Phase separation methods for protein purification: A meta-analysis of purification performance and cost-effectiveness.

Protein purifications based on phase separations (e.g., precipitation and liquid-liquid extraction) have seen little adoption in commercial protein drug production. To identify barriers, we analyzed the purification performance and economics of 290 phase separation purifications from 168 publications. First, we found that studies using Design of Experiments for optimization achieved significantly greater mean yield and host cell protein log10 removal values than those optimizing one factor at a time (11.5% and 53% increases, respectively). Second, by modeling each reported purification at scales from 10 to 10,000 kg product/year and comparing its cost-effectiveness versus chromatography, we found that cost-effectiveness depends strongly on scale: the fraction of phase separations predicted to be cost-effective at the 10, 100, and 1000 kg/year scales was 8%, 15%, and 43%, respectively. Total cost per unit product depends inversely on input purity, with phase separation being cheaper than chromatography at the 100 kg/year scale in 100% of cases where input purity was ≤ 1%, compared to about 25% of cases in the dataset as a whole. Finally, we identified a simple factor that strongly predicts phase separation process costs: the mass ratio of reagents versus purified product (the "direct materials usage rate"), which explains up to 58% of variation in cost per unit of purified product among all 290 reports, and up to 98% of variation within particular types of phase separation.

An Economical and Versatile High-Throughput Protein Purification System Using a Multi-Column Plate Adapter.

Protein purification is imperative to the study of protein structure and function and is usually used in combination with biophysical techniques. It is also a key component in the development of new therapeutics. The evolving era of functional proteomics is fueling the demand for high-throughput protein purification and improved techniques to facilitate this. It was hypothesized that a multi column plate adaptor (MCPA) can interface multiple chromatography columns of different resins with multi-well plates for parallel purification. This method offers an economical and versatile method of protein purification that can be used under gravity or vacuum, rivaling the speed of an automated system. The MCPA can be used to recover milligram yields of protein by an affordable and time efficient method for subsequent characterization and analysis. The MCPA has been used for high-throughput affinity purification of SH3 domains. Ion exchange has also been demonstrated via the MCPA to purify protein post Ni-NTA affinity chromatography, indicating how this system can be adapted to other purification types. Due to its setup with multiple columns, individual customization of parameters can be made in the same purification, unachievable by the current plate-based methods.

Intact Protein Mass Spectrometry for Therapeutic Protein Quantitation, Pharmacokinetics, and Biotransformation in Preclinical and Clinical Studies: An Industry Perspective.

Recent advancements in immunocapture methods and mass spectrometer technology have enabled intact protein mass spectrometry to be applied for the characterization of antibodies and other large biotherapeutics from in-life studies. Protein molecules have not been traditionally studied by intact mass or screened for catabolites in the same manner as small molecules, but the landscape has changed. Researchers have presented methods that can be applied to the drug discovery and development stages, and others are exploring the possibilities of the new approaches. However, a wide variety of options for assay development exists without clear recommendation on best practice, and data processing workflows may have limitations depending on the vendor. In this perspective, we share experiences and recommendations for current and future application of mass spectrometry for biotherapeutic molecule monitoring from preclinical and clinical studies.

Morphology optimization and assessment of the performance limits of high-porosity nanostructured polymer monolithic capillary columns for proteomics analysis.

This study targets the synthesis of high external-porosity poly(styrene-co-divinylbenzene) monolithic support structures with macropore and globule sizes in the sub-micron range, aiming at the realization of high-speed and high-resolution gradient separations of intact proteins and peptides. The thermodynamic and kinetic aspects of the free-radical polymerization synthesis were adjusted by tuning the porogen to monomer ratio, the porogen ratio, the initiator content, and polymerization temperature. Next, column morphology was linked to eddy-dispersion and mobile-phase mass-transfer contributions and the chromatographic performance limits were benchmarked against conventional packed columns and silica monoliths. Polymer monolithic structures yielding a separation impedance as low as 976 were created allowing to generate N > 1,000,000 (for an unretained marker), albeit the expense of very long analysis times. Decreasing the macropore and globule sizes below a certain threshold led to significant increase in eddy dispersion, as globular entities agglomerate, and a small number of large flow-through pores permeate the overall fine interconnected polymer network with small diameter flow-through pores. The potential of monolith chromatography for proteomics application is demonstrated with a ballistic 6 s gradient separation of intact proteins and a high-resolution nanoLC-Orbitrap mass spectrometric analysis of a tryptic E. coli digest applying a coupled-column system.

