The effect of sodium dodecyl sulfate and anion‐exchange silica gel on matrix‐assisted laser desorption/ionization mass spectrometric analysis of proteins

Sodium dodecyl sulfate (SDS), an anionic surfactant, is widely used in peptide and protein sample preparation. When the sample is analyzed by matrix‐assisted laser desorption/ionization mass spectrometry (MALDI‐MS), this surfactant can often cause signal suppression. We have previously reported an on‐probe sample preparation method using a suspension of anion‐exchange silica gel and sinapinic acid (i.e., gel‐SA suspension) as a matrix, thereby greatly improving the MALDI signal detection of the protein solutions containing SDS. In this study, we found that a certain amount of SDS enhanced the MALDI signal intensity for protein samples. This effect was also observed when using sodium decyl sulfate and sodium tetradecyl sulfate instead of SDS. Furthermore, this on‐probe sample preparation method using both SDS and the gel‐SA suspension improved the detection limit of protein samples in the MALDI‐MS analysis by about ten‐fold as compared to that of protein samples without SDS and the gel‐SA suspension. This method can be applied not only to the MALDI‐MS analysis of samples containing SDS, but also to the examination of proteins at femtomole levels or insoluble proteins such as membrane proteins. Copyright © 2009 John Wiley & Sons, Ltd.     

Ion-pair chromatography on a porous graphitic carbon stationary phase for the analysis of twenty underivatized protein amino acids

The analysis of twenty underivatized protein amino acids has been achieved on porous graphitic carbon packing material (Hypercarb). Five perfluoroalkyl carboxylic acids (trifluoroacetic, heptafluorobutyric, nonafluoropentanoic, tridecafluoroheptanoic and pentadecafluorooctanoic acid) have been studied as ion-pairing reagent. Several parameters (equilibration time, quantities adsorbed onto the chromatographic support, concentration and nature of the ion-pairing reagent, as well as temperature effect) have been studied leading to the complete separation of these compounds in gradient elution mode. Evaporative light scattering detector has allowed the detection of these non UV–visible absorbent molecules. The chromatographic methodology developed can also be easily coupled with pneumatically assisted electrospray mass spectrometry.     

Removal of sodium dodecyl sulfate from protein samples prior to matrix-assisted laser desorption/ionization mass spectrometry

Sodium dodecyl sulfate (SDS) is widely used for protein solubilization and for separation of proteins by SDS polyacrylamide gel electrophoresis (SDS-PAGE). However, SDS interferes with other techniques used for characterization of proteins, such as mass spectrometry (MS) and amino acid sequencing. In this paper, we have compared three procedures to remove SDS from proteins, including chloroform/methanol/water extraction (C/M/W), cold acetone extraction and desalting columns, in order to find a rapid and reproducible procedure that provides sufficient reduction of SDS and high recovery rates for proteins prior to matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOFMS). A 1000-fold reduction of SDS concentration and a protein recovery at approximately 50% were obtained with the C/M/W procedure. The cold acetone procedure gave a 100-fold reduction of SDS and a protein recovery of approximately 80%. By using desalting columns, the removal of SDS was 100-fold, with a protein recovery of nearly 50%. Both the C/M/W and the cold acetone methods provided sufficient reduction of SDS, high recovery rates of protein and allowed the acquisition of MALDI spectra. The use of n-octyl-beta-D-glucopyranoside in the protein sample preparation enhanced the MALDI signal for protein samples containing more than 2 10(-4)% SDS, after the C/M/W extraction. Following the cold acetone procedure, the use of n-octylglucoside was found to be necessary in order to obtain spectra, but they were of lower quality than those obtained with the C/M/W method, probably due to higher residual amounts of SDS.     

