Mineral oil-, glycerol-, and Vaseline-coated plates as matrix-assisted laser desorption/ionization sample supports for high-throughput peptide analysis

A novel protocol for rapid and high-quality sample preparation prior to matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) has been developed by coating bare stainless steel plates with one of three adhesives: mineral oil, glycerol, or Vaseline. The advantages of these three adhesive coats are that they take little time to both prepare and wipe away, hold the matrices to prevent them from flying from the support, reduce the background matrix, and affect neither the resolution of the peptide peaks nor the accuracy of their determined molecular masses. Consequently, the signal intensity, detection limit, and tolerance of the analytes to contaminants on the three adhesive-coated plates are improved. In the two strategies of on-plate desalting and concentration of the peptide mixture, all three adhesives reduced the loss of peptides, especially in the case of larger molecular mass peptides. The microscope and stereomicroscope images of the deposited droplets showed that after dropping onto the adhesive coats, the droplets formed a reduced spot size, were more homogeneous, and showed sticky crystallization. Therefore, this is an easy-to-use, reproducible, highly sensitive, tolerant (to salts), and high-throughput method of peptide sample preparation for MALDI-TOF MS analysis.     

On-line biological sample cleanup for electrospray mass spectrometry using sol-gel columns

Using a slight overpressure, a urine sample is loaded onto a monolithic photopolymerized sol-gel column that has been derivatized with hydrophobic carbon chains and then the complex urine matrix is washed with aqueous solution. A buffer containing organic solvent is used to elute the adsorbed peptides by an applied voltage and the sample is then introduced into a mass spectrometer by sheath flow electrospray. The importance of desalting this type of sample is demonstrated by an experiment that shows that the signal intensity of a test solution with neurotensin, sprayed directly into the mass spectrometer, decreased from 4.5x10(4) cps to no detectible signal when just 10% urine is added to the sample solution. We suggest that this procedure may find general application for desalting biological samples prior to mass spectrometric analysis.     

An in-gel digestion procedure that facilitates the identification of highly hydrophobic proteins by electrospray ionization-mass spectrometry analysis

A procedure is described for in-gel tryptic digestion of proteins that allows the direct analysis of eluted peptides in electrospray ionization (ESI) mass spectrometers without the need of a postdigestion desalting step. It is based on the following principles: (a) a thorough desalting of the protein in-gel before digestion that takes advantage of the excellent properties of acrylamide polymers for size exclusion separations, (b) exploiting the activity of trypsin in water, in the absence of inorganic buffers, and (c) a procedure for peptide extraction using solvents of proven efficacy with highly hydrophobic peptides. Quality of spectra and sequence coverage are equivalent to those obtained after digestion in ammonium bicarbonate for hydrophilic proteins detected with Coomassie blue, mass spectrometry-compatible silver or imidazole-zinc but are significantly superior for highly hydrophobic proteins, such as membrane proteins with several transmembrane domains. ATPase subunit 9 (GRAVY 1.446) is a membrane protein channel, lipid-binding protein for which both the conventional in-gel digestion protocol and in solution digestion failed. It was identified with very high sequence coverage. Sample handling after digestion is notably simplified as peptides are directly loaded into the ESI source without postdigestion processing, increasing the chances for the identification of hydrophobic peptides.     

Fullerene-C60-modified edge plane pyrolytic graphite electrode for the determination of dexamethasone in pharmaceutical formulations and human biological fluids

Electrochemical behaviour of dexamethasone at the fullerene-C(60)-modified pyrolytic graphite electrode (PGE) has been investigated using Osteryoung square wave voltammetry (SWV). Compared to a bare PGE and fullerene-C(60)-modified glassy carbon electrode (GCE), the fullerene-C(60)-modified edge plane PGE exhibited an apparent shift of the peak potential to less negative potentials with a marked enhancement in the current response of dexamethasone. The peak potential was linearly dependent on pH with dE(p)/dpH as 59 mV/pH. Calibration plot having good linearity with a correlation coefficient 0.9983 is obtained in the concentration range of 0.05-100 microM and the sensitivity of the method has been found to be 0.685 microA microM(-1). The detection limit is estimated to be 5.5 x 10(-8)M. The electrode showed good sensitivity, stability and reproducibility. The practical analytical utility of the method is illustrated by quantitative determination of dexamethasone in several commercially available pharmaceutical formulations and human blood plasma of patients being treated with dexamethasone. HPLC method was used to compare the results obtained for the quantitative estimation of dexamethasone in biological fluids.     

