A desalting approach for MALDI-MS using on-probe hydrophobic self-assembled monolayers

A Surface Pattern on MALDI Steel Plate for One-Step In-Situ Self-Desalting and Enrichment of Peptides/Proteins

We report a novel strategy to achieve simultaneous one-step in-situ self-desalting and enrichment (OISE) of peptides/proteins on a facilely fabricated patterned MALDI steel plate with a circular paraffin-steel-polystyrene structure. The OISE plate could efficiently segregate salts from both analytes and matrices while retaining both analyte and matrix concentrate, and facilitating them to form homogeneous co-crystals on the centrally located polystyrene pattern. With the OISE plate, high quality and reproducible spectra could be obtained for low abundance peptides even in the presence of high salt concentrations (200 mM NH₄HCO₃, 1 M NaCl, or 400 mM urea). Using this strategy, a significant sensitivity enhancement was gained over traditional MALDI plate. The practical utility of this method was further demonstrated by the successful profiling of BSA digests and human serum. Graphical Abstract ᅟ.

Rapid fabrication of functionalized plates for peptides, glycopeptides and protein purification and mass spectrometry analysis

A rapid and simple approach for fabricating a disposable functionalized membrane on matrix-assisted laser desorption ionization (MALDI) targets, glass, or plastic substrates, without using complex mechanical protocols or chemical reactions, was developed for sample enrichment and mass spectrometry analysis. By coating functionalized-silica particles on a polydimethylsiloxane (PDMS)-coated plate, these particles can form a monolayer of materials on the PDMS membrane for sample handling without peeling off. An octadecyl(C18)-functionalized plate was fabricated by coating porous C18-silica particles on a PDMS-coated plate. The C18 particle-coated PDMS plate (CP plate) has better sensitivity than C18 tips and magnetic nanoparticles, along with a higher sample recovery (64.3 ± 4.9%) compared to the C18 tip method, when analyzing trace amounts of 5 fm BSA digest samples. The CP plate shows significantly higher urea/SDS removal efficiency on the cell lysate proteome compared to C18 tips. The capacity of the C18 spot (∼2.8 mm in diameter) on the CP plate was ∼10 μg of BSA digests. A hydrophilic particle-coated PDMS plate was also fabricated and successfully used for glycopeptide enrichment and matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) analysis.

Magnetic metal–organic frameworks for selective enrichment and exclusion of proteins for MALDI-TOF MS analysis

We firstly report magnetic metal–organic frameworks for selective enrichment and exclusion of proteins for MALDI-TOF MS analysis.

Desalting by crystallization: detection of attomole biomolecules in picoliter buffers by mass spectrometry

Sensitive detection of biomolecules in small-volume samples by mass spectrometry is, in many cases, challenging because of the use of buffers to maintain the biological activities of proteins and cells. Here, we report a highly effective desalting method for picoliter samples. It was based on the spontaneous separation of biomolecules from salts during crystallization of the salts. After desalting, the biomolecules were deposited in the tip of the quartz pipet because of the evaporation of the solvent. Subsequent detection of the separated biomolecules was achieved using solvent assisted electric field induced desorption/ionization (SAEFIDI) coupled with mass spectrometry. It allowed for direct desorption/ionization of the biomolecules in situ from the tip of the pipet. The organic component in the assistant solvent inhibited the desorption/ionization of salts, thus assured successful detection of biomolecules. Proteins and peptides down to 50 amol were successfully detected using our method even if there were 3 × 10(5) folds more amount of salts in the sample. The concentration and ion species of the salts had little influence on the detection results.

Importance of the matrix and the matrix/sample ratio in MALDI-TOF-MS analysis of cathelicidins obtained from porcine neutrophils

Qualitative and quantitative mass spectrometric studies of biomolecules for example proteins, peptides, or lipids contained in biological samples like physiologic fluids are very important for many fields of science such as medicine, veterinary medicine, biology, biochemistry, molecular biology, or environmental sciences. In the last two decades, MALDI TOF MS — matrix-assisted laser desorption mass spectrometry, proved to be an especially convenient tool for these analyses. The main advantages of this method are its rapidity and high sensitivity which is particularly appreciated in the case of studies of complex biological specimen. A major challenge for many researchers is to maximize this sensitivity, among others, by appropriate procedures of sample preparation for the measurement. The objective of this work was to optimize these procedures, selecting the optimal matrix and optimum proportions of the sample and the matrix solution in a mixture of both solutions, aiming at the achievement of the maximum intensity of ion current. In this respect, five low molecular mass cathelicidins were studied: prophenin-2, protegrins 1–3, PR-39. All of them were obtained directly from the porcine blood. As a result of studies, the authors determined such experimental conditions when the intensity of investigated ionic current had the highest value.

