated trypsin digestion by exploiting these phenomena.