Thin-Layer Matrix Sublimation with Vapor-Sorption Induced Co-Crystallization for Sensitive and Reproducible SAMDI-TOF MS Analysis of Protein Biosensors

Coupling immunoassays on self-assembled monolayers (SAMs) to matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry (MS) provides improved assay selectivity compared with traditional photometric detection techniques. We show that thin-layer-transfer (TLT) of ??-cyano-4-hydroxycinnaminic acid (CHCA) MALDI matrix via vacuum sublimation followed by organic solvent-based vapor-sorption induced co-crystallization (VIC) results in unique matrix/analyte co-crystallization tendencies that optimizes assay reproducibility and sensitivity. Unique matrix crystal morphologies resulted from VIC solvent vapors, indicating nucleation and crystal growth characteristics depend upon VIC parameters. We observed that CHCA microcrystals generated by methanol VIC resulted in >10× better sensitivity, increased analyte charging, and improved precision compared with dried droplet measurements. The uniformity of matrix/analyte co-crystallization across planar immunoassays directed at intact proteins yielded low spectral variation for single shot replicates (18.5?% relative standard deviation, RSD) and signal averaged spectra (<10?% RSD). We envision that TLT and VIC for MALDI-TOF will enable high-throughput, reproducible array-based immunoassays for protein molecular diagnostic assays in diverse biochemical and clinical applications.     

Rapid screening of anthocyanins in berry samples by surfactant-mediated matrix-assisted laser desorption/ionization time-of-flight mass spectrometry

Surfactant-mediated matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS) has been used for the identification of flavonoids from three berry extracts: lowbush blueberry (Vaccinium angustifolium), lingonberry (Vaccinium vitis-idaea), and blackberry (Rubus armeniacus). The addition of the surfactant led to suppression of matrix ions from both alpha-cyano-4-hydroxycinnamic acid (CHCA) and 2',4',6'-trihydroxyacetophenone (THAP). This is the first case of this method being successfully employed with a matrix other than CHCA. It was observed that CHCA led to a great deal of fragmentation of the sugar moiety from glycosides, whereas THAP produced more intact glycoside molecules, and thus leads to better characterization of the flavonoids in a berry sample. The flavonoids were characterized and quantified by liquid chromatography/electrospray ionization mass spectrometry (LC/ESI-MS) with UV detection. Although MALDI-TOF-MS did not lead to the identification of as many flavonoids, it did enable us to identify many anthocyanin glycosides. Quantification was achieved and demonstrated that use of the THAP matrix can enable quantification of the intact glycosides with relative standard deviation (RSD) values of less than 10% with surfactant addition. These results are comparable with LC results. MALDI-TOF-MS with THAP matrix thus provided a rapid method for the qualitative screening of these compounds. It took only a few minutes, greatly reducing the analysis time from that in traditional LC/MS methods.     

Evaluation of matrix‐assisted laser desorption/ionization (MALDI) preparation techniques for surface characterization of intact Fusarium spores by MALDI linear time‐of‐flight mass spectrometry

Unambiguous identification of mycotoxin‐producing fungal species as Fusarium is of great relevance to agriculture and the food‐producing industry as well as in medicine. Protein profiles of intact fungal spores, such as Penicillium, Aspergillus and Trichoderma, derived from matrix‐assisted laser desorption/ionization time‐of‐flight mass spectrometry (MALDI‐TOF MS) were shown to provide a rapid and straightforward method for species identification and characterization. In this study, we applied this approach to five different Fusarium spp. strains which are known to affect the growth of different grain plants. To obtain a suitable MALDI matrix system and sample preparation method, thin‐layer, dried‐droplet and sandwich methods and several MALDI matrices, namely CHCA, DHB, FA, SA and THAP dissolved in various solvent mixtures (organic solvents such as ACN, MeOH, EtOH and iPrOH and for the aqueous phase water and 0.1% TFA), were evaluated in terms of mass spectrometric pattern and signal intensities. The most significant peptide/protein profiles were obtained with 10 mg ferulic acid (FA) in 1 mL ACN/0.1% TFA (7:3, v/v) used as matrix system. Mixing the spores with the matrix solution directly on the MALDI target (dried‐droplet technique) resulted in an evenly distributed spores/matrix crystal layer, yielding highly reproducible peptide/protein profiles from the spore surfaces. Numerous abundant ions throughout the investigated m/z range (m/z 1500–15 000) could be detected. Differences in the obtained mass spectral patterns allowed the differentiation of spores of various Fusarium species. Copyright © 2009 John Wiley & Sons, Ltd.     

