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.     

Phosphoric acid as a matrix additive for MALDI MS analysis of phosphopeptides and phosphoproteins

Phosphopeptides are often detected with low efficiency by MALDI MS analysis of peptide mixtures. In an effort to improve the phosphopeptide ion response in MALDI MS, we investigated the effects of adding low concentrations of organic and inorganic acids during peptide sample preparation in 2,5-dihydroxybenzoic acid (2,5-DHB) matrix. Phosphoric acid in combination with 2,5-DHB matrix significantly enhanced phosphopeptide ion signals in MALDI mass spectra of crude peptide mixtures derived from the phosphorylated proteins alpha-casein and beta-casein. The beneficial effects of adding up to 1% phosphoric acid to 2,5-DHB were also observed in LC-MALDI-MS analysis of tryptic phosphopeptides of B. subtilis PrkC phosphoprotein. Finally, the mass resolution of MALDI mass spectra of intact proteins was significantly improved by using phosphoric acid in 2,5-DHB matrix.     

Two-layer sample preparation: a method for MALDI-MS analysis of complex peptide and protein mixtures

The analytical performance of matrix-assisted laser desorption/ionization (MALDI) mass spectrometry for direct analysis of peptide and protein mixtures is strongly dependent on the sample and matrix preparation. A two-layer sample preparation method is demonstrated to be very effective for analyzing complex mixtures. In this method, the first layer on the MALDI probe is the densely packed matrix microcrystals formed by fast solvent evaporation of a matrix solution. A mixture solution containing both matrix and sample is then deposited onto the first layer to form uniform analyte/matrix micrococrystals. It is found that the addition of matrix to the second-layer sample solution proves to be critical in analyzing mixtures of peptides and proteins covering a broad mass range. The effect of solvent conditions for preparing the second-layer solution is discussed. The application of this method is demonstrated for the analysis of cow's milk where milk proteins as well as peptide fragments produced from proteins by indigenous proteinases are detected. Direct analyses of peptides and proteins from a bacteria extract and crude egg white are also illustrated.     

Two-layer sample preparation method for MALDI mass spectrometric analysis of protein and peptide samples containing sodium dodecyl sulfate

Sodium dodecyl sulfate (SDS) is widely used in protein sample workup. However, many mass spectrometric methods cannot tolerate the presence of this strong surfactant in a protein sample. We present a practical and robust technique based on a two-layer matrix/sample deposition method for the analysis of protein and peptide samples containing SDS by matrix-assisted laser desorption ionization mass spectrometry (MALDI-MS). The two-layer method involves the deposition of a mixture of sample and matrix on top of a thin layer of matrix crystals. It was found that for SDS-containing samples, the intensity of the MALDI signals can be affected by the conditions of sample preparation: on-probe washing, choice of matrix, deposition method, solvent system, and protein-to-SDS ratio. However, we found that, under appropriate conditions, the two-layer method gave reliable MALDI signals for samples with levels of SDS up to approximately 1%. The applications of this method are demonstrated for MALDI analysis of hydrophobic membrane proteins as well as bacterial extracts. We envision that this two-layer method capable of handling impure samples including those containing SDS will play an important role in protein molecular weight analysis as well as in proteome identification by MALDI-MS and MS/MS.     

Device for the reversed-phase separation and on-target deposition of peptides incorporating a hydrophobic sample barrier for matrix-assisted laser desorption/ionization mass spectrometry