Surfactant-assisted synthesis,characterizations, and room temperature ammonia sensing mechanism of nanocrystalline CuO

CuO nanocrystalline powder has been synthesized by a sol?gel auto combustion route with cetyltrimethylammonium bromide (CTAB) as cationic surfactant, and sodium dodecyl sulphate (SDS) as anionic surfactant. The powder samples are characterized by TGA/DTA, XRD, FESEM, and TEM techniques. Thermal analysis of the dried gel samples shows that addition of surfactant in the precursor increases the heat of reaction, which is evolved in the decomposition of metal citrate complex. The CTAB and SDS addition in the reaction mixture lowers the average crystallite size to few tens of nanometer. Surfactant doping in precursor causes a variation in lattice strain and changes to its type to compressive. CuO nanoparticles are bound together into facets–like weakly aggregated clusters, as indicated by FESEM images. TEM micrographs indicate the porous, nearly spherical particles having crystallite size around 7 and 18 nm for CTAB and SDS surfactant assisted CuO samples respectively. CuO nanoparticles assembled as thick film have been tested for their response to 100 ppm ammonia gas at room temperature. Cationic surfactant assisted sample shows maximum response to ammonia as compared to anionic surfactant. The CTAB assisted sensor shows almost completes recovery in 500 s whereas SDS assisted sample shows 75% recovery in the same time. The ammonia response of the films obeys the Elovich equation. The response rate of sensor is found to be maximum for CTAB assisted CuO films as compared to other samples. The kinetics of the response reaction shows that the ionic surfactants assisted CuO follows second order reaction kinetics.     

Retention properties of internal-surface reversed-phase silica packing and recovery of drugs from human plasma

The properties of internal-surface reversed-phase silica packings developed for use in high-performance liquid chromatography, were investigated with regard to the effects of mobile phase conditions (pH, ionic strength, nature and concentration of organic modifiers, ion-pairing agent and surfactant) on the retention of some selected compounds having different polarities. The results indicated that pi-electron interactions play the main role in solute retention, although it is weaker than that on phenylsilica supports, and that weak cation-exchange properties exert a secondary effect on the retention of ionic solutes. The ion-pairing effect was found to be markedly weakened in mobile phases containing an anionic counter ion. In contrast, the addition of a surfactant (SDS) caused a marked increase in the retention of certain drugs at low pH and expanded the pH range of the mobile phase applicable to plasma samples. Based on these findings, the separation and recovery of several drugs (probenecid, lidocaine, cefpiramide and cefaclor) from human plasma were investigated, with emphasis on their protein bindings. The contour chromatogram of human plasma is also demonstrated in relation to the selection of the detection wavelength.     

Stacking of unlabeled sodium dodecyl sulfate-proteins within a fluorimetrically detected moving boundary, electroelution and mass spectrometric identification

The previously reported fluorimetric detection of sodium dodecyl sulfate (SDS)-protein in the presence of cascade blue in agarose gel electrophoresis using barbital buffer was found to be equally feasible in the absence of the fluorescent marker and using Tris-Tricinate buffer, provided that SDS was loaded with the sample but not contained in the catholyte. That fluorescent detection is thought to be due to the formation of a moving boundary between leading SDS and trailing barbital, or Tricinate buffer. This hypothesis is supported by the following evidence: (i) The fluorometrically detected band disappears with addition of SDS to the catholyte; (ii) band area is proportional to protein and/or SDS load; (iii) mobility of SDS-proteins differing in mass is the same at agarose concentrations up to 3%; (iv) lowering of protein mobility by increase in gel concentration and/or increase in the size of the SDS-protein leads to band disappearance. Fluorescent detection of the band is like to be nonspecific and due to the light scattering properties of a stack comprising moving boundaries of any analytes with net mobilities intermediate between SDS (or micellar SDS) and the trailing buffer constituent at their regulated very high concentrations. The steady-state stack of SDS-proteins in the size range of 14.4-45.0 kDa, and the transient stack of an SDS-protein of 66.2 kDa have lent themselves to electroelution and characterization by mass of the proteins after removal of SDS and buffer exchange using matrix assisted laser desorption/ionization-time of flight (MALDI-TOF)-mass spectrometry. The possibility to form a stack of protein between leading SDS and trailing buffer anions under conditions of weak molecular sieving (open-pore gel and small-sized protein) contributes to the understanding of moving boundaries in gel electrophoresis, but in view of the narrowly defined conditions, under which this stack forms, is of limited practical significance for the gel electrophoresis of SDS-proteins.     