Concentration and desalting of peptide and protein samples with a newly developed C18 membrane in a microspin column format.

Protein identification plays an important role in today's academic and industrial proteomic research. Commonly used methods for the separation of proteins from complex samples include liquid chromatography (e.g., ion exchange, reversed-phase, hydrophobic interaction), or types of gel electrophoresis (e.g., 1d and 2d PAGE). Relevant proteins separated in the latter way are often cut out, cleaved with trypsin "in gel," and the resulting peptide mixtures combined with matrix and spotted onto a target plate for matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-ToF-ms) analysis. Subsequently, proteins can be identified by comparison of the resulting peptide mass fingerprints against different databases.(1) since the success of protein identification can be enhanced by the desalting and concentration of the samples, an innovative C18-membrane was incorporated into a microspin column (Vivapure C18 micro spin column, Vivascience AG, Hannover, Germany) to analyze its performance for sample preparation prior to MALDI-ToF-ms. Rapid concentration of single or multiple 200-microl volumes through an available membrane only 2 mm in diameter allowed for analysis of very dilute samples. We observed the successful and rapid desalting of urea-containing protein samples at 100 fmol/mul up to a mass of approximately 70 KDA and the concentration of digest peptides from a solution of 1 fmol/microl using C18-membrane technology.     

Unique anthranilic acid chemistry facilitates profiling and characterization of Ser/Thr-linked sugar chains following hydrazinolysis

A novel method for the analysis of Ser/Thr-linked sugar chains was made possible by the virtue of unique anthranilic acid (AA, 2-aminobenzoic acid [2AA]) chemistry for labeling carbohydrates in aqueous salt solutions (K. R. Anumula, Anal. Biochem. 350 (2006) 1-23). The protocol for profiling of Ser/Thr carbohydrates by hydrazinolysis was made simple by eliminating intermediary isolation steps involved in a sample preparation such as desalting and various chromatographic purification schemes. A 6-h hydrazinolysis was carried out at 60 degrees C for O-linked oligosaccharides and at 95 degrees C for total oligosaccharides (N-linked with some O-linked). Following evaporation of hydrazine (<10 min), the oligosaccharides were N-acetylated and derivatized with AA in the same reaction mixture containing salts. Presumably, the glycosyl-hydrazines/hydrazones present in the mixture did not interfere with AA labeling. Because AA is the most fluorescent and highly reactive tag for labeling carbohydrates, the procedures described are suitable for the analysis of a limited amount of samples ( approximately 5 microg) by the current high-resolution high-performance liquid chromatography (HPLC) methods. HPLC conditions developed for the separation of O-linked sugar chains based on size on an amide column were satisfactory for quantitative profiling and characterization. Common O-linked sugar chains found in fetuin, equine chorionic gonadotropin, and glycophorin can be analyzed in less than 50 min. In addition, these fast profiling methods were comparable to profiling by PNGase F (peptide N-glycosidase from Flavobacterium meningosepticum) digestion in terms of time, effort, and simplicity and also were highly reproducible for routine testing. The procedures for the release of sugar chains by hydrazinolysis at the microgram level, labeling with fluorescent tag AA, and profiling by HPLC should be useful in characterization of carbohydrates found in glycoproteins.     