On-plate self-desalting and matrix-free LDI MS analysis of peptides with a surface patterned sample support

A hydrophobic-hydrophilic-hydrophobic pattern has been produced on the surface of a silicon substrate for selective enrichment, self-desalting, and matrix-free analysis of peptides in a single step. Upon sample application, the sample solution is first confined in a small area by a hydrophobic F-SAM outer area, after which salt contaminants and peptides are selectively enriched in the hydrophilic and hydrophobic areas, respectively. Simultaneously, matrix background noise is significantly reduced or eliminated because of immobilization of matrix molecules. As a result, the detection sensitivity is enhanced 20-fold compared with that obtained using the usual MALDI plate, and interference-free detection is achieved in the low m/z range. In addition, peptide ions can be identified unambiguously in the presence of NH₄HCO₃ (100 mM), urea (1 M), and NaCl (1 M). When the device was applied to the analysis of BSA digests, the peptide recovery and protein identification confidence were greatly improved.

On-plate selective enrichment and self-desalting of peptides/proteins for direct MALDI MS analysis

In this paper, a new technique has been proposed to achieve simultaneous peptides/proteins enrichment and wash-free self-desalting on a novel sample support with a circle hydrophobic-hydrophilic-hydrophobic pattern. Upon deposition, the sample solution is first concentrated in a small area by repulsion of the hydrophobic outer layer, and then, the peptides/proteins and coexisting salt contaminants are selectively captured in different regions of the pattern through strong hydrophobic and hydrophilic attractions, respectively. As a result, the detection sensitivity is improved by 2 orders of magnitude better than the use of the traditional MALDI plate, and high-quality mass spectra are obtained even in the presence of NaCl (1 M), NH(4)HCO(3) (100 mM), or urea (1 M). The practical application of this method is further demonstrated by the successful analysis of myoglobin digests with high sequence coverage, demonstrating the great potential in proteomic research.

On-plate desalting and SALDI-MS analysis of peptides with hydrophobic silicate nanofilms on a gold substrate

We report the use of silicate nanofilms for on-plate desalting and subsequently direct laser desorption/ionization-mass spectrometric (LDI-MS) analysis of peptides. A hydrophobic octadecyltrichlorosilane (OTS) monolayer is formed on a calcinated nanofilm on a gold substrate to facilitate sample deposition and interaction with the surface that allows effective removal of MS-incompatible contaminants such as salts and surfactants by simple on-plate washing while the peptides are retained on the spot. By elimination of interferences from matrix-related ions and contaminants, sensitivity of MS analysis has been enhanced over ca. 20 times, leading to improved detection of peptides at the low-femtomolar level. A high recovery rate of the peptides is obtained by using relatively rough nanofilms, which are prepared through a modified layer-by-layer deposition/calcination process. The performance of the films has been investigated with peptide samples in the presence of high salts (NaCl and sodium acetate) and urea. Compared to matrix-assisted laser desorption/ionization analysis with CHCA matrix, LDI with on-plate desalting offers marked improvement for analysis of peptides due to low background ions and reduction of sample complexity. Additionally, selective capture of the hydrophobic components of a protein can be achieved, providing a highly useful strategy for specific peptide enrichment. LDI with on-plate desalting approach has also been successfully applied to peptide analysis from protein digests.

Cysteine-capped ZnSe quantum dots as affinity and accelerating probes for microwave enzymatic digestion of proteins via direct matrix-assisted laser desorption/ionization time-of-flight mass spectrometric analysis

Fluorescent semiconductor quantum dots (QDs) exhibit great potential and capability for many biological and biochemical applications. We report a simple strategy for the synthesis of aqueous stable ZnSe QDs by using cysteine as the capping agent (ZnSe-Cys QDs). The ZnSe QDs can act as affinity probes to enrich peptides and proteins via direct matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOFMS) analysis. This nanoprobe could significantly enhance protein signals (insulin, ubiquitin, cytochrome c, myoglobin and lysozyme) in MALDI-TOFMS by 2.5-12 times compared with the traditional method. Additionally, the ZnSe-Cys QDs can be applied as heat absorbers (as accelerating probes) to speed up microwave-assisted enzymatic digestion reactions and also as affinity probes to enrich lysozyme-digested products in MALDI-TOFMS. Furthermore, after the enrichment experiments, the solutions of ZnSe-Cys QDs mixed with proteins can be directly deposited onto the MALDI plates for rapid analysis. This approach shows a simple, rapid, efficient and straightforward method for direct analysis of proteins or peptides by MALDI-TOFMS without the requirement for further time-consuming separation processes, tedious washing steps or laborious purification procedures. The present study has demonstrated that ZnSe-Cys QDs are reliable and potential materials for rapid, selective separation and enrichment of proteins as well as accelerating probes for microwave-digested reactions for proteins than the regular MALDI-MS tools. Additionally, we also believe that this work may also inspire investigations for applications of QDs in the field of MALDI-MS for proteomics.