Step-Wise Assessment and Optimization of Sample Handling Recovery Yield for Nanoproteomic Analysis of 1000 Mammalian Cells.

Protein and peptide adhesion is a major factor contributing to sample loss during proteomic sample preparation workflows. Sample loss often has detrimental effects on the quality of proteomic analysis by compromising protein identification and data reproducibility. When starting with a low sample amount, only the most abundant proteins can be identified, which often offers little insights for biological research. Although the general idea about severe sample loss from low amount of starting material is widely presumed in the proteomics field, quantitative assessment on the impact of sample loss has been poorly investigated. In the present study, we have quantitatively assessed sample loss during each step of a conventional in-solution sample preparation workflow using bicinchoninic acid (BCA) and targeted LC/MS/MS protein and peptide assays. According to our assessment, for starting materials of ∼1000 mammalian cells, surface adhesion, along with desalting and speed-vacuum drying steps, all contribute heavily to sample loss, in particular for low-abundance proteins. With this knowledge, we have adapted slippery liquid infused porous surface (SLIPS) treatment, commercial LoBind tubes, and in-line desalting during sample processing. With these improvements, we were able to use a conventional in-solution sample handling method to identify on average 829 proteins with 1000 U2OS osteosarcoma cells (∼100 ng) with 75-min LC/MS/MS runs, an 11-fold increase in protein identification. Our optimized in-solution workflow is straightforward and also much less equipment- and technique-demanding than other advanced sample preparation protocols in the field.

An assessment of the impact of extraction and digestion protocols on multiplexed targeted protein quantification by mass spectrometry for egg and milk allergens.

The unintentional presence of even trace amounts of certain foods constitutes a major hazard for those who suffer from food allergies. For many food industries, product and raw ingredient surveillance forms part of their risk assessment procedures. This may require the detection of multiple allergens in a wide variety of matrices. Mass spectrometry offers a possible solution for the quantification of multiple allergens in a single analysis. The capability of MS to quantify many peptides from a complex protein digestion is well known. However, a lack of matrix certified reference materials has made the optimisation of extraction and digestion conditions for multiplexed allergen quantification difficult to assess. Here, we report a systematic study, using preliminary screening followed by a Design of Experiments approach, to find the optimal buffer and digestion conditions for detecting milk and egg protein markers in a model processed food matrix. Five of the most commonly used buffers, two chaotropic reagents and two reducing reagents were assessed for the optimal extraction of multiple protein markers. While the choice of background buffer had little impact, the use of chaotropic and reducing reagents showed significant benefits for the extraction of most proteins. A full factorial design experiment was applied to the parameters shown to have a significant impact on protein recovery. These studies suggest that a single optimal set of extraction conditions enabling the quantitative recovery of all proteins is not easily achieved. Therefore, although MS is capable of the simultaneous quantification of many peptides in a single run, greater consideration of protein extraction is required before these are applied for multiplex allergen quantification in food matrices. Graphical abstract.

A Multichannel Gel Electrophoresis and Continuous Fraction Collection Apparatus for High-Throughput Protein Separation and Characterization.

We developed a multichannel gel electrophoresis system that continuously collects fractions as protein bands migrate to the bottom of gel columns. The device uses several short linear gel columns, each of a different percent acrylamide, to achieve a separation power similar to that of a long gradient gel. A "counter-free-flow" elution technique allows continuous and simultaneous fraction collection from multiple channels at low cost. Using the system with SDS-PAGE, 300 µg samples of protein can be separated and eluted into 48-96 fractions over a mass range of 10-150 kDa in 2.5 h. Each eluted protein can be recovered at 50% efficiency or higher in ~500 µL. The system can also be used for native gel electrophoresis, but protein aggregation limits the loading capacity to about 50 µg per channel and reduces resolution. This system has the potential to be coupled with mass spectrometry to achieve high-throughput protein identification.