Single-strand conformation polymorphism analysis of genetic variation in Labiostrongylus longispicularis from kangaroos

Single-strand conformation polymorphism (SSCP) analysis was employed to screen for sequence heterogeneity in the second internal transcribed spacer (ITS-2) of ribosomal (r) DNA of Labiostrongylus longispicularis, a parasitic strongylid nematode occuring in some species of kangaroo in different geographical regions of Australia. The results showed that most of the nematodes screened had different SSCP profiles, which were subsequently shown to correspond to polymorphisms and/or an indel in the ITS-2 sequence. These variable sites related mainly to unpaired regions of the predicted secondary structure of the precursor rRNA molecule. SSCP profiles could be used to distinguish L. longispicularis in Macropus robustus robustus (New South Wales) from L. longispicularis in Macropus robustus erubescens and Macropus rufus (South Australia). This difference corresponded to a transversional change in the ITS-2 sequence at alignment position 82. The study demonstrated clearly the effectiveness of SSCP analysis for future large-scale population genetic studies of L. longispicularis in order to test the hypothesis that L. longispicularis from different geographical regions represents multiple sibling species.     

Novel approach to enhance sensitivity in surface‐assisted laser desorption/ionization mass spectrometry imaging using deposited organic‐inorganic hybrid matrices

Sample pretreatment is key to obtaining good data in matrix‐assisted laser desorption/ionization mass spectrometry imaging (MALDI‐MSI). Although sublimation is one of the best methods for obtaining homogenously fine organic matrix crystals, its sensitivity can be low due to the lack of a solvent extraction effect. We investigated the effect of incorporating a thin film of metal formed by zirconium (Zr) sputtering into the sublimation process for MALDI matrix deposition for improving the detection sensitivity in mouse liver tissue sections treated with olanzapine. The matrix‐enhanced surface‐assisted laser desorption/ionization (ME‐SALDI) method, where a matrix was formed by sputtering Zr to form a thin nanoparticle layer before depositing MALDI organic matrix comprising α‐cyano‐4‐hydroxycinnamic acid (CHCA) by sublimation, resulted in a significant improvement in sensitivity, with the ion intensity of olanzapine being about 1800 times that observed using the MALDI method, comprising CHCA sublimation alone. When Zr sputtering was performed after CHCA deposition, however, no such enhancement in sensitivity was observed. The enhanced sensitivity due to Zr sputtering was also observed when the CHCA solution was applied by spraying, being about twice as high as that observed by CHCA spraying alone. In addition, the detection sensitivity of these various pretreatment methods was similar for endogenous glutathione. Given that sample preparation using the ME‐SALDI‐MSI method, which combines Zr sputtering with the sublimation method for depositing an organic matrix, does not involve a solvent, delocalization problems such as migration of analytes observed after matrix spraying and washing with aqueous solutions as sample pretreatment are not expected. Therefore, ME‐Zr‐SALDI‐MSI is a novel sample pretreatment method that can improve the sensitivity of analytes while maintaining high spatial resolution in MALDI‐MSI.     

A second‐generation ionic liquid matrix‐assisted laser desorption/ionization matrix for effective mass spectrometric analysis of biodegradable polymers

A second generation ionic liquid matrix (ILM), N,N‐diisopropylethylammonium α‐cyano‐4‐hydroxycinnamate (DEA‐CHCA), was developed for the characterization of polar biodegradable polymers. It is compared with five solid matrices typically used for the characterization of these polymers and one other new ILM. It is shown that use of the ILM, DEA‐CHCA, allows maximum signal with minimum laser intensity which minimizes polymer degradation. In these conditions, the DEA‐CHCA ILM is able to assist in the ionization of analytes in an efficient but soft manner. These qualities produce spectra that allow an accurate and sensitive determination of the number average molecular weights, weight average m.w., and polydispersity index of labile polar polymers. With such polymers, many solid matrices produce spectra showing extensive polymer degradation leading to the underestimation of molecular weights. The distribution of intact analyte peaks obtained with the ILM DEA‐CHCA allows for identification of the fine structure of complex copolymers. ILMs were much less susceptible to effects of extraction delay times on molecular weight determination than were solid matrices. The liquid nature of the matrix is an important reason for the outstanding results obtained for labile analyte polymers. No comparable results could be obtained with any known solid matrices or other ILMs. In many cases, the manufacturers' listed molecular weights and polydispersity measurements for biodegradable polymers are determined by size‐exclusion chromatography and the data obtained by that method may differ considerably from the high‐precision matrix‐assisted laser desorption/ionization time‐of‐flight mass spectrometry (MALDI‐TOF‐MS) results presented here. Copyright © 2009 John Wiley & Sons, Ltd.     