Nanoparticles for Selective Laser Desorption/Ionization in Mass Spectrometry

The selective desorption/ionization of analytes using nanomaterials is investigated using metallic nanoparticles. By replacing the sodium citrate capping of gold nanoparticles with self-assembled monolayers, we are able to both enhance analyte ionization and selectively capture analytes. Capping gold nanoparticles with a monolayer of 4-mercaptobenzoic acid enhances analyte ionization while greatly decreasing chemical noise resulting from alkali adducted species. Selective capture and sequential desorption/ionization of the peptide bradykinin (1–7) from a two peptide mixture is achieved using β-cyclodextrin capped gold nanoparticles. Finally, by switching from gold to silver nanoparticles, we are able to ionize both folic acid and amphotericin B. These results demonstrate that through careful control of nanoparticle surface chemistry and composition one can achieve selective analyte ionization for MS applications.

Self-assembled-monolayer-modified silicon substrate to enhance the sensitivity of peptide detection for AP-MALDI mass spectrometry

A self-assembled-monolayer-modified silicon substrate was successfully used to enhance the sensitivity of peptide detection for atmospheric pressure-matrix-assisted laser desorption/ionization mass spectrometry (AP-MALDI/MS). The effect of surface modification of silicon wafer samples with NH(2) and OH functional groups was investigated. In addition, solvent effects for the preparation of modified NH(2)-functionalized surfaces were examined. The sensitivities for the two peptides were significantly improved, increasing between 12 and 160 times, for bradykinin and gramicidin, respectively, on an NH(2)-modified silicon surface prepared in toluene, over that on a conventional gold substrate. The limits of detection (LODs) for bradykinin and gramicidin using the conventional gold substrate in AP-MALDI/MS experiments were > 0.011 microM and 110 microM, respectively. Using our SAM approach, the LODs for bradykinin and gramicidin in AP-MALDI/MS can be improved to 0.93 nM and 0.33 microM, respectively. This SAM approach for AP-MALDI/MS is simple and sensitive, and can be used for high-throughput analysis.

Rapid and automatic on-plate desalting protocol for MALDI-MS: using imprinted hydrophobic polymer template

A novel protocol of rapid and automatic on-plate desalting (OPD) and peptide concentration for 2-DE-MALDI-MS has been developed by the approach of templating the hydrophobic polymer solution over Kapton-etched mask. For the template technique, small hydrophobic polymer [linear poly(methyl methacrylate) (PMMA), PMMA derivatized with fullerene-C60 (PMMA-C60), linear polystyrene (PSt), or PSt derivatized with fullerene-C60 (PSt-C60)] spots (990 microm od) are patterned at the centers of stainless MALDI plate wells (1400 microm id). Tryptic-peptide solution with no predesalting was dropped onto the central hydrophobic spots, resulting in a concentration of proteolytic peptides on the hydrophobic polymer surface with a reduced spot size. The dried peptide layer was then covered subsequently with over-volume matrix solution, causing the removal of redissolved salts from the spot center to the spot edge by means of a natural "outward flow." The proposed OPD protocol exhibited a dramatic enhancement in S/N up to 850 for 14 fmol BSA digests in the coexistence of 100 mM salts, compared with barely detectable peaks in ordinary way. This analysis has shown that the success rate of identification was increased by two-fold for low abundance proteins in the human liver tissue with no need for the conventional ZipPlate desalting strategy.

Tailoring nanoparticle surface chemistry to enhance laser desorption ionization of peptides and proteins

Gold nanoparticles capped with 4-aminothiophenol have been employed for laser desorption ionization mass spectrometry of biomolecules. We demonstrate that the capped nanoparticles increase ion yields, decrease ion fragmentation, and increase the useful analyte mass range when compared to other nanoparticle systems. These results will allow for further development of nanoparticles with both targeting and enhanced ionization abilities to aid in biomarker screening.

Wash-free in-situ self-desalting and peptide enrichment by block copolymer analyzed with MALDI-TOFMS

A novel technique of simultaneous peptide enrichment and wash-free in-situ self-desalting for MALDI analysis is reported, where a newly synthesized block copolymer with a microphase-separated configuration is applied to embed salts with its hydrophilic domain of poly(ethylene oxide) and concentrate peptides with its hydrophobic domain of polysulfone.