Ultrarapid Sodium Dodecyl Sulfate Polyacrylamide Mini-Gel Electrophoresis.

We describe here an ultrafast method for electrophoresing proteins on SDS-PAGE. Previously we reported a method to complete SDS-PAGE and immunoblotting in an hour, including electrophoresing proteins at 70°C in 10 min. Here we show that we can electrophorese molecular weight standards and bovine serum albumin on a 4-20% gradient gel in well under 10 min using heated (44 °C) Laemmli running buffer and high voltage.

A robust, cost-effective method for DNA, RNA and protein co-extraction from soil, other complex microbiomes and pure cultures.

The soil microbiome is inherently complex with high biological diversity, and spatial heterogeneity typically occurring on the submillimetre scale. To study the microbial ecology of soils, and other microbiomes, biomolecules, that is, nucleic acids and proteins, must be efficiently and reliably co-recovered from the same biological samples. Commercial kits are currently available for the co-extraction of DNA, RNA and proteins but none has been developed for soil samples. We present a new protocol drawing on existing phenol-chloroform-based methods for nucleic acids co-extraction but incorporating targeted precipitation of proteins from the phenol phase. The protocol is cost-effective and robust, and easily implemented using reagents commonly available in laboratories. The method is estimated to be eight times cheaper than using disparate commercial kits for the isolation of DNA and/or RNA, and proteins, from soil. The method is effective, providing good quality biomolecules from a diverse range of soil types, with clay contents varying from 9.5% to 35.1%, which we successfully used for downstream, high-throughput gene sequencing and metaproteomics. Additionally, we demonstrate that the protocol can also be easily implemented for biomolecule co-extraction from other complex microbiome samples, including cattle slurry and microbial communities recovered from anaerobic bioreactors, as well as from Gram-positive and Gram-negative pure cultures.

An efficient method for FITC labelling of proteins using tandem affinity purification.

Fluorescence-based assays are extremely diverse, sensitive and robust experimental methods for investigating the conformational changes, enzyme kinetics, dynamics and molecular interactions. A prerequisite for most of these experimental approaches is to label the protein of interest with one or more extrinsic fluorophores with desired photophysical properties. Fluorescein isothiocyanate (FITC), due to its high quantum efficiency and conjugate stability, is most widely used fluorescence labelling reagent for such experimental approaches. However, the bottlenecks in this labelling reaction is requirement of high protein concentration, maintenance of protein stability during the labelling process as well as high background fluorescence due to ineffective removal of unreacted FITC, prior to fluorescence studies. Therefore, to overcome these inadequacies or limitations, we have modified the existing protocol by introducing tandem affinity purification tags at the N- and C-terminus of target protein. Using this modified method, we have efficiently labelled target protein with significant decrease in precipitation, degradation and background fluorescence of unreacted FITC. This facile and rapid technique may also be used as a basis for labelling procedures with other fluorophores and hence has a broad application in spectroscopic studies.

Facile and green fabrication of cation exchange membrane adsorber with unprecedented adsorption capacity for protein purification.

Fabricating membrane adsorbers with high adsorption capacity and appreciable throughput for the separation and purification of protein products is challenging in biomedical and pharmaceutical industries. Herein, we report the synthesis of a novel membrane adsorber by functionalizing a nylon microfiltration membrane with alginate dialdehyde (ADA) followed by sulphonic addition, without any solvent usage, and its successful application in the purification of lysozyme. Taking advantage of abundant dual cation exchange (CEX) groups on sulphonic-ADA (S-ADA) ligands, this novel S-ADA-nylon membrane adsorber showed an unprecedented static binding capicity of 286mg/mL for lysozyme adsorption. Meanwhile, the prepared membrane adsorber could be easily regenerated (complete protein elution) under mild conditions and be reused at least for five times. Featured with a unique selectivity, the S-ADA-nylon membrane also captured lysozyme from chicken egg white solution with a high purity (100%) and a high recovery of 98%. The purified lysozyme showed similar specific activity as commercial product. The present work provides a facile, green and low-cost approach for the preparation of high-performance membrane adsorbers, which has a great potential in protein production.