Effects of common surfactants on protein digestion and matrix-assisted laser desorption/ionization mass spectrometric analysis of the digested peptides using two-layer sample preparation

While surfactants are commonly used in preparing protein samples, their presence in a protein sample can potentially affect the enzymatic digestion process and the subsequent analysis of the resulting peptides by mass spectrometry. The extent of the tolerance of matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) to surfactant interference in peptide analysis is very much dependent on the matrix/sample preparation method. In this work the effects of four commonly used surfactants, namely n-octyl glucoside (OG), Triton X-100 (TX-100), 3-[(3-cholamidopropyl)dimethylammonio]-1-propanesulfonate (CHAPS) and sodium dodecyl sulfate (SDS), for biological sample preparation on trypsin digestion and MALDI-MS of the resulting digest are examined in detail within the context of using a two-layer method for MALDI matrix/sample preparation. Non-ionic and mild surfactants, such as OG, TX-100 or CHAPS, are found to have no significant effect on trypsin digestion with surfactant concentrations up to 1%. However, TX-100 and CHAPS interfere with the subsequent peptide analysis by MALDI-MS and should be removed prior to peptide analysis. OG is an MS-friendly surfactant and no effect is observed for MALDI peptide analysis. The effect of SDS on trypsin digestion in terms of the number of peptides generated and the overall protein sequence coverage by these peptides is found to be protein dependent. The use of SDS to solubilize hydrophobic membrane proteins, followed by trypsin digestion in the presence of 0.1% SDS, results in a peptide mixture that can be analyzed directly by MALDI-MS. These peptides are shown to provide better sequence coverage compared with those obtained without the use of SDS in the case of bacteriorhodopsin, a very hydrophobic transmembrane protein. This work illustrates that MALDI-MS with the two-layer sample preparation method can be used for direct analysis of protein digests with no or minimum sample cleanup after proteins are digested in a solution containing surfactants.     

Effect of Sample Preparation on the Detection and Quantification of Selected Nuts Allergenic Proteins by LC-MS/MS

The detection and quantification of nut allergens remains a major challenge. The liquid chroma-tography tandem mass spectrometry (LC-MS/MS) is emerging as one of the most widely used methods, but sample preparation prior to the analysis is still a key issue. The objective of this work was to establish optimized protocols for extraction, tryptic digestion and LC-MS analysis of almond, cashew, hazelnut, peanut, pistachio and walnut samples. Ammonium bicar-bonate/urea extraction (Ambi/urea), SDS buffer extraction (SDS), polyvinylpolypyrroli-done (PVPP) extraction, trichloroacetic acid/acetone extraction (TCA/acetone) and chloro-form/methanol/sodium chloride precipitation (CM/NaCl) as well as the performances of con-ventional tryptic digestion and microwave-assisted breakdown were investigated. Overall, the protein extraction yields ranged from 14.9 ± 0.5 (almond extract from CM/NaCl) to 76.5 ± 1.3% (hazelnut extract from Ambi/urea). Electrophoretic profiling showed that the SDS extraction method clearly presented a high amount of extracted proteins in the range of 0–15 kDa, 15–35 kDa, 35–70 kDa and 70–250 kDa compared to the other methods. The linearity of the LC-MS methods in the range of 0 to 0.4 µg equivalent defatted nut flour was assessed and recovery of internal standards GWGG and DPLNV(d8)LKPR ranged from 80 to 120%. The identified bi-omarkers peptides were used to relatively quantifier selected allergenic protein form the inves-tigated nut samples. Considering the overall results, it can be concluded that SDS buffer allows a better protein extraction from almond, peanut and walnut samples while PVPP buffer is more appropriate for cashew, pistachio and hazelnut samples. It was also found that conventional overnight digestion is indicated for cashew, pistachio and hazelnut samples, while microwave assisted tryptic digestion is recommended for almond, hazelnut and peanut extracts.     