Preparation of C60‐functionalized magnetic silica microspheres for the enrichment of low‐concentration peptides and proteins for MALDI‐TOF MS analysis

In this work, for the first time, a novel C60‐functionalized magnetic silica microsphere (designated C60‐f‐MS) was synthesized by radical polymerization of C60 molecules on the surface of magnetic silica microspheres. The resulting C60‐f‐MS microsphere has magnetite core and thin C60 modified silica shell, which endow them with useful magnetic responsivity and surface affinity toward low‐concentration peptides and proteins. As a result of their excellent magnetic property, the synthesized C60‐f‐MS microspheres can be easily separated from sample solution without ultracentrifuge. The C60‐f‐MS microspheres were successfully applied to the enrichment of low‐concentration peptides in tryptic protein digest and human urine via a MALDI‐TOF MS analysis. Moreover, they were demonstrated to have enrichment efficiency for low‐concentration proteins. Due to the novel materials maintaining excellent magnetic properties and admirable adsorption, the process of enrichment and desalting is very fast (only 5 min), convenient and efficient. As it has been demonstrated in the study, newly developed fullerene‐derivatized magnetic silica materials are superior to those already available in the market. The facile and low‐cost synthesis as well as the convenient and efficient enrichment process of the novel C60‐f‐MS microspheres makes it a promising candidate for isolation of low‐concentration peptides and proteins even in complex biological samples such as serum, plasma, and urine or cell lysate.     

Nanometer-scale immobilization of polysaccharides on hydrophobic polymer plates in supercritical fluoroform/water emulsions

Hydrophilic polysaccharides such as dextran and hyaluronan were immobilized on a hydrophobic polystyrene (PSt) plate by a nanometer-scale surface penetration method in the emulsion of aqueous solutions in supercritical fluoroform (scCHF3). Since a supercritical fluid has high diffusiveness, water emulsions of polysaccharides can penetrate into the polymer surface. Dextran was surface-penetrated by two different methods: (1) the penetration of sucrose as a glucose donor and then the enzymatic polymerization to dextran near the surface catalyzed by dextransucrase, and (2) the direct penetration of dextran polymer into the PSt plate. The contact angle for water of the dextran-penetrated PSt plate was decreased to 78 degrees from 95 degrees of the untreated plate. The surface coverage and the penetration depth of polysaccharides could be obtained to be 10-30% and 10-20 nm, respectively, by X-ray photoelectron spectroscopy. These values could be controlled by the pressure of scCHF3. The transparency of the PSt dish did not change after the dextran penetration. Dextrans on the PSt plate could be elongated enzymatically by dextransucrase in the presence of sucrose as a glucose donor, and be detected by the enzyme-linked biotin-avidin assay. When anionic hyaluronan was surface-penetrated on the PSt plate instead of the neutral dextran, the plate showed the specific adhesion for human T-cells having hyaluronan receptors.     

Establishment of a 2-D human urinary proteomic map in IgA nephropathy

Immunoglobulin A nephropathy (IgAN) is the most common form of immune complex-mediated glomerulonephritis worldwide. Although chronic renal failure develops in considerable numbers of IgAN patients, the exact etiology has not yet been clearly elucidated. To establish the urinary protein map of IgAN, we performed a urinary proteomic analysis. Thirteen patients with IgAN and 12 normal controls were recruited. Morning midstream spot urine samples were used with Centriprep ultrafiltration for concentration and desalting. 2-DE was performed and compared between IgAN and normal control, and urinary proteins were identified by MALDI-TOF MS. A large number of protein spots were identified in IgAN and normal control samples, with means of 311 spots and 174 spots, respectively. Approximately 216 protein spots were detected as differentially expressed in IgAN. Among these, 82 spots were over-expressed, and 134 spots were under-expressed compared to normal controls. A total of 84 differentially expressed spots, representing 59 different proteins, were finally identified in IgAN. We have established a urinary proteomic map of IgAN and this result helps in the identification. Further study is needed to determine the potential pathogenic role of these proteins.     