Ten-Minute Protein Purification and Surface Tethering for Continuous-Flow Biocatalysis.

Nature applies enzymatic assembly lines to synthesize bioactive compounds. Inspired by such capabilities, we have developed a facile method for spatially segregating attached enzymes in a continuous-flow, vortex fluidic device (VFD). Fused Hisn -tags at the protein termini allow rapid bioconjugation and consequent purification through complexation with immobilized metal affinity chromatography (IMAC) resin. Six proteins were purified from complex cell lysates to average homogeneities of 76 %. The most challenging to purify, tobacco epi-aristolochene synthase, was purified in only ten minutes from cell lysate to near homogeneity (>90 %). Furthermore, this "reaction-ready" system demonstrated excellent stability during five days of continuous-flow processing. Towards multi-step transformations in continuous flow, proteins were arrayed as ordered zones on the reactor surface allowing segregation of catalysts. Ordering enzymes into zones opens up new opportunities for continuous-flow biosynthesis.

A low cost and palm-size analyzer for rapid and sensitive protein detection by AC electrokinetics capacitive sensing.

Specific detection of protein biomarkers has a wide range of applications in areas such as medical science, diagnostics, and pharmacology. Quantitative detection of protein biomarkers in biological media, such as serum, is critically important in detecting disease or physiological malfunction, or tracking disease progression. Among various detection methods, electrical detection is particularly well suited for point-of-care (POC) specific protein detection, being of low cost, light weight and small form factor. A portable system for sensitive and quantitative detection of protein biomarkers will be highly valuable in controlling and preventing diseases outbreaks. Recently, an alternating current electrokinetic (ACEK) capacitive sensing method has been reported to demonstrate very promising performance on rapid and sensitive detection of specific protein from serum. In this work, a low cost and portable analyzer with good accuracy is developed to use with ACEK capacitive sensing to produce a true POC technology. The development of a board-level capacitance readout system is presented, as well as the adaption of the protocol for use with ACEK capacitive sensing. Results showed that the developed system could achieve a limit of detection of 10ng/mL, comparable to a sophisticated benchtop instrument. With its small size and light-weight similar to a smart phone, the developed system is ready to be applicable to POC diagnostics. Further, the readout system can be readily expanded for multichannel monitoring and telecommunication capabilities.

Batch affinity adsorption of His-tagged proteins with EDTA-based chitosan.

Affinity adsorption purification of hexahistidine-tagged (His-tagged) proteins using EDTA-chitosan-based adsorption was designed and carried out. Chitosan was elaborated with ethylenediaminetetraacetic acid (EDTA), and the resulting polymer was characterized by FTIR, TGA, and TEM. Different metals including Ni(2+), Cu(2+), and Zn(2+) were immobilized with EDTA-chitosan, and their capability to the specific adsorption of His-tagged proteins were then investigated. The results showed that Ni(2+)-EDTA-chitosan and Zn(2+)-EDTA-chitosan had high affinity toward the His-tagged proteins, thus isolating them from protein mixture. The target fluorescent-labeled hexahistidine protein remained its fluorescent characteristic throughout the purification procedure when Zn(2+)-EDTA-chitosan was used as a sorbent, wherein the real-time monitor was performed to examine the immigration of fluorescent-labeled His-tagged protein. Comparatively, Zn(2+)-EDTA-chitosan showed more specific binding ability for the target protein, but with less binding capacity. It was further proved that this purification system could be recovered and reused at least for 5 times and could run on large scales. The presented M(2+)-EDTA-chitosan system, with the capability to specifically bind His-tagged proteins, make the purification of His-tagged proteins easy to handle, leaving out fussy preliminary treatment, and with the possibility of continuous processing and a reduction in operational cost in relation to the costs of conventional processes.

Quality assessment and antiplasmodial activity of West African Cochlospermum species.

