Construction of a comprehensive beer proteome map using sequential filter‐aided sample preparation coupled with liquid chromatography tandem mass spectrometry

The quality traits of beer, which include flavor, texture, foam stability, gushing, and haze formation, rely on contributions from beer proteins and peptides. Large‐scale proteomic analysis of beer is gaining importance, not only with respect to authenticity of raw material in beer but also to improve quality control during beer production. In this work, foam proteins were first isolated from beer by virtue of their high hydrophobicity. Then sequential filter‐aided sample preparation coupled with liquid chromatography and tandem mass spectrometry was used to analyze both beer protein and foam protein. Finally, 4692 proteins were identified as beer proteins, and 3906 proteins were identified as foam proteins. In total, 7113 proteins were identified in the beer sample. Several proteins contributing to beer quality traits, including lipid transfer protein, serpin, hordein, gliadin, and glutenin, were detected in our proteins list. This work constructed a comprehensive beer proteome map that may help to evaluate potential health risks related to beer consumption in celiac patients.     

Improvement of a sample preparation method assisted by sodium deoxycholate for mass‐spectrometry‐based shotgun membrane proteomics†

In current shotgun‐proteomics‐based biological discovery, the identification of membrane proteins is a challenge. This is especially true for integral membrane proteins due to their highly hydrophobic nature and low abundance. Thus, much effort has been directed at sample preparation strategies such as use of detergents, chaotropes, and organic solvents. We previously described a sample preparation method for shotgun membrane proteomics, the sodium deoxycholate assisted method, which cleverly circumvents many of the challenges associated with traditional sample preparation methods. However, the method is associated with significant sample loss due to the slightly weaker extraction/solubilization ability of sodium deoxycholate when it is used at relatively low concentrations such as 1%. Hence, we present an enhanced sodium deoxycholate sample preparation strategy that first uses a high concentration of sodium deoxycholate (5%) to lyse membranes and extract/solubilize hydrophobic membrane proteins, and then dilutes the detergent to 1% for a more efficient digestion. We then applied the improved method to shotgun analysis of proteins from rat liver membrane enriched fraction. Compared with other representative sample preparation strategies including our previous sodium deoxycholate assisted method, the enhanced sodium deoxycholate method exhibited superior sensitivity, coverage, and reliability for the identification of membrane proteins particularly those with high hydrophobicity and/or multiple transmembrane domains.     

Cyclic sample pooling using two‐dimensional liquid chromatography system enhances coverage in shotgun proteomics

We report a cyclic sample pooling technique devised in two‐dimensional liquid chromatography–electrospray ionization mass spectrometry (LC‐ESI‐MS) shotgun proteomics that renders deeper proteome coverage; we combined low pH reversed‐phase (RP) LC in trifluoroacetic acid in the first dimension, followed by cyclic sample pooling of the eluate and low‐pH RP‐LC in formic acid in the second dimension. The new protocol has a significantly higher resolving power suitable for LC‐ESI‐MS/MS shotgun proteomics. Copyright © 2013 John Wiley & Sons, Ltd.     

Trends in sample preparation for classical and second generation proteomics

Sample preparation is a fundamental step in the proteomics workflow. However, it is not easy to find compiled information updating this subject. In this paper, the strategies and protocols for protein extraction and identification, following either classical or second generation proteomics methodologies, are reviewed. Procedures for: tissue disruption, cell lysis, sample pre-fractionation, protein separation by 2-DE, protein digestion, mass spectrometry analysis, multidimensional peptide separations and quantification of protein expression level are described.     

Improved in‐solution trypsin digestion method for methanol–chloroform precipitated cellular proteomics sample