Detection of Amine Impurity and Quality Assessment of the MALDI Matrix α-Cyano-4-Hydroxy-Cinnamic Acid for Peptide Analysis in the amol Range

We have studied sample preparation conditions to increase the reproducibility of positive UV-MALDI-TOF mass spectrometry of peptides in the amol range. By evaluating several α-cyano-4-hydroxy-cinnamic acid (CHCA) matrix batches and preparation protocols, it became apparent that two factors have a large influence on the reproducibility and the quality of the generated peptide mass spectra: (1) the selection of the CHCA matrix, which allows the most sensitive measurements and an easier finding of the “sweet spots,” and (2) the amount of the sample volume deposited onto the thin crystalline matrix layer. We have studied in detail the influence of a contaminant, coming from commercial CHCA matrix batches, on sensitivity of generated peptide mass spectra in the amol as well as fmol range of a tryptic peptide mixture. The structure of the contaminant, N,N-dimethylbutyl amine, was determined by applying MALDI-FT-ICR mass spectrometry experiments for elemental composition and MALDI high energy CID experiments utilizing a tandem mass spectrometer (TOF/RTOF). A recrystallization of heavily contaminated CHCA batches that reduces or eliminates the determined impurity is described. Furthermore, a fast and reliable method for the assessment of CHCA matrix batches prior to tryptic peptide MALDI mass spectrometric analyses is presented.

High-speed counter-current chromatography for the study of defense metabolites in wheat. Characterization of 5,6-O-methyl trans-aconitic acid

High-speed counter-current chromatography (HSCCC) methods were developed for the study of induced defense metabolites in wheat (Triticum aestivum) against powdery mildew (Blumeria graminis f. sp. tritici). A single HSCCC purification step afforded extraction of mg-quantities of an induced compound with antifungal activity. Subsequent LC-MS and NMR analyses have led to the characterization of 5,6-O-methyl trans-aconitic acid, the first such report of this compound in a plant species. The inducible nature of aconitic acid was evidenced by comparing the metabolite profiles of leaf extracts from plants treated or not with soluble silicon and infected or not with powdery mildew. In a second step, dual-mode HSCCC was used to enhance the separation of other forms of aconitic acid in wheat. Based on these results, it was concluded that 5,6-O-methyl trans-aconitic acid plays an important role as a defense molecule in wheat plants and that HSCCC is a powerful separation method for purifying such compounds from complex plant-pathogen interactions.     

Single drop microextraction as a concentrating probe for rapid screening of low molecular weight drugs from human urine in atmospheric-pressure matrix-assisted laser desorption/ionization mass spectrometry

The present work reports the development of a new analytical procedure for simple and rapid screening of low molecular weight drugs (<500 Da) from human urine samples by atmospheric-pressure matrix-assisted laser desorption/ionization mass spectrometry (AP-MALDI-MS) combined with single drop microextraction (SDME). The success of the proposed method is due to the use of methyltrioctylammonium chloride (MTOAC) as additive to avoid the noise arising from the matrix ions (alpha-cyano-4-hydroxycinnamic acid (CHCA)). SDME also aided in alleviating the interferences arising from other matrix ions present in the urine samples prior to AP-MALDI-MS analysis. Factors affecting the extraction efficiency of drugs, such as selection of solvent, stirring speed, extraction time, exposure volume of extraction phase and salt addition, have been optimized. The optimum molar ratio of CHCA/MTOAC that gave the minimum background noise of CHCA ions was 700:1. The limit of detection (LOD) and relative standard deviation (RSD) of the method were in the ranges 0.3-1.6 microM and 7.8-11.4%, respectively. The SDME method was compared with liquid-liquid extraction (LLE) and hollow fiber liquid-phase microextraction (HF-LPME) to evaluate the compatibility of the present method in the extraction of drugs from urine samples. The role of MTOAC as matrix ion signal suppressor and SDME as analyte-separating device in the rapid screening of low molecular weight drugs from human urine samples using AP-MALDI/MS has been reported.     