The separation of peptide mixtures from proteolytic cleavage is often necessary prior to mass spectrometry (MS) to enhance sensitivity and peptide mapping coverage. When buffers, salts, and other higher abundance peptides/contaminants are present, competition for charge during the electrospray ionization and matrix-assisted laser desorption/ionization (MALDI) processes can lead to ion suppression for the targeted analyte(s). In this note, a simple reversed-phase microcolumn sample separation and deposition device (Sep-Dep) is described. The use of this device improves or renders possible the analysis of complex or contaminated peptide mixtures by MALDI-MS. The method is simple and inexpensive and utilizes single-use low-cost Geloader-type columns packed with reversed-phase material. The device described utilizes an open column, allowing for a gradient or narrow-step gradient to be applied by any solvent delivery system or manually with a pipet. A key feature of the device is a deposition chamber that can be custom-built to hold any MALDI target. The Sep-Dep device is attached directly to an in-house vacuum line and draws solvent from the open-ended LC column. The elution of separated peptides is performed directly onto a target that has been treated with a hydrophobic barrier. This barrier effectively isolates fractions and improves the quality and morphology of the matrix crystals. The method produces efficient separations of proteolytic peptides, significantly reducing signal suppression effects in MALDI.     

Characterization of synthetic polymers by MALDI-TOF/MS: investigation into new methods of sample target preparation and consequence on mass spectrum finger print

Characterization of synthetic polymers by Matrix assisted laser desorption (MALDI) is limited by the solubility of different oligomers in a suitable solvent, and the fingerprint of the mass spectrum is affected by the properties of solvents employed (eg., pH, secondary solvents, evaporation) during sample target preparation. If solvents are not used during sample target preparation, then solvent properties should not play an important role in determining the quality of the MALDI mass spectrum. We report here two solventless approaches for sample target preparation. It was observed that Poly(ethylene glycol) 6000 (PEG) showed the same molecular mass distribution in different modes of sample target preparation. Fluorinated polymer used in these studies was affected by sample target preparation protocol and by target surface. Pyrolysis of PEG oligomers was observed in all the methods of sample target preparation. The desorbed high mass neutral oligomers fragment to give small oligomers which are then cationized by the desolvation of the cationized matrix clusters. Moreover, the origin of the matrix clusters (i.e., formed in the condensed phase or in the gas phase) determines the relative intensities of PEG oligomers cationized by sodium or potassium.     

Coupling of protein HPLC to MALDI-TOF MS using an on-target device for fraction collection, concentration, digestion, desalting, and matrix/analyte cocrystallization

Multidimensional protein chromatography offers an alternative to gel-based separations for large-scale proteomic analyses of highly complex mixtures. However, these liquid separations divide the original mixtures into multitudes of discrete samples, each of which may require numerous steps of sample manipulation, such as fraction collection, buffer exchange, protease digestion, peptide desalting, and, in the case of MALDI-MS, matrix and analyte cocrystallization on target. When traditional high-flow liquid chromatography is used, large volumes of solvent must also be removed from fractions to maximize MS sensitivity. Although robotic liquid-handling devices can facilitate these steps and reduce analyst/sample contact, they remain prototypic and expensive. Here, we explore the use of a novel, one-piece elastomeric device, the BD MALDI sample concentrator, which affixes to a MALDI target to create a prestructured 96-well sample array on the target surface. We have developed methodologies to process high-flow HPLC fractions by collecting them directly into the elastomeric device and then subjecting them to sequential on-target sample concentration, buffer exchange, digestion, desalting, and matrix/analyte cocrystallization for MALDI-MS analyses. We demonstrate that this methodology enables the rapid digestion and analysis of low amounts of proteins and that it is effective in the characterization of an HPLC-fractionated protein mixture by MALDI-TOF MS followed by peptide mass fingerprinting.     

Characterization and performance of MALDI on a triple quadrupole mass spectrometer for analysis and quantification of small molecules

The usefulness of MALDI for small-molecule work has been limited by matrix chemical interference in the mass range of interest, tedious sample preparation, and various crystallization and sample deposition issues. We report instrument characterization and small-molecule quantification performance data from a high repetition rate laser MALDI ion source coupled to a triple quadrupole mass spectrometer. The high repetition rate laser improves sensitivity and precision and allows a proportional increase in sample throughput. Tandem mass spectrometry is used to discriminate the signal from the high chemical background caused by the MALDI matrix. Successful quantification requires use of an internal standard and a means of sample cleanup for typical in vitro sample compositions. This instrument combination and analysis technique is relatively insensitive to sample crystal quality and spot homogeneity. Quantitative performance results are characterized for 53 small-molecule pharmaceutical compounds and compared to those obtained by ESI-MS/MS. Further comparison between MALDI and ESI is examined, and the potential for high-throughput MALDI-MS/MS quantification is demonstrated.     