Methanol–chloroform based protein precipitation is an essential step in many liquid chromatography–tandem mass spectrometry‐based cellular proteomics applications. However, re‐solubilization of the total protein precipitate is difficult using regular in‐solution digestion protocol. Sodium deoxycholate is reported as an efficient surfactant for re‐solubilization of membrane fractions. In this study, we demonstrated an application combining methanol–chloroform based protein precipitations and deoxycholic acid assisted re‐solubilization of pellets to evaluate the improvement of protein identifications in mass spectrometry‐based bottom‐up proteomics. We evaluated the modified method using an equal amount of Raw 264.7 mouse macrophage cell lysate. Detailed in‐solution trypsin digestion studies were presented on methanol–chloroform precipitated samples with or without deoxycholic acid treatments and compared with popular sample digestion methods. A mass spectrometric analysis confirmed an 82% increase in protein identification in deoxycholic acid‐treated samples compared to other established methods. Furthermore, liquid chromatography–tandem mass spectrometry analysis of an equal amount of proteins from methanol–chloroform precipitated, and methanol–chloroform/deoxycholic acid‐treated macrophage cell lysate showed a 14% increase and 27% unique protein identifications. We believe this improved digestion method could be a complementary or alternative method for mammalian cell sample preparations where sodium dodecyl sulfate based lysis buffer is frequently used.     

Automated sample preparation for CE‐SDS

Traditionally, CE with SDS (CE‐SDS) places many restrictions on sample composition. Requirements include low salt content, known initial sample concentration, and a narrow window of final sample concentration. As these restrictions require buffer exchange for many sample types, sample preparation is often tedious and yields poor sample recoveries. To improve capacity and streamline sample preparation, an automated robotic platform was developed using the PhyNexus Micro‐Extractor Automated Instrument (MEA) for both the reduced and nonreduced CE‐SDS assays. This automated sample preparation normalizes sample concentration, removes salts and other contaminants, and adds the required CE‐SDS reagents, essentially eliminating manual steps during sample preparation. Fc‐fusion proteins and monoclonal antibodies were used in this work to demonstrate benefits of this approach when compared to the manual method. With optimized conditions, this application has demonstrated decreased analyst “hands on” time and reduced total assay time. Sample recovery greater than 90% can be achieved, regardless of initial composition and concentration of analyte.     

Novel method for preparation of poly(benzoxazinone‐imide)

A novel method was developed to prepare poly(benzoxazinone‐imide) by the dealcoholization of poly(amide‐imide), having pendent ethoxycarbonyl groups, which was prepared from poly(amide acid). The poly(amide acid) was prepared from the reaction of pyromellitic dianhydride and 4,4′‐diamino‐6‐ethoxycarbonyl benzanilide. The curing behavior of the poly(amide acid) was monitored by DSC, which indicated the presence of two broad endotherms, one with maximum at 153 °C due to imide‐ring formation and the other with maximum at 359 °C due to benzoxazinone‐ring formation. The poly(amide acid) was thermally treated at 300 °C/1 h to get poly(amide‐imide) with pendent ester groups, then at 350 °C/2 h to convert into poly(benzoxazinone‐imide) by dealcoholization. Viscoelastic measurements of the poly(amide‐imide) showed that the storage modulus dropped at about 280 °C with glass‐transition temperature (T_g ) at about 340 °C. The storage modulus of poly(benzoxazinone‐imide), however, was almost constant up to 400 °C and no T_g was detected below 400 °C. Also, the tensile modulus and tensile strength of the poly(benzoxazinone‐imide) was much higher than that of the poly(amide‐imide). The 5% decomposition of poly(benzoxazinone‐imide) film was at 535 °C, which reflects its excellent thermal stability. Also, poly(benzoxazinone‐imide) showed more hydrolytic stability against alkali in comparison to polyimides. © 2000 John Wiley & Sons, Inc. J Polym Sci A: Polym Chem 38: 1647–1655, 2000     

Improved sample preparation method for glycan analysis of glycoproteins by CE‐LIF and CE‐MS

CE is a high‐resolution separation technique broadly used in the biotechnology industry for carbohydrate analysis. The standard sample preparation protocol for CE analysis of glycans released from glycoproteins generally requires derivatization times of overnight at 37°C, using ≥100 fold excess of fluorophore reagent, 8‐aminopyrene‐1,3,6‐trisulfonic‐acid, if the sample is unknown, or it is a regulated biotherapeutic product, possibly containing terminal sialic acid(s). In this paper, we report on significant improvements for the standard CE sample preparation method of glycan analysis. By replacing the conventionally used acetic acid catalyst with citric acid, as low as 1:10 glycan to fluorophore molar ratio (versus the typical 1:≥100 ratio) maintained the >95% derivatization yield at 55°C with only 50 min reaction time. Terminal sialic acid loss was negligible at 55°C during the derivatization process, and indicating that the kinetics of labeling at 55°C was faster than the loss of sialic acid from the glycan. The reduced relative level of 8‐aminopyrene‐1,3,6‐trisulfonic‐acid simplified the removal of excess reagent, important in both CE‐LIF (electrokinetic injection bias) and CE‐MS (ion suppression). Coupling CE‐ ESI‐MS confirmed that the individual peaks separated by CE corresponded to single glycans and increased the confidence of structural assignment based on glucose unit values.     