Proteome profile of salt gland‐rich epidermis extracted from a salt‐tolerant tree species

Preparation of proteins from salt‐gland‐rich tissues of mangrove plant is necessary for a systematic study of proteins involved in the plant's unique desalination mechanism. Extraction of high‐quality proteins from the leaves of mangrove tree species, however, is difficult due to the presence of high levels of endogenous phenolic compounds. In our study, preparation of proteins from only a part of the leaf tissues (i.e. salt gland‐rich epidermal layers) was required, rendering extraction even more challenging. By comparing several extraction methods, we developed a reliable procedure for obtaining proteins from salt gland‐rich tissues of the mangrove species Avicennia officinalis. Protein extraction was markedly improved using a phenol‐based extraction method. Greater resolution 1D protein gel profiles could be obtained. More promising proteome profiles could be obtained through 1D‐LC‐MS/MS. The number of proteins detected was twice as much as compared to TUTS extraction method. Focusing on proteins that were solely present in each extraction method, phenol‐based extracts contained nearly ten times more proteins than those in the extracts without using phenol. The approach could thus be applied for downstream high‐throughput proteomic analyses involving LC‐MS/MS or equivalent. The proteomics data presented herein are available via ProteomeXchange with identifier PXD001691.     

Effect of the addition of diammonium citrate to <Emphasis Type="Italic">α</Emphasis>-cyano-4-hydroxycinnamic acid (CHCA) matrix for the detection of phosphorylated peptide in phosphorylation reactions using cell and tissue lysates

The ionization of phosphorylated peptides is usually suppressed by non-phosphorylated peptides when alpha-cyano-4-hydroxycinnamic acid (CHCA) is used as a matrix for matrix-assisted laser desorption/ionization-time-of-Flight (MALDI-TOF) mass spectrometry analysis. In the present study, we examined the effect of diammonium citrate addition to the CHCA matrix on the detection of phosphorylated peptides. Substrates for protein kinase C (PKC) and c-Src were synthesized and phosphorylated by reaction with cell and tissue lysate samples. The addition of diammonium citrate to the CHCA matrix increased the sensitivity for distinguishing phosphorylated peptides from background noise. However, the effect depended on substrate concentration.     

Improved spectra for MALDI MSI of peptides using ammonium phosphate monobasic in MALDI matrix

MALDI mass spectrometry imaging (MSI) enables analysis of peptides along with histology. However, there are several critical steps in MALDI MSI of peptides, 1 of which is spectral quality. Suppression of MALDI matrix clusters by the aid of ammonium salts in MALDI experiments is well known. It is asserted that addition of ammonium salts dissociates potential matrix adducts and thereafter decreases matrix cluster formation. Consequently, MALDI MS sensitivity and mass accuracy increase. Up to our knowledge, a limited number of MALDI MSI studies used ammonium salts as matrix additives to suppress matrix clusters and enhance peptide signals. In this work, we investigated the effect of ammonium phosphate monobasic (AmP) as alpha‐cyano‐4‐hydroxycinnamic acid (α‐CHCA) matrix additive in MALDI MSI of peptides. Prior to MALDI MSI, the effect of varying concentrations of AmP in α‐CHCA was assessed in bovine serum albumin tryptic digests and compared with the control (α‐CHCA without AmP). Based on our data, the addition of AmP as matrix additive decreased matrix cluster formation regardless of its concentration, and specifically, 8 mM AmP and 10 mM AmP increased bovine serum albumin peptide signal intensities. In MALDI MSI of peptides, both 8 and 10 mM AmP in α‐CHCA improved peptide signals especially in the mass range of m/z 2000 to 3000. In particular, 9 peptide signals were found to have differential intensities within the tissues deposited with AmP in α‐CHCA (AUC > 0.60). To the best of our knowledge, this is the first MALDI MSI of peptides work investigating different concentrations of AmP as α‐CHCA matrix additive to enhance peptide signals in formalin‐fixed paraffin‐embedded (FFPE