Ammonium dodecyl sulfate as an alternative to sodium dodecyl sulfate for protein sample preparation with improved performance in MALDI mass spectrometry

Sodium dodecyl sulfate (SDS) is a strong surfactant that is widely used in protein sample preparation. While protein and peptide samples containing up to approximately 1% SDS can be analyzed by matrix-assisted laser desorption/ionization mass spectrometry (MALDI MS) using a two-layer matrix/sample deposition method, the presence of SDS in a protein sample generally degrades mass resolution and mass measurement accuracy. This degradation in performance is found to be related to the formation of sodium-protein adducts in the MALDI process. If the instrument resolving power is insufficient to separate these adduct peaks from the protonated molecular ion peak, peak broadening is observed in the protein molecular ion region, and as a result, the peak centroid shifts to a higher mass. In this work, we present a method using ammonium dodecyl sulfate as a viable alternative to SDS for protein sample preparation with much improved MALDI MS performance. Three non-sodium-based dodecyl sulfate surfactants, ammonium dodecyl sulfate (ADS), hydrogen dodecyl sulfate, and tris(hydroxymethyl)aminomethane dodecyl sulfate were investigated. Of the three surfactants tested, it is found that ADS gives the best performance in MALDI. For proteins with moderate molecular masses (i.e., up to approximately 25 kDa), the presence of ADS in a protein sample does not result in significant degradation in mass resolution and accuracy, and the protonated molecular ion peak is the dominant peak in the MALDI spectrum. The ammonium adduct ions dominate the MALDI spectra when the protein mass exceeds approximately 25 kDa; however, ADS still gives better results than SDS. The behavior of ADS in gel electrophoresis was also investigated. It is shown that cell extracts dissolved in ADS can be separated by normal SDS-polyacrylamide gel electrophoresis by simply mixing them with the SDS sample buffer. The application of ADS as the surfactant for protein solubilization with improved performance in MALDI analysis is demonstrated in the study of a detergent insoluble fraction from a Raji/CD9 B-cell lymphocyte lysate.     

A solid sample preparation method that reduces signal suppression effects in the MALDI analysis of peptides

Here we report on the application of a solid-solid (SS) sample preparation protocol for the MALDI analysis of peptides and multicomponent peptide mixtures. Our results with a series of model peptides indicate that a SS MALDI sample preparation protocol is useful for the analysis of peptides in the 1-3 kDa mass range. MALDI mass spectra recorded for peptides in this size range using a SS sample preparation were of a quality comparable to spectra recorded using a conventional dried-droplet (DD) sample preparation. Our results with several model peptide mixtures indicate that one advantage of a SS sample preparation protocol for the MALDI analysis of peptides is that it can significantly reduce signal suppression effects in multicomponent mixtures. MALDI results obtained using a SS sample preparation protocol are also more reproducible than results obtained using a conventional DD sample preparation protocol.     

Identification of individual proteins in complex protein mixtures by high-resolution, high-mass-accuracy MALDI TOF-mass spectrometry analysis of in-solution thermal denaturation/enzymatic digestion

Identification of individual proteins in complex protein mixtures by high-resolution (HR), high-mass-accuracy matrix-assisted laser desorption/ionization (MALDI) time-of-flight mass spectrometry (TOF-MS) is demonstrated for synthetic protein mixtures. Instead of chemical denaturation, thermal denaturation followed by in-solution trypsin digestion is used to achieve uniform digestion of the constituents of the protein mixture. Protein identification is carried out using protein database searches with search scoring systems, which seems more effective than conventional peptide mass mapping without using a scoring system. Identification of individual proteins by MALDI HR-TOF-MS peptide mass mapping dramatically reduces data acquisition/analysis time and does not require special equipment for sample preparation/transfer prior to mass spectral analysis.     