An improved sample preparation method for the sensitive detection of peptides by MALDI‐MS

We describe here an optimization study of the sample preparation conditions for sensitive detection of peptides by matrix‐assisted laser desorption/ionization mass spectrometry (MALDI‐MS). Among many factors in the conditions, we varied the percent acetonitrile in the peptide solution, the percent acetonitrile in the matrix solution and the α‐cyano‐4‐hydroxycinnamic acid (CHCA) concentration in the matrix solution. CHCA was chosen because it is the most frequently used matrix for analyzing peptides. The well‐established dried‐droplet method was employed for sample deposition. The examined range of the concentration of CHCA was from 0.01 to 10 mg/ml, and the MeCN content of the solvent for matrix/analyte was 10% to 50%. The indicator for the detection sensitivity was the S/N ratio of the peaks of peptides used. Highly increased sensitivity (100‐ to 1000‐fold) was observed for the optimal CHCA concentration of 0.1 mg/ml in 20% MeCN/0.1% aq. trifluoroacetic acid (TFA), as compared with the conventional concentration (10 mg/ml) in 50% MeCN/0.1% aq. TFA. For example, the limit of detection of human ACTH 18–39 was 10 amol/well for the optimal condition but 10 fmol/well for the conventional condition. The optimal condition (0.1 mg/ml CHCA in 20% MeCN/0.1% aq. TFA) was verified with five model peptides and provided significant improvement in sensitivity (by two to three orders of magnitude) compared with the conventional conditions. Optimizing the CHCA concentration and solvent composition significantly improved the detection sensitivity in the analysis of peptides by MALDI‐MS. Copyright © 2013 John Wiley & Sons, Ltd.     

Desulfurization of cysteine‐containing peptides resulting from sample preparation for protein characterization by mass spectrometry

In this study, we have examined two cysteine modifications resulting from sample preparation for protein characterization by mass spectrometry (MS): (1) a previously observed conversion of cysteine into dehydroalanine, now found in the case of disulfide mapping and (2) a novel modification corresponding to conversion of cysteine into alanine. Using model peptides, the conversion of cysteine into dehydroalanine via β‐elimination of a disulfide bond was seen to result from the conditions of typical tryptic digestion (37°C, pH 7.0–9.0) without disulfide reduction and alkylation. Furthermore, the surprising conversion of cysteine into alanine was shown to occur by heating cysteine‐containing peptides in the presence of a phosphine (tris(2‐carboxyethyl)phosphine hydrochloride (TCEP)). The formation of alanine from cysteine, investigated by performing experiments in H₂O or D₂O, suggested a radical‐based desulfurization mechanism unrelated to β‐elimination. Importantly, an understanding of the mechanism and conditions favorable for cysteine desulfurization provides insight for the establishment of improved sample preparation procedures of protein analysis. Copyright © 2010 John Wiley & Sons, Ltd.     

Poly(N‐vinylpyrrolidone)‐Modified Surfaces for Biomedical Applications

Poly(N‐vinylpyrrolidone) (PVP), an important water soluble synthetic polymer, has many desirable properties including low toxicity, chemical stability, and good biocompatibility. Since PVP is hemocompatible and physiologically inactive, it has been used as a blood plasma substitute. Surface modification with PVP has been investigated extensively over the past few years as a means of preventing nonspecific protein adsorption. PVP may therefore be seen as a promising antifouling surface modifier comparable to poly(ethylene glycol) (PEG). In this review, various approaches for the design and preparation of PVP‐modified surfaces are summarized and potential biomedical applications of these PVP‐modified materials are indicated. Finally, some perspectives on future research on PVP for surface modification are discussed.