SECM visualization of spatial variability of enzyme-polymer spots. 1. Discretisation and interference elimination using artificial neural networks

Enzyme-polymer layers immobilized on an electrode surface often serve as basis for amperometric biosensors. Caused by the formation process they show spatial variability in the polymer thickness which corresponds to a variability of immobilized enzyme activity. The relationship between topography and localized enzymatic activity of enzyme-polymer spots was studied using scanning electrochemical microscopy (SECM) in the feedback mode and generator-collector mode. Discretisation with a grid size corresponding to the scanning parameters defined substructures which can be treated as individual microsensors with specific response characteristics. The local responses are mainly governed by the polymer thickness but also influenced by neighbouring sites. Thus, discretisation allowed us to treat an enzyme-polymer spot with dimensions of about 300 microm diameter like an array of more than 400 individual microsensors. Using suitable selection criteria and multivariate calibration it was possible to identify sensing sites which are optimal for the determination of glucose. It was demonstrated that an artificial neural network which was trained with the data provided by SECM images well predicted glucose concentration in the presence of ascorbic acid.     

Effects of bile salts on the adsorption of a hydrophobic mutagen to dietary fiber

The effect of the bile salts, sodium cholate, deoxycholate, glycocholate and taurocholate, on the solubility in aqueous solution of the hydrophobic, environmental mutagen, 1,8-dinitropyrene (DNP), was examined. In the absence of bile salts, the DNP appeared to precipitate out of solution, whereas bile salts at a concentration of greater than or equal to 4 mM maintained the DNP in solution. In the presence of the model dietary fiber, alpha-cellulose, the DNP absorbed to this preferentially. Bile salts reduced this adsorption at low alpha-cellulose levels, but had little effect at high alpha-cellulose levels. The implication of these results is that bile salts have solubilising properties that could affect the distribution of hydrophobic molecules, including mutagens, in the digestive tract.     

猫爪草提取物对结核分枝杆菌临床分离株的可能作用靶标

利用双向电泳技术, 对猫爪草提取物作用前后的结核分枝杆菌临床分离株的全细胞蛋白表达图谱进行差异比较和分析, 发现其中22个蛋白质斑点的浓度具有差异,利用基质辅助激光解吸/电离飞行时间质谱技术, 对其中4个表达明显下调和1个明显上调的蛋白质斑点进行分析鉴定, 获得5个明确的肽质量指纹图谱.通过数据库检索, 确定这5个蛋白质分别为S-腺苷甲硫氨酸合成酶、吲哚-3-甘油磷酸合酶、烯酰-CoA水合酶、琥珀酰辅酶A合成酶和60 kD的分子伴侣2.其中前4个分子是首次报道参与结核分枝杆菌的重要生理活动.该结果有助于了解猫爪草提取物对结核分枝杆菌生理的影响, 为进一步确定中药猫爪草提取物对结核分枝杆菌的作用靶标和机理提供了基础.     

Evaluation of three different protocols of protein extraction for Arabidopsis thaliana leaf proteome analysis by two-dimensional electrophoresis

This work was performed to compare three precipitation protocols of protein extraction for 2-DE proteomic analysis using Arabidopsis leaf tissue: TCA-acetone, phenol, and TCA-acetone-phenol. There were no statistically significant differences in protein yield between the three methods. Samples were subjected to 2-DE in the 5 to 8 pH and 14-80 kDa ranges. The TCA-acetone-phenol protocol provided the best results in terms of spot focusing, resolved spots, spot intensity, unique spots detected, and reproducibility. In all, 93 qualitative or quantitative statistically significant differential spots were found between the three protocols. The 2-DE map of TCA-acetone-phenol extracts presented more resolved spots above 40 kDa, with no pI-dependent differences observed between the three protocols. 54 spots were selected for trypsin digestion, and the peptides were analyzed by MALDI-TOF-TOF MS. After database search using peptide mass fingerprinting, and MS/MS combined search, 30 proteins were identified, the proteins from chloroplastic photosynthetic and carbohydrate metabolism being those most highly represented. From these data, we were able to conclude that each extraction protocol had its main features. Considering this, the workflow of any standard comparative proteomic experiment should include the optimization and adaptation of the protein extraction protocol to the plant tissue and to the particular objective pursued.     