The present study focuses on development of phytochemical methods for quality assessment of two West-African Cochlospermum species (Cochlospermum planchonii and Cochlospermum tinctorium) traditionally used for malaria treatment in Burkina Faso. Antimalarial activity of preparations from dried rhizomes (decoction) was tested against the chloroquine-sensitive Plasmodium strain 3D7 using the histidine-rich protein II (HRP2) drug susceptibility assay and compared with extract preparations using organic solvents of different polarity. Two main apocarotenoids were isolated from rhizomes of C. planchonii and unambiguously identified as dihydrocochloxanthine and cochloxanthine by spectroscopic methods. Comparative HPLC analyses of thirty-nine (39) samples from markets and from collections in natural habitats of both species showed a high variability in the accumulation of cochloxanthines and related carotenoids which were proven to be characteristic for rhizomes of both species and generally absent in leaves. Furthermore, content of total phenolics and antioxidant activities (DPPH and FRAP) as well as haemolytic activity of various extracts was tested. The HPLC method presented here was validated and provides a good separation of both compounds including 10 minor carotenoids. Extracts from both species and pure cochloxanthine offered pronounced antioxidant activities and weak haemolytic activity while, in contrast, dihydrocochloxanthine had a strong haemolytic effect at the highest concentration analysed. However, cochloxanthine as well as dihydrocochloxanthine showed erythroprotective effects against the haemolytic activity of the reference saponin. Moderate antiplasmodial activity between 16 and 63 µg/ml were observed with all tested extracts, and lower IC50 values were obtained with pure dihydrocochloxanthine (IC50=6.9 µg/ml), cochloxanthine (IC50=6.8 µg/ml), the DCM fraction (IC50=2.4 µg/ml) and the ethyl acetate fraction (IC50=11.5µg/ml) derived from a methanolic extract of C. planchonii. This study shows a major variability of carotenoid content and antiplasmodial activity of both C. planchonii and C. tinctorium. The high haemolytic activity of dihydrocochloxanthine (at 100 µg/ml) should be considered as a selection criterion for choosing species phenotypes for treatment.

Separation of macromolecular proteins and rejection of toxic heavy metal ions by PEI/cSMM blend UF membranes.

The charged surface modifying macromolecule (cSMM) was blended into the casting solution of poly(ether imide) (PEI) to prepare surface modified ultrafiltration membranes by phase inversion technique. The separation of proteins including bovine serum albumin, egg albumin, pepsin and trypsin was investigated by the fabricated membranes. On increasing cSMM content, solute rejection decreases whereas membrane flux increases. The pore size and surface porosity of the 5 wt% cSMM blend PEI membranes increases to 41.4 Å and 14.8%, respectively. Similarly, the molecular weight cut-off of the membranes ranged from 20 to 45 kDa, depending on the various compositions of the prepared membranes. The toxic heavy metal ions Cu(II), Cr(III), Zn(II) and Pb(II) from aqueous solutions were subjected to rejection by the prepared blended membrane with various concentration of polyethyleneimine (PETIM) as water soluble polymeric ligand. It was found that the rejection behavior of metal ion depends on the PETIM concentration and the stability complexation of metal ion with ligand.

Artificial neural network for charge prediction in metabolite identification by mass spectrometry.

Collision-induced dissociation (CID) is widely used in mass spectrometry to identify biologically important molecules by gaining information about their internal structure. Interpretation of experimental CID spectra always involves some form of in silico spectra of potential candidate molecules. Knowledge of how charge is distributed among fragments is an important part of CID simulations that generate in silico spectra from the chemical structure of the precursor ions entering the collision chamber. In this chapter we describe a method to obtain this knowledge by machine learning.

Applications of low-flow LC-SRM for the analysis of large molecules in pharmaceutical R&D.

Although ligand-binding assays are frequently employed to measure large molecules, the use of LC-SRM assays is increasingly popular due to the inherent selectivity advantage and the ability to operate without exquisitely selective antibodies. Until recently LC-SRM assays have been unable to compete with ligand-binding assays in terms of sensitivity. However, the use of low-flow chromatography prior to mass spectrometry has played a crucial role in increasing the sensitivity of LC-SRM platforms and enabling measurements of large molecules that had previously been unmeasurable. In this article, we highlight some technical advances, describe strategies for employing low-flow chromatography, and review recent literature that describes implementation of low-flow LC-SRM to support large-molecule analysis in pharmaceutical R&D.