     

Three-layer matrix/sample preparation method for MALDI MS analysis of low nanomolar protein samples

A robust and sensitive sample preparation method is presented for matrix-assisted laser desorption ionization (MALDI) mass spectrometric analysis of low nanomolar concentrations of proteins containing high amounts of common salts and buffers. This method involves the production of densely packed sub-micrometer matrix crystals by depositing a matrix solution on top of a matrix seed-layer prepared on a MALDI target. A sub-microliter aliquot of analyte solution is then directly added to the top of the matrix crystals to form a thin-layer. alpha-Cyano-4-hydroxycinnamic acid (4-HCCA) is used as matrix and demonstrated to give better performance than other commonly used matrices, such as 2,5-dihydroxybenzoic acid (DHB), 2-(4-hydroxy-phenylazo) benzoic acid (HABA), or sinapinic acid. This three-layer method is shown to be superior to the other MALDI sample preparation methods, particularly for handling low nanomolar protein solutions containing salts and buffers.     

Developing front‐end devices for improved sample preparation in MS‐based proteome analysis

Chemical analysis has long relied on instrumentation, from the simplest (eg, burets) to the more sophisticated (eg, mass spectrometers) to facilitate precision measurements. Regardless of their complexity, the development of a new instrumental device can be a valued approach to address problems in science. In this perspective, we outline the process of novel device design, from early phase conception to the manufacturing and testing of the tool or gadget. Focus is placed on the development of improved front‐end devices to facilitate protein sample manipulations ahead of mass spectrometry, which therefore augment the proteomics workflow. Highlighted are some of the many training secrets, choices, and challenges that are inherent to the often iterative process of device design. In hopes of inspiring others to pursue instrument design to address relevant research questions, we present a summary list of points to consider prior to innovating their own devices.     

Agarose‐ and alginate‐based biopolymers for sample preparation: Excellent green extraction tools for this century

Recently, there has been considerable interest in the use of miniaturized sample preparation techniques before the chromatographic monitoring of the analytes in unknown complex compositions. The use of biopolymer‐based sorbents in solid‐phase microextraction techniques has achieved a good reputation. A great variety of polysaccharides can be extracted from marine plants or microorganisms. Seaweeds are the major sources of polysaccharides such as alginate, agar, agarose, as well as carrageenans. Agarose and alginate (green biopolymers) have been manipulated for different microextraction approaches. The present review is focused on the classification of biopolymer and their applications in multidisciplinary research. Besides, efforts have been made to discuss the state‐of‐the‐art of the new microextraction techniques that utilize commercial biopolymer interfaces such as agarose in liquid‐phase microextraction and solid‐phase microextraction.     

Coupling of CE‐MS for protein and peptide analysis

The review is focused on the latest developments in the analysis of proteins and peptides by capillary electrophoresis techniques coupled to mass spectrometry. First, the methodology and instrumentation are overviewed. In this section, recent progress in capillary electrophoresis with mass spectrometry interfaces and capillary electrophoresis with matrix‐assisted laser desorption/ionization is mentioned, as well as separation tasks. The second part is devoted to applications—mainly bottom‐up and top‐down proteomics. It is obvious that capillary electrophoresis with mass spectrometry methods are well suited for peptide and protein analysis (proteomic research) and it is described how these techniques are complementary and not competitive with the often used liquid chromatography with mass spectrometry methods.     

Ile‐Lys‐Val‐ala‐Val (IKVAV) peptide for neuronal tissue engineering

Despite the great advances in microsurgery, some neural injuries cannot be treated surgically. Stem cell therapy is a potential approach for treating neuroinjuries and neurodegenerative disease. Researchers have developed various bioactive scaffolds for tissue engineering, exhibiting enhanced cell viability, attachment, migration, neurite elongation, and neuronal differentiation, with the aim of developing functional tissue grafts that can be incorporated in vivo. Facilitating the appropriate interactions between the cells and extracellular matrix is crucial in scaffold design. Modification of scaffolds with biofunctional motifs such as growth factors, drugs, or peptides can improve this interaction. In this review, we focus on the laminin‐derived Ile‐Lys‐Val‐Ala‐Val peptide as a biofunctional epitope for neuronal tissue engineering. Inclusion of this bioactive peptide within a scaffold is known to enhance cell adhesion as well as neuronal differentiation in both 2‐dimensional and 3‐dimensional environments. The in vivo application of this peptide is also briefly described.