A two-dimensional gel database of rat liver proteins useful in gene regulation and drug effects studies.

A standard two-dimensional (2-D) protein map of Fischer 344 rat liver (F344MST3) is presented, with a tabular listing of more than 1200 protein species. Sodium dodecyl sulfate (SDS) molecular mass and isoelectric point have been established, based on positions of numerous internal standards. This map has been used to connect and compare hundreds of 2-D gels of rat liver samples from a variety of studies, and forms the nucleus of an expanding database describing rat liver proteins and their regulation by various drugs and toxic agents. An example of such a study, involving regulation of cholesterol synthesis by cholesterol-lowering drugs and a high-cholesterol diet, is presented. Since the map has been obtained with a widely used and highly reproducible 2-D gel system (the Iso-Dalt system), it can be directly related to an expanding body of work in other laboratories.     

Electrophoretically driven SDS removal and protein fractionation in the shotgun analysis of membrane proteomes

SDS is mostly used to enhance the solubilization and extraction of membrane proteins due to its strong detergency and low cost. Nevertheless, SDS interferes with the subsequent procedures and needs to be removed from the samples. In this work, a special gradient gel electrophoresis (GGE) system was developed to remove SDS from the SDS-solubilized protein samples. As a proof-of-principle experiment, the GGE system was designed to be composed of an agarose loading layer, six polyacrylamide fractionation layers with different concentrations and a high-concentration polyacrylamide sealing layer. The advantages of the GGE system are that it not only can electrophoretically remove SDS efficiently so that the protein loss resulted from the repeated gel washing after electrophoresis was avoided, but also can reduce the complexity of the sample, prevent the precipitation of proteins after loading and avoid the loss of proteins with low molecular weight during the electrophoresis. Using GGE system, about 85% of SDS in the sample and gel was electrophoretically removed and the proteins were fractionated. Compared with the two representative gel-based sample cleanup methods reported in literature, GGE-based strategy significantly improved the identification efficiency of proteins in terms of the number and coverage of the identified proteins.     

High-performance size-exclusion chromatography of polypeptides on a TSK G2000SW column in acidic mobile phases

Polypeptides subjected to high-performance liquid chromatography on a TSK G2000SW column in acidic mobile phases of low ionic strength underwent a combination of size exclusion and ion exclusion from the matrix. The distribution coefficient (Kd) of each polypeptide was dependent upon the concentration of ion-pairing agent present and increased as the concentration of ion-pairing agent increased. The fractionation range of the column could thus be manipulated by altering the concentration of acid in the mobile phase. The nature of the ion-pairing acid, in terms of hydrophilic or hydrophobic ion pairing, also had an effect on the chromatography, such that hydrophobic ion-pairing agents lead to increased Kd values, especially in the case of the most basic polypeptides. To account for these results it is proposed that the TSK GSW matrix is cationic at low pH, and that ion pairing suppresses the ion exclusion experienced by cationic polypeptides under these conditions.     

Effects of substrate surfaces in matrix‐assisted laser desorption/ionization mass spectrometry

For matrix‐assisted laser desorption/ionization (MALDI) mass spectra, undesirable ion contamination can occur due to the direct laser excitation of substrate materials (i.e., laser desorption/ionization (LDI)) if the samples do not completely cover the substrate surfaces. In this study, comparison is made of LDI processes on substrates of indium and silver, which easily emit their own ions upon laser irradiation, and conventional materials, stainless steel and gold. A simultaneous decrease of ion intensities with the number of laser pulses is observed as a common feature. By the application of an indium substrate to the MALDI mass spectrometry of alkali salts and alkylammonium salts mixed with matrices, 2,5‐dihydroxybenzoic acid (DHB) or N‐(4‐methoxybenzylidene)‐4‐butylaniline (MBBA), the mixing of LDI processes can be detected by the presence of indium ions in the mass spectra. This method has also been found to be useful for investigating the intrinsic properties of the MALDI matrices: DHB samples show an increase in the abundance of fragment ions of matrix molecules and cesium ions with the number of laser pulses irradiating the same sample spot; MBBA samples reveal a decrease in the level of background noise with an increase in the thickness of the sample layer. Copyright © 2009 John Wiley & Sons, Ltd.     