Thermoresponsive MALDI probe surfaces as a tool for protein on-probe purification

Thin film depositions of rf plasma polymerized N-isopropylacrylamide (ppNIPAM) show a phase transition temperature below which the polymer surface is hydrophilic, and protein nonadsorptive, and above which the polymer surface is hydrophobic, and protein-retentive. Results presented here demonstrate that this thermoresponsive plasma polymer can be coated on the surface of a MALDI probe and subsequently used for on-probe biomolecule cleanup. Specifically, a contaminated biomolecule can be applied to the ppNIPAM coated MALDI probe surface at a temperature above the phase transition temperature, washed using solvent also held above the phase transition temperature, and then analyzed by reducing the probe temperature to room temperature before adding the MALDI matrix. With the use of this approach, it is demonstrated that cytochrome c contaminated with 0.3% SDS, which yields only a very weak MALDI ion signal as directly deposited, can be purified on-probe using the thermoresponsive plasma polymer to improve significantly the ion signal. It is further shown that the decontamination of whole cell protein extracts from cyanobacteria is augmented through the use of the ppNIPAM coated MALDI probe.

Methods for samples preparation in proteomic research

Sample preparation is one of the most crucial processes in proteomics research. The results of the experiment depend on the condition of the starting material. Therefore, the proper experimental model and careful sample preparation is vital to obtain significant and trustworthy results, particularly in comparative proteomics, where we are usually looking for minor differences between experimental-, and control samples. In this review we discuss problems associated with general strategies of samples preparation, and experimental demands for these processes.

Letter: Lanthanum-calcium-manganate (La0.67Ca0.33MnO3) nanoparticle assisted affinity probes for MALDI MS analysis of proteins

Matrix-assisted laser desorption/ionization mass spectrometry (MALDI MS) has been used extensively for the analysis of -intact proteins and for proteomics. Proteins or proteomics analyses with low molecular mass range have some limitations because of background interference from the salt or surfactant ions. Lanthanum-calcium- manganate La(0.67)Ca(0.33)MnO(3) nanoparticles (LCMONPs) have been used as the matrix-assisting material after surface modification to reduce the salt or surfactant interference. The detectable mass range was tested in the range of 800-16,000 Da. The surface-modified LCMONPs have affinity with protein molecules through ionic or electrostatic interaction at pH 4.0. The nanoparticles mixed with proteins give a spectrum with a large signal-to-noise ratio for the analytes, and effectively eliminate the noise from interfering salt or surfactant ions. The results indicate that surface-modified La(0.67)Ca(0.33)MnO(3) nanoparticles can be used with MALDI matrix for proteins to eliminate the excessive noise of selective surfactants or salt ions from the MALDI spectrum.

In situ AP/MALDI-MS characterization of anchored matrix metalloproteinases

Several different procedures are available for the immobilization of proteins on solid supports, as many advantages derive from this approach, such as the possibility to develop new protein solid-state assays. Enzymes that are anchored on gold surfaces can interact with several different molecules in a tag-free environment, opening the way to surface plasmon resonance (SPR) investigations. Nevertheless, it is often important to know the identity of the affinity-retained analyte, and mass spectrometric analysis, via its unique molecular mass identification, represents a very valuable complementary method. There are many pieces of evidence to suggest that matrix metalloproteinases (MMPs) are involved in normal and pathological processes, including embryogenesis, wound healing, inflammation, arthritis and cancer, but presumably also exhibiting other functions. The search for new inhibitors of MMPs has prompted research towards the development of new solid-state assays for the rapid evaluation of MMP activity. We have already reported the possibility of measuring the activity of MMP-1 anchored on solid support by coupling SPR with ESI-MS analysis. In this work, we show the in situ atmospheric pressure (AP) MALDI-MS characterization of MMPs anchored on a gold chip with known surface coverage. The study extends the MS analysis to different proteins, and sequence coverage is reported for different digestion and MS procedures.

Material-enhanced laser desorption/ionization (MELDI)--a new protein profiling tool utilizing specific carrier materials for time of flight mass spectrometric analysis

Over the past couple of years, proteomics pattern analysis has emerged as an effective method for the early diagnosis of diseases such as ovarian, breast, or prostate cancer, without identification of single biomarkers. MALDI-TOF MS, for example, offers a simple approach for fast and reliable protein profiling, especially by using carrier materials with various physical and chemical properties, in combination with a MALDI matrix. This approach is referred to as material-enhanced laser desorption/ionization (MELDI). In this paper, we report the development and application of derivatized carrier materials [cellulose, silica, poly(glycidyl methacrylate/divinylbenzene) (GMA/DVB) particles, and diamond powder] for fast and direct MALDI-TOF MS protein profiling. The applicability of MELDI for rapid protein profiling was evaluated with human serum samples. These carriers, having various hydrophobicities, resulted in characteristic mass fingerprints, even if all materials were derivatized with iminodiacetic acid (IDA) to yield an immobilized metal affinity chromatography (IMAC) functionality. Our study demonstrates that analyzing complex biological samples, such as human serum, by employing different MELDI carrier materials yielded type- and size-dependent performance variation.