Boron nitride as desalting material in combination with phosphopeptide enrichment in shotgun proteomics

Hydrophilic peptides in shotgun proteomics have been shown to be problematic in conventional chromatography. Typically, C18 solid phase extraction or peptide traps are used for desalting the sample prior to mass spectrometry analysis, but the capacity to retain hydrophilic peptides is not very high, causing a bias toward more hydrophobic peptides. This is particularly problematic in phosphoproteomic studies. We tested the compatibility of commercially available boron nitride as a novel material for peptide desalting. Boron nitride can be used to recover a wide range of peptides with different physicochemical properties comparable to combined C18 and graphite carbon material.     

Monoliths for microfluidic devices in proteomics

We report here on the preparation of monolithic capillary columns in view to their integration in a microsystem for on-chip sample preparation before their on-line analysis by electrospray and mass spectrometry (ESI-MS). These monolithic columns are based on polymer materials and consist of reverse phases for peptide separation and/or desalting. They were prepared using lauryl methacrylate (LMA), ethylene dimethacrylate (EDMA) as well as a suitable porogenic mixture composed of cyclohexanol and ethylene glycol. The resulting stationary phases present thus a C12-functionality. The LMA-based columns were first prepared in a capillary format using capillary tubing of 75 microm i.d. and tested in nanoLC-MS experiments for the separation of a commercial Cytochrome C digest composed of 12 peptidic fragments whose isoelectric point values and hydrophobic character cover a wide range. The LMA-based columns were capable of separating the peptidic fragments and their performances were seen to be similar as those of standard commercial columns dedicated to proteomic purposes with calculated separation efficiencies up to 145 x 10(3) plates/m. Monolithic LMA-based phases were then successfully polymerized in microchannels fabricated using the negative photoresist SU-8. After the polymerization, the systems were seen to withstand the pressures applied during the nanoLC-MS separation tests that were carried out in the same conditions as for the monolithic capillary columns. The pressure drop during these tests of the in-microchannel monoliths was as high as 50 bar; however, the separation was not as good as for a capillary format which could be accounted for by the monolith dimensions.     

Triton X-114 cloud point extraction to subfractionate blood plasma proteins for two-dimensional gel electrophoresis

A simple and reproducible procedure for enrichment of a plasma protein subfraction suitable for two-dimensional polyacrylamide gel electrophoresis (2DE) was developed, using a Triton X-114-based cloud point extraction (CPE). Appropriate conditions for such a CPE procedure were found by SDS-PAGE to be a plasma protein concentration of about 10 mg/ml in 3% (w/v) Triton X-114. 2DE of proteins obtained by CPE of 400 μl of human plasma revealed about 200 spots constituting a spot pattern very different from the pattern of total plasma. The CPE procedure only had a limited contribution to the technical variation. Identification of about 60 spots, representing only 22 proteins, revealed that several proteins in the obtained subfraction were present in more isoforms or modifications. Among these were apolipoproteins (A-1, D, E, L1, and M), haptoglobin-related protein, phosphatidylcholine-sterol acyltransferase, serum amyloid A, and serum paraoxonase/arylesterase 1, which are proteins of a hydrophobic nature, as in plasma they relate to lipoprotein particles. Thus, Triton X-114-based CPE is a simple plasma prefractionation tool, attractive for detailed 2DE studies of hydrophobic plasma proteins and their isoforms or modifications.     

Transport in rat vessel walls. II. Macromolecular leakage and focal spot size growth in rat arteries and veins

Transendothelial lipid transport into and spread in the subendothelial intima of large arteries, and subsequent lipid accumulation, appear to start plaque formation. We experimentally examine transendothelial horseradish peroxidase (HRP) transport in vessels that are usually, e.g., pulmonary artery (PA), or almost always, e.g., inferior vena cava (IVC), atherosclerosis resistant vs. disease prone, e.g., aorta, vessels. In these vessels, HRP traverses the endothelium at isolated, focal spots, rather than uniformly, for short circulation times. For femoral vein HRP introduction, PA spots have 30-s radii [ approximately 53.2 microm (SD 10.4); compare aorta: 54.6 microm (SD 8.75)] and grow quickly from 30 s to 1 min (40%, P<0.05) and more slowly afterward (P>0.05). This trend resembles the aorta, suggesting the PA has a similarly sparse intima. With carotid artery (CA) HRP introduction, the 30-s spot (132.86 +/- 37.32 microm) is far larger than the PAs, grows little ( approximately 28%, P<0.05) from 30 to 60 s, and is much flatter than the artery curves. Transverse electron microscopic sections after approximately 10 min HRP circulation show thin, intense staining immediately beneath both vessels' endothelia with an almost step change to diffuse staining beyond. This indicates the existence of a sparse, subendothelial intima, even when there is no internal elastic lamina (IVC). This motivates a simple model that translates growth rates into lower bounds for the flow through focal leaks. The model results and our earlier wall and medial hydraulic conductivity data explain these spot growth curves and point to differences in transport patterns that might be relevant in understanding the immunity of IVC to disease initiation.     

Assessment of protein spot components applying correspondence analysis for peptide mass fingerprint data

Proteins separated by two-dimensional gel electrophoresis (2-DE) may be distributed over several spots. Otherwise, one spot may contain more than one component. The same protein occurring in several spots supposedly represents differently modified protein species that might be of biological relevance. Identification of spots with peptide mass fingerprinting and database searching leads only to the detection of the major spot components. If a spot also contains additional minor protein components, quantitation of spots with protein staining techniques or antibody detection becomes misleading. In order to find spots containing minor components we applied correspondence analysis, a multivariate data exploration method, to peptide mass fingerprint data. Correspondence analysis using peak lists revealed groups of spots containing the same protein with their characteristic mass-to-charge ratio (m/z) values. In order to detect different protein spot components an interactive threshold setting and removal of m/z values with subsequent recalculation of the correspondence analysis using our software tool CorrAn are performed. The usefulness of this methodical approach was shown by a data set of peptide mass fingerprints of 284 spots of Helicobacter pylori 26695 separated by 2-DE.     

Conformational Analysis of the β-amyloid Peptide Fragment, β(12-28)

Abstract NMR and CD spectroscopy have been used to examine the conformation of the peptide, β(12-28), (VHHQKLVFFAEDVGSNK) in aqueous and 60% TFE/40% H(2)0 solution at pH 2.4. In 60% TFE solution, the peptide is helical as confirmed by the CD spectrum and by the pattern of the NOE cross peaks detected in the NOESY spectrum of the peptide. In aqueous solution, the peptide adopts a more extended and flexible conformation. Broadening of resonances at low temperature, temperature-dependent changes in the chemical shifts of several of the CH(α) resonances and the observation of a number of NOE contacts between the hydrophobic side-chain protons of the peptide are indicative of aggregation in aqueous solution. The behavior of β(12-28) in 60% TFE and in aqueous solution are consistent with the overall conformation and aggregation behavior reported for the larger peptide fragment, β(1-28) and the parent β-amyloid peptide.     

Prediction of quaternary structure by analysis of hot spot residues in protein-protein interfaces: the case of anthranilate phosphoribosyltransferases

It is an important goal of computational biology to correctly predict the association state of a protein based on its amino acid sequence and the structures of known homologues. We have pursued this goal on the example of anthranilate phosphoribosyltransferase (AnPRT), an enzyme that is involved in the biosynthesis of the amino acid tryptophan. Firstly, known crystal structures of naturally occurring homodimeric AnPRTs were analyzed using the Protein Interfaces, Surfaces, and Assemblies (PISA) service of the European Bioinformatics Institute (EBI). This led to the identification of two hydrophobic “hot spot” amino acids in the protein-protein interface that were predicted to be essential for self-association. Next, in a comprehensive multiple sequence alignment (MSA), naturally occurring AnPRT variants with hydrophilic or charged amino acids in place of hydrophobic residues in the two hot spot positions were identified. Representative variants were characterized in terms of thermal stability, enzymatic activity, and quaternary structure. We found that AnPRT variants with charged residues in both hot spot positions exist exclusively as monomers in solution. Variants with hydrophilic amino acids in one hot spot position occur in both forms, monomer and dimer. The results of the present study provide a detailed characterization of the determinants of the AnPRT monomer-dimer equilibrium and show that analysis of hot spots in combination with MSAs can be a valuable tool in prediction of protein quaternary structures.