Studies of keratins in tongue coating samples of hepatitis B patients by mass spectrometry

Pooled tongue coating samples from 64 hepatitis B patients and 24 healthy adults were studied and a major band of differential proteins was found by sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS‐PAGE). The differential proteins in this band were identified and proved to be keratins by liquid chromatography/tandem mass spectrometry (LC/MS/MS) and Western blot analysis. Furthermore, relative quantification of the identified keratins was performed via using stable isotopic labeling and matrix‐assisted laser desorption/ionization time‐of‐flight mass spectrometry (MALDI‐TOF MS), showing the higher expression level of these keratins in tongue coating samples of hepatitis B patients than healthy adults. These results provided additional information to understand the medical diagnosis depending on the tongue coating. Copyright © 2009 John Wiley & Sons, Ltd.     

Sequential electroelution and mass spectroscopic identification of intact sodium dodecyl sulfate-proteins labeled with 5(6)-carboxyfluorescein-N-hydroxysuccinimide ester

A gel electrophoresis apparatus capable of scanning the migration path fluorometrically and of computer-directed electroelution of bands was applied to the mass spectrometric identification of sequentially electroeluted 5(6)-carboxyfluorescein-N-hydrosuccinimide ester (FLUOS)-labeled sodium dodedyl sulfate (SDS)-proteins. The masses of four electroeluted SDS-proteins under study determined by matrix assisted laser desorption/ionization-time of flight (MALDI-TOF) spectrometry are changed by 1% due to their reaction with FLUOS in a 1:5 molar ratio of protein:label, allowing for the identification of the labeled intact proteins on the basis of mass. More importantly, the partial (10 or 50%) derivatization of proteins with FLUOS does not preclude their tryptic hydrolysis, and identification of the protein on the basis of the mass spectrometric analysis of its tryptic peptides. Potentially, the procedure allows for the automated mass spectrometric identification of SDS-proteins globally labeled with FLUOS and electrophoretically separated, without need for any gel sectioning.     

Determination of fluorescent whitening agents in environmental waters by solid-phase extraction and ion pair liquid chromatography-tandem mass spectrometry

A comprehensive method for the trace determination of four stilbene-type disulfonate and one distyrylbiphenyl-type fluorescent whitening agents (FWAs) in environmental water samples was developed and validated. Various solid-phase extraction (SPE) cartridges were investigated. The newly developed Oasis WAX (weak mixed-mode anion exchange and reversed-phase sorbent) SPE cartridge provides the optimal sample extraction results. The analytes were then identified and quantitated by liquid chromatography-electrospray ionization tandem mass spectrometry (HPLC-ESI-MS-MS) in negative ionization mode, applying di-n-hexylammonium acetate (DHAA) as the ion-pairing reagent in mobile phase. Limits of quantitation (LOQs) were established between 4 and 18 ng/l in 50 ml of water samples. Intrabatch and interbatch precision with their accuracy at two concentration levels were also investigated. Precision for these five FWAs, as indicated by RSD, proved to be less than 13 and 11%, respectively, for intra- and interbatch. Accuracy, expressed as the mean recovery, was between 68 and 97%. The method was finally applied to environmental water samples, showing the occurrence of five FWAs in both river water and wastewater treatment plant (WWTP) effluent samples.     

Improved MALDI-TOF imaging yields increased protein signals at high molecular mass

Matrix assisted laser desorption ionization (MALDI) mass spectrum images are created from an array of mass spectra collected over a tissue surface. We have increased the mass range of proteins that can be detected in tissue sections from kidneys, heart, lung and brain of different rodent species by a modification of the sandwich technique, which involves co-crystallizing matrix with analyte. A tissue section is placed upon a drop of sinapinic acid matrix dissolved in 90% ethanol and 0.5% Triton X-100. Once the matrix has dried, a seed layer of sinapinic crystals is added as a dispersion in xylene. Additional layers of sinapinic acid are added as solutions in 90% ethanol followed by 50% acetonitrile. Numerous peaks with signal to noise ratio of four or greater are observed between 25 kDa to 50 kDa. This represents approximately 10 times as many peaks as are detected using traditional matrix spotting and spraying.     