Porous anodic alumina membrane as a sample support for MALDI-TOF MS analysis of salt-containing proteins

Matrix-assisted laser desorption/ionization time-of-flight mass spectrometric (MALDI-TOF MS) analysis of proteins in salt-containing solution was performed for the first time using porous anodic alumina (PAA) membrane as sample support. The resulting spectral quality of proteins under standard sample preparation conditions was superior to that of normal metal sample stages. Analysis of phosphate-doped protein solutions indicated that porous anodic alumina membranes as a target yielded better results than a metallic target for salt-containing solutions. Because of the biocompatibility of the PAA, proteins can be adsorbed on the PAA and thus a washing process can be introduced to remove the salts from the PAA target before MS analysis. This desalting step significantly enhanced spectral quality, and better signal-to-noise ratios were obtained. The present technique is promising for proteomics research.

On-Probe Sample Preparation without Washes for Matrix-Assisted Laser Desorption/Ionization Mass Spectrometry Using an Anion Exchange Medium

When the mass spectra of biological samples (proteins, peptides, and so on) are obtained routinely by matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS), a serious problem is the reduction of the ionization efficiency by impurities, such as buffer salts and detergents. We focused our attention on devising a method to maintain the ionization efficiency of protein samples, even in the presence of sodium dodecyl sulfate (SDS), without any extra purification step. Although no protein ion peaks are observed in the presence of 2.5% SDS with the usual methods, the addition of a granular anion exchange silica gel to the matrix solution allowed the protein ion peaks to be obtained with an excellent signal-to-noise ratio. Together with other supporting experiments, we suggest that the positively charged surface (the basic environment derived from the anion exchange groups) and the roughness of the particles were important for good ionization in the presence of a high SDS concentration. For a very uneven surface, the SDS might be absorbed into the particle interiors during the process of cocrystallization with the matrix and analytes, which is known as the molecular sieve effect, and the SDS concentration in the surface crystalline film might be reduced. As a result, we developed an on-probe sample preparation method without washes for MALDI, using a strong anion exchange silica gel. This method is applicable even in the presence of 2.5% SDS, and is not only very simple but also inexpensive, because it can be used with the standard MALDI target plates.

Use of polymer-modified MALDI-MS probes to improve analyses of protein digests and DNA

The use of sample probe surfaces patterned with 200-microm-diameter spots of hydrophilic, charged polymers significantly enhances the analysis of protein digests and DNA by MALDI-MS. Selective adsorption on these polymer-modified surfaces allows collection of specific proteolytic peptides, while subsequent rinsing of the deposited sample removes contaminants. In the case of partially digested myoglobin, the mass spectrum obtained using a sample probe modified with polyanionic functionalities permits detection of 22 proteolytic fragments, while analysis using a stainless steel MALDI sample probe gives only 11 detectable fragments. Similarly, during the analysis of bovine serum albumin digests, the use of several different surface-modified MALDI sample probes increases sequence coverage from 61.3 to 74.5%. Detection of phosphorylated peptides can be quite challenging during analyses of phosphoprotein digests by MALDI-MS because these anionic proteolytic fragments have low ionization efficiencies. However, MALDI signals from the phosphorylated proteolytic fragments sometimes increase dramatically when using a sample probe surface modified by a polycation (polyethylenimine or poly(acrylic acid) complexed with Fe(3+)). The signal enhancement apparently occurs because the positive surface selectively binds the phosphorylated peptides. The use of patterned, polycationic surfaces also shows great promise for selective adsorption and decontamination of DNA samples; a simple water rinse diminishes or eliminates the formation of multi-ion adducts, thereby improving mass resolution during subsequent analysis by MALDI-MS.