Producing highly charged ions without solvent using laserspray ionization: a total solvent-free analysis approach at atmospheric pressure

First examples of highly charged ions in mass spectrometry (MS) produced from the solid state without using solvent during either sample preparation or mass measurement are reported. Matrix material, matrix/analyte homogenization time and frequency, atmospheric pressure (AP) to vacuum inlet temperature, and mass analyzer ion trap conditions are factors that influence the abundance of the highly charged ions created by laserspray ionization (LSI). LSI, like matrix-assisted laser desorption/ionization (MALDI), uses laser ablation of a matrix/analyte mixture from a surface to produce ions. Preparing the matrix/analyte sample without the use of solvent provides the ability to perform total solvent-free analysis (TSA) consisting of solvent-free ionization and solvent-free gas-phase separation using ion mobility spectrometry (IMS) MS. Peptides and small proteins such as non-β-amyloid components of Alzheimer's disease and bovine insulin are examples in which LSI and TSA were combined to produce multiply charged ions, similar to electrospray ionization, but without the use of solvent. Advantages using solvent-free LSI and IMS-MS include simplicity, rapid data acquisition, reduction of sample complexity, and the potential for an enhanced effective dynamic range. This is achieved by more inclusive ionization and improved separation of mixture components as a result of multiple charging.     

Toward prediction: using chemometrics for the optimization of sample preparation in MALDI-TOF MS of synthetic polymers

In recent years, matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) has become a powerful tool for the study of synthetic polymers although its mechanism is still not understood in detail. Sample preparation plays the key role in obtaining reliable MALDI mass spectra, in particular, the proper choice of matrix, cationization reagent, and solvent. There is still no general sample preparation protocol for MALDI analysis of synthetic polymers. For known synthetic polymers, such as polystyrenes and other frequently investigated polymers, application tables in review articles might be a guide for selecting a MALDI matrix, cationization reagent, and solvent. For unknown polymers (polymers which were not analyzed by MALDI-TOF MS before but whose structures are in part known from the manufacturing process and from NMR analysis as well), the selection of matrix and solvent is based upon the polarity-similarity principle. Chemometric methods provide a useful tool for the investigation of sample preparation because huge data sets can be evaluated in short time, that is, for extracting relevant information and for classification of samples, as well. Furthermore, chemometrics provide a suitable way for the selection of a proper matrix, cationization reagent, and solvent. In this paper, a prediction model is presented using the partial least-squares (PLS) regression. By applying the model, the suitability of appropriate (nontested) combinations (matrix, cationization reagent, solvent) can be predicted for a certain synthetic polymer based upon the investigation of a few combinations. This model may help find suitable combinations in a short time and serve as a starting point for the investigation of unknown polymers. Results are exemplary presented for polystyrene PS2850.     

Optimization of sample preparation for peptide sequencing by MALDI-TOF photofragment mass spectrometry

This paper describes the optimization of sample preparation for MALDI 193-nm photofragment ion time-of-flight mass spectrometry to sequence small to medium-sized peptides from peptide mixtures. We show that matrix additives, such as fructose and phenylbutyric acid have a dramatic effect on the abundance of fragment ions observed in the post-source decay spectra. A dried-droplet MALDI matrix consisting of 1:1 alpha-cyano-4-hydroxycinnamic acid/fructose proves to be an excellent matrix for photodissociation because [M + H]+ ions are formed with low internal energies, and the photofragment ion spectrum contains high abundances of sequence-informative ions. The addition of fructose appears to improve overall sample homogeneity and durability, as compared to conventional alpha-cyano-4-hydroxycinnamic acid dried-droplet preparations. MALDI-TOF photodissociation is then used to selectively sequence the peptides bradykinin (RPPGFSPFR), des-Arg9 bradykinin (RPPGFSPF), and substance P-amide (RPKPQQFFGLM-NH2) from a mixture of five peptides.     

Heterogeneity within MALDI samples as revealed by mass spectrometric imaging

While matrix-assisted laser desorption/ionization mass spectrometry (MALDI MS) has revolutionized the manner by which many large molecules are characterized, the highly variable appearance of MALDI mass spectra remains a concern. We have developed MALDI-based imaging as a diagnostic tool for examining the relationships between preparation strategy, sample morphology, and spectral quality. The imaging protocol involves the automated acquisition of mass spectra at 400-1600 positions within a single sample, followed by off-line processing and image display. Several sample types have been characterized, including a simple peptide mixture prepared in dried droplets of 2,5-dihydroxybenzoic acid and in thin films of alpha-cyano-4-hydroxycinnamic acid as well as a complex biological sample consisting of intact peptidergic neurons from the marine mollusk Aplysia californica. Imaging experiments provide a wealth of unbiased information concerning sample defects, spectral reproducibility, mass accuracy, differential analyte distributions, and the validity of internal standards.     

Dual desorption electrospray ionization-laser desorption ionization mass spectrometry on a common nanoporous alumina platform for enhanced shotgun proteomic analysis

A gold coated nanoporous alumina surface was used for dual ionization mode mass spectrometric analysis using desorption electrospray ionization (DESI) and laser desorption ionization (LDI). DESI and LDI mass spectrometry (MS) from the nanoporous alumina surface were compared with conventional electrospray ionization (ESI) mass spectrometry and matrix assisted laser desorption ionization (MALDI) for analysis of tryptic digests of proteins. Combined use of DESI and LDI offer greater peptide coverage than either method alone and comparable peptide coverage as with dual MALDI and ESI. This dual ionization technique using a common platform with same sample spot demonstrates a potential time and cost-effective tool for improved shotgun proteomic analysis.     

Combining liquid chromatography with MALDI mass spectrometry using a heated droplet interface

A novel interfacing technology is described to combine solution-based separation techniques such as liquid chromatography (LC) with matrix-assisted laser desorption ionization (MALDI) mass spectrometry. The interface includes a transfer tube having an inlet and an outlet, the inlet being adapted to accept the LC effluents and the outlet being adapted to form continuously replaced, hanging droplets of the liquid stream, and a MALDI sample plate mounted below the outlet of the transfer tube for collecting the droplets. The liquid stream in the transfer tube is heated to a temperature sufficient to cause partial evaporation of the carrier solvent from the hanging droplets. The droplets are dislodged to the MALDI plate, which is heated to above the boiling point of the carrier solvent to cause further evaporation of the carrier solvent from the collected droplets. It is found that analytes can be fractionated and deposited to a sample spot of 0.8 mm in diameter when a liquid flow rate of up to 50 microL/min and a fractionation interval of 1 min/spot are used. Flow rate of up to 200 microL/min can be used with a deposition sample spot of 2.4 mm in diameter on a commercial MALDI target. This heated droplet interface does not introduce sample loss, and the detection sensitivity of LC/MALDI is similar to that of standard MALDI, i.e., low femtomoles for peptide analysis with a microliter sample deposition. It is compatible with microbore and narrow-bore column separation, thus allowing the injection of a larger amount of sample for separation and analysis, compared to a capillary column LC/MALDI system. The detection dynamic range is shown to be in the order of 10(6) for peptide mixture analysis, which is 4 orders of magnitude greater than standard MALDI. The application of this interface for combining LC with MALDI MS/MS is demonstrated in the proteome analysis of water-soluable protein components of E. coli K12 extracts.     

Fractionation and solvent-free MALDI-MS analysis of polymers using liquid adsorption chromatography at critical conditions in combination with a multisample on-target homogenization/transfer sample preparation method

A solvent-free homogenization/transfer matrix-assisted laser desorption/ionization (MALDI) mass spectrometry (MS) method is described for the preparation and precise transfer of up to 100 samples simultaneously on a single MALDI plate. This method is demonstrated using a poly(ethylene oxide) (PEO) mixture consisting of different molecular weights (500-6000) and end groups (PEO, dimethoxy-PEO, monomethoxy monomethacrylate-PEO, and dimethacrylate-PEO) that was fractionated using liquid adsorption chromatography at critical conditions. Off-line fractionation is performed prior to the on-target homogenization/transfer solvent-free sample preparation and MALDI mass analysis. The miniaturization of the solvent-free MALDI approach allowed analysis of less than 2 microg per PEO component per fraction corresponding to approximately 200 pmol for PEO 6000. The amounts of polymer sample used for LC separation and the quality of the MS results are equivalent to the "dry spray" method; however, three times more fractions were collected and analyzed with the newly developed hyphenated approach. The off-line method eliminates optimization of, for example, spray conditions or spreading of organic solvents on the MALDI plate that occurs with droplet deposition methods. The widespread applications of MALDI make this solvent-free, multisample method particularly important as it expands the capabilities for obtaining mass measurements with great efficiencies in areas with increased sample numbers. In addition, the solvent-free method is well suited for automated MALDI analysis as it virtually eliminates the "dead-spot" phenomenon.     

MALDI MS peptide mapping performance by in-gel digestion on a probe with prestructured sample supports

Matrix-assisted laser desorption/ionization (tandem) mass spectrometry (MALDI MS) is widely used in protein chemistry and proteomics research for the identification and characterization of proteins isolated by polyacrylamide gel electrophoresis. In an effort to minimize sample handling and increase sample throughput, we have developed a novel in-gel digestion protocol where sample preparation is performed directly on a MALDI probe with prestructured sample support. The protocol consists of few sample-handling steps and has minimal consumption of reagents, making the protocol sensitive, timesaving, and cost-efficient. Performance of the on-probe sample preparation protocol was demonstrated by analysis of a set of rat liver proteins obtained from a fluorescently stained (Cy3 and SyproRuby) two-dimensional polyacrylamide gel. The success rate of protein identification by on-probe tryptic digestion and MALDI peptide mass mapping was 89%. The on-probe in-gel digestion procedure provided superior sensitivity and peptide mass mapping performance as compared to our standard in-gel digestion protocol. The on-probe digestion technique resulted in significantly improved amino acid sequence coverage of proteins, mainly due to efficient recovery and detection of large (>1.5 kDa) hydrophobic peptides. These observations indicate that numerous tryptic peptides are lost when using the standard in-gel digestion methods and sample preparation techniques for MALDI MS. This study also demonstrates that the on-probe digestion protocol combined with MALDI tandem mass spectrometry provides a robust platform for proteomics research, including protein identification and determination of posttranslational modifications.     

Importance of solubility in the sample preparation of poly(ethylene terephthalate) for MALDI TOFMS

The role of solubility in the sample preparation process for matrix-assisted laser desorption/ionization (MALDI) mass spectrometry is demonstrated for oligomeric and medium molar mass poly(ethylene terephthalate) (PET). For low molar mass oligomers (PET-1), minor discrimination effects were observed when the sample was not completely in solution. MALDI spectra of medium molar mass PET, representative of the entire molar mass distribution, were obtained only when a good solvent for PET was used, such as 1,1,1,3,3,3-hexafluoro-2-propanol (commonly referred to as HFIP), as the sample preparation solvent and dithranol as the matrix. The azeotropic composition of 70:30 CH(2)Cl(2)/HFIP better solubilizes the more nonpolar matrixes, which enables more latitude in selecting sample preparation conditions than pure HFIP. Segregation effects were observed when the azeotrope mixture was diluted with tetrahydrofuran, resulting in large molar mass distribution discrimination effects in the MALDI spectra. Dilution with CH(2)Cl(2) resulted in a significant decrease in the overall signal intensity for the entire polymer distribution. With each attempt to dilute the azeotrope, the sample after solvent evaporation was visibly heterogeneous, which resulted in shot-to-shot variability. Both examples demonstrate the importance of constant solvent composition during solvent evaporation. The compatibility of matrix and polymer was explored using relative HPLC retention times. Consistent with previous work in our laboratories, it was found that the matrix/polymer combination that has the closest match of retention time resulted in the best MALDI signal intensity.