Rapid and sensitive determination of ethylenediaminetetraacetic acid and diethylenetriaminepentaacetic acid in water samples by ion-pair reversed-phase liquid chromatography--electrospray tandem mass spectrometry

A new method is presented for the quantitative determination of ethylenediaminetetraacetic acid (EDTA) and diethylenetriaminepentaacetic acid (DTPA) from aqueous samples without an enrichment step. It consist of the formation of the Fe(III) complexes of EDTA and DTPA, liquid-chromatography with a volatile ion-pairing agent and determination by electrospray ionization-tandem mass spectrometry (ESI-MS/MS). Limits of quantification (LOQ) of 1.0 and 0.6 microgL(-1) for EDTA and DTPA were obtained, allowing the direct injection of most aqueous environmental samples without any preceding enrichment. With a more recent mass spectrometer, the LOQ could be further decreased by almost one order of magnitude. Parallel analysis of real samples by a standardized method employing enrichment, derivatization and GC-MS analysis yielded comparable results. The method was applied to the determination of both complexing agents in several wastewater, surface water and drinking water samples, showing that EDTA is an omnipresent contaminant in partially closed water cycles.     

Direct profiling and imaging of peptides and proteins from mammalian cells and tissue sections by mass spectrometry

Mass spectrometry can be used to map the distribution of targeted compounds in tissue, providing important molecular information in many areas of biological research. Matrix assisted laser desorption/ionization - time of flight - mass spectrometry (MALDI-TOF-MS) is well suited for the analysis of tissue samples with a spatial resolution of about 30 microm for compounds in a mass range from 1000 to over 50 000 Da. Direct analysis of tissue sections requires spotting or coating of the tissue with a matrix compound typically sinapinic acid or other cinnamic acid analogs. A raster of this sample by the laser beam and subsequent mass analysis of the desorbed ions can record molecular intensities throughout the section. The overall process is illustrated by profiling and imaging of mouse epididymis sections where protein activity changes markedly throughout the section.     

MALDI质谱检测蛋白质与富勒醇的非共价复合物

基质辅助激光解吸电离(MALDI)质谱由于受到酸性基质、样品制备、激光诱导聚合和基质加合物的形成等条件的限制而难以用于非共价复合物的检测.本文以芥子酸为基质,观察到蛋白质与富勒醇的特殊相互作用,一些质谱特征,如质量数迁移、宽的加合峰和定量结合比表明,在蛋白质和富勒醇之间形成了特殊的非共价复合物.其中,血红蛋白与富勒醇的结合比是1:4,而肌红蛋白与富勒醇的结合比是1:1.实验结果表明:富勒醇可用来保护血红蛋白,有在酸性介质中防止其分解的作用.因此,通过在基质组份中添加特性有机化合物保护被测样品,有可能实现用MALDI质谱测定四级结构蛋白质的分子量.     

MALDI‐TOF mass spectrometry of hordeins: rapid approach for identification of malting barley varieties

A procedure for identification of malting barley varieties using matrix‐assisted laser desorption/ionization time‐of‐flight mass spectrometry (MALDI‐TOF MS) of ethanol‐soluble barley proteins (hordeins) is described. The hordeins were first extracted from milled barley grains by several extraction protocols (using different extraction agents and conditions). Hordein extracts were then analyzed directly via MALDI‐TOF MS without any preliminary purification or separation step, and the protein profiles of analyzed hordein extracts were compared in order to find out the most suitable extraction procedure for mass spectrometric analysis. The optimized procedure was successfully applied to identification of 13 malting barley varieties. Our results revealed that the proposed mass spectrometry‐based approach provides characteristic mass patterns of extracted hordeins, which can be advantageously used for barley variety identification. Copyright © 2009 John Wiley & Sons, Ltd.