Carbon nanotubes as adsorbent of solid-phase extraction and matrix for laser desorption/ionization mass spectrometry

A method with carbon nanotubes functioning both as the adsorbent of solid-phase extraction (SPE) and the matrix for matrix assisted laser desorption/ionization mass spectrometry (MALDI-MS) to analyze small molecules in solution has been developed. In this method, 10 microL suspensions of carbon nanotubes in 50% (vol/vol) methanol were added to the sample solution to extract analytes onto surface of carbon nanotubes because of their dramatic hydrophobicity. Carbon nanotubes in solution are deposited onto the bottom of tube with centrifugation. After removing the supernatant fluid, carbon nanotubes are suspended again with dispersant and pipetted directly onto the sample target of the MALDI-MS to perform a mass spectrometric analysis. It was demonstrated by analysis of a variety of small molecules that the resolution of peaks and the efficiency of desorption/ionization on the carbon nanotubes are better than those on the activated carbon. It is found that with the addition of glycerol and sucrose to the dispersant, the intensity, the ratio of signal to noise (S/N), and the resolution of peaks for analytes by mass spectrometry increased greatly. Compared with the previously reported method by depositing sample solution onto thin layer of carbon nanotubes, it is observed that the detection limit for analytes can be enhanced about 10 to 100 times due to solid-phase extraction of analytes in solution by carbon nanotubes. An acceptable result of simultaneously quantitative analysis of three analytes in solution has been achieved. The application in determining drugs spiked into urine has also been realized.

Digital Microfluidics with In-Line Sample Purification for Proteomics Analyses with MALDI-MS

An in-line sample purification method for MALDI-MS, which relies on the electrowetting-on-dielectric (EWOD)-based technique for digital microfluidics, is reported. In this method, a droplet containing peptides and impurities is moved by EWOD and deposited onto a Teflon-AF surface. A droplet of water is subsequently moved over the spot, where it dissolves and removes the impurities. A droplet containing MALDI matrix is then moved to the spot, which is analyzed by MALDI-MS. This purification method reduces the number of salt adduct peaks caused by low concentrations of impurities (e.g., 20 mM sodium phosphate), and reduces or eliminates the catastrophic effects of high concentrations of impurities (e.g., 8 M urea). The method was used to purify spots made by depositing multiple droplets of contaminated peptides. Spectra from the purified spots showed an increase in the S/N ratio as a function of the number of droplets deposited; when not purified, the S/N ratio remained constant regardless of the number of droplets. Finally, the method was used to purify protein digests for peptide mass fragment (PMF) searches, and was shown to be more efficient than the conventional method of purification with reversed-phase-packed pipet tips. We anticipate this new, in-line sample purification technique for EWOD-MALDI-MS will enable development of integrated high-throughput proteomics analysis methodologies.

Attomole peptide analysis by high-pressure matrix-assisted laser desorption/ionization Fourier transform mass spectrometry

A new high-pressure matrix-assisted laser desorption/ionization (HP-MALDI) source for FTMS has recently been described (O'Connor et al. J. Am. Soc. Mass Spectrom., in press). Improvements to the source design, including the incorporation of a new high-pressure gas channel plate, resulted in ions devoid of metastable fragmentation and also in increased sensitivity compared to the HP-MALDI prototype source design. The focus of this contribution is the evaluation of the current HP-MALDI FTMS configuration. The use of nonconductive sample surfaces, such as Parafilm and Teflon, was explored, and spectra from 30 amol of peptide applied to these surfaces were routinely obtained. In addition, the current limit of detection for this configuration is demonstrated to be 300 zmol for the phosphopeptide RRREEE(pS)EEEAA using multishot accumulation of the ions from 15 laser shots in the hexapole and 1 scan. In addition, the performance of the new HP-MALDI FTMS configuration and its potential application for high-throughput proteomics analyses are discussed.

Surface-MALDI mass spectrometry in biomaterials research

Matrix-assisted laser desorption ionization mass spectrometry (MALDI-MS) has been used for over a decade for the determination of purity and accurate molecular masses of macromolecular analytes, such as proteins, in solution. In the last few years the technique has been adapted to become a new surface analysis method with unique capabilities that complement established biomaterial surface analysis methods such as XPS and ToF-SSIMS. These new MALDI variant methods, which we shall collectively summarize as Surface-MALDI-MS, are capable of desorbing adsorbed macromolecules from biomaterial surfaces and detecting their molecular ions with high mass resolution and at levels much below monolayer coverage. Thus, Surface-MALDI-MS offers unique means of addressing biomaterial surface analysis needs, such as identification of the proteins and lipids that adsorb from multicomponent biological solutions in vitro and in vivo, the study of interactions between biomaterial surfaces and biomolecules, and identification of surface-enriched additives and contaminants. Surface-MALDI-MS is rapid, experimentally convenient, overcomes limitations in mass resolution and sensitivity of established biochemical techniques such as SDS-PAGE, and can in some circumstances be used for the quantitative analysis of adsorbed protein amounts. At this early stage of development, however, limitations exist: in some cases proteins are not detectable, which appears to be related to tight surface binding. This review summarizes ways in which Surface-MALDI-MS methods have been applied to the study of a range of issues in biomaterials surfaces research.

Quantitative Submonolayer Spatial Mapping of Arg-Gly-Asp-Containing Peptide Organomercaptan Gradients on Gold with Matrix-Assisted Laser Desorption/Ionization Mass Spectrometry

Peptides containing the tripeptide sequence Arg-Gly-Asp (RGD) have the ability to bind to members of the integrin superfamily of cell-surface receptors and direct cellular adhesion and haptotaxis. The goal of this work is the development of a rapid and effective method for the quantitative submonolayer spatial composition mapping of surfaces displaying molecular assemblies of RGD-containing organomercaptan peptides on a Au surface using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-MS). Quantitation of the RGD peptide is achieved by determining the peak intensity of the protonated molecular ion, (M + H)+, relative to the (M + H)+ peak for an internal standard, which is similar chemically but with glutamic acid (E) substituted for aspartic acid (D). Using optimized sample preparation procedures, a bilinear calibration was obtained between the quantitative peak intensity ratio and the mole fraction of the RGD-containing peptide. Quantitative compositions were determined with relative standard deviations of <10%, even in the presence of 10x spot-to-spot variations in the absolute signal intensities, by using this internal standard approach. This MALDI-MS quantitative analysis method was employed to probe variable-width two-component counterpropagating electrochemically generated gradients of the two peptides, prepared by coupling in-plane electrochemical potential gradients with the electrosorption reactions of organothiols to vary the composition laterally. The measured lateral composition profiles match the quasi-linear potential gradient model and yield profiles that overlap to a high degree of fidelity in potential space. Thus, MALDI-MS spatial composition mapping should become a powerful tool for the preparation of designed surfaces facilitating the study of cellular adhesion and motility and cell-cell interactions.

Non-specific, on-probe cleanup methods for MALDI-MS samples

High concentrations of contaminants such as salts and surfactants are often present in biological samples to solubilize or stabilize analytes such as proteins. Unfortunately, the presence of those contaminants often precludes direct analysis by MALDI-MS. Selective adsorption of analytes directly on modified MALDI probes, followed by rinsing to remove contaminants, overcomes this problem. This review focuses on various modifications of MALDI probes to allow the adsorption of proteins and DNA, even in a large excess of salt or surfactant. Interfaces deposited on the MALDI probes to adsorb analytes include films of commercial polymers, thin layers of matrix crystals, self-assembled monolayers, and ultrathin polymer films. Hydrophobic and ionic interactions both effect analyte adsorption on those interfaces, and patterned interfaces allow the concentration and purification of analyte molecules.

Analysis of Self-Assembled Monolayer Interfaces by Electrospray Mass Spectrometry: A Gentle Approach

A general mass spectrometry technique for the characterization of alkanethiol-modified surfaces is presented. Alkanethiol self-assembled onto a gold surface (in this case, peptides were attached to the gold surface via a thiolate bond) was reductively desorbed in 0.05 M KOH in the presence of octadecyl-derivatized silica gel. The peptide adsorbed onto the silica gel, whereupon it could be filtered, washed to remove any salts, and then eluted using a mixture of 4:1 v/v methanol/water. The eluant containing the peptide was injected into a Fourier transform ion-cyclotron resonance mass spectrometer (FTICR/MS) via electrospray ionization. The spectrum showed no fragmentation of the peptide, demonstrating the gentleness of the technique. This simple procedure is not limited to FTICR/MS and could be adapted to other mass spectrometers.

In situ liquid-liquid extraction as a sample preparation method for matrix-assisted laser desorption/ionization MS analysis of polypeptide mixtures

A novel liquid-liquid extraction (LLE) procedure was investigated for preparation of peptide and protein samples for matrix-assisted laser desorption/ionization mass spectrometry (MALDI MS). LLE using ethyl acetate as the water-immiscible organic solvent enabled segregation of hydrophobic and hydrophilic polypeptides in mixtures, thereby reducing the complexity of mass spectra obtained by MALDI MS. The LLE technique was optimized for rapid and sensitive in situ (on-target) sample preparation for MALDI MS analysis of proteins and peptides at low-picomole and subpicomole levels. Addition of MALDI matrix to the organic solvent enhanced the efficiency of the LLE-MALDI MS method for analysis of hydrophobic peptides and proteins. LLE-MALDI MS enabled the detection of the hydrophobic membrane protein bacteriorhodopsin as a component in a simple protein mixture. Peptide mixtures containing phosphorylated, glycosylated, or acylated peptides were successfully separated and analyzed by the in situ LLE-MALDI MS technique and demonstrate the potential of this method for enhanced separation and structural analysis of posttranslationally modified peptides in proteomics research.

Enhanced affinity capture MALDI-TOF MS: orientation of an immunoglobulin G using recombinant protein G

Although immobilization of antigen-specific immunoglobulins onto matrix-assisted laser desorption/ionization (MALDI) targets allows the specific detection and enrichment of an antigen from complex biological fluids, the process of antibody immobilization is not optimal. The principal reason is that the antibody can bind to the template in various orientations, many of which block antigen recognition. An affinity capture MALDI mass spectrometry methodology was developed by covalently immobilizing an Fc receptor (recombinant protein G) onto MALDI gold targets for the purpose of orientating an immunoglobulin G, with the Fab domains pointing away from the target surface. The pregnancy and cancer marker, human chorionic gonadotropin beta core fragment (hCGbetacf), was our chosen test substance. To optimize the methodology, different surface densities of protein G and immunoglobulin were achieved by employing varying concentrations for immobilization. Captured amounts of hCGbetacf were compared using an external standard (cytochrome c). Orientation of immunoglobulin resulted in an approximately 3-fold increase in MALDI signal compared to using randomly immobilized antibody. Higher antibody concentrations resulted in diminished MALDI signals, which were explained by steric hindrance. Purification and enrichment of hCGbetacf was achieved from a test solution containing contaminant peptides and proteins using oriented immunoglobulins on-target.

Determination of beta-2 microglobulin levels in plasma using a high-throughput mass spectrometric immunoassay system

A high-throughput mass spectrometric immunoassay (MSIA) system for the analysis of proteins directly from biological fluids is reported. A 96-well-format robotic workstation equipped with antibody-derivatized affinity pipet tips was used for the parallel extraction of specific proteins from samples and subsequent deposition onto 96-well arrayed matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOFMS) targets. Interferences from nonspecifically bound proteins were minimized through choice of appropriate affinity pipet tip derivatization chemistries. Sample preparation for MALDI-TOFMS was enhanced through the use of hydrophobic/hydrophilic contrasting targets, which also presented functionalities found to promote matrix/analyte crystal growth. Automated mass spectrometry was used in the unattended acquisition of data, resulting in an analysis rate of approximately 100 samples/h (biological fluid-->data). The quantitative MSIA of beta2m levels present in human plasma samples is given as illustration.

Monitoring the expression and purification of recombinant proteins by MALDI-TOF mass spectrometry

1Samples coming from biologic sources usually contain several contaminants that interfere seriously with Mass Spectrometry (MS) measurements. In this paper we report the application of MALDI-TOF MS to monitor recombinant protein expression and purification. The technique is based on the use of a C18 resin to clean and concentrate proteins in batch. The utility of this method is demonstrated for samples coming from different bacterial cultures expressing secreted and intracellular proteins ranging from 4 to 53 kDa. MALDI-TOF MS of peptide and proteins can be accomplished directly from complex bacterial cultures or from any purification step in a few minutes using the conventional stainless steel sample targets, allowing for a nearly instantaneous monitoring of the nature and integrity of recombinant expression products.

Application of nonporous polyurethane (PU) membranes and porous PU thin films as sample supports for MALDI-MS of wheat proteins

Non-porous polyurethane (PU) membranes and porous PU thin films are used as sample supports for MALDI-TOFMS. Mass spectra obtained are compared with those acquired using metal targets and the crushed matrix method. The compounds characterized are wheat proteins which consist of moderately water-soluble gliadins, and of water-insoluble low molecular weight (LMW) and high molecular weight (HMW) glutenins. Mass spectra obtained using the PU supports are in general of good quality, and this method of sample preparation is the most convenient for sample handling. In the case of gliadins and LMW glutenins, the spectra obtained on PU are comparable with those obtained using metal supports. Isolation of the LMW and HMW wheat proteins characterized in this study requires the use of buffers incompatible with MALDI. Spectra of samples containing buffer components on PU supports are of better quality than those obtained using the crushed matrix method. This effect is attributed to stronger protein binding onto the PU supports, which allows for extensive washing and removal of water soluble buffer components. The PU film, when cast onto a MALDI probe, is porous and flat in topology. The differences in surface characteristics between the PU film and the PU membrane result in slight variations in the mass spectra. The extent of surface charging, observed significantly using 50 µm thick PU membranes, decreases with 25 µm membranes and becomes insignificant with PU thin films. An important advantage of using the PU supports is the possibility of preparing samples on the film or membrane in the field and of analysing them at a later time. This is especially important when samples are susceptible to chemical degradation in solution. These proteins are known to degrade while stored in solution. We have thus incorporated the use of PU membrane–film supports into our routine analysis of these proteins.Key words: gliadins, glutenins, MALDI, membrane supports, polymeric supports, time-of-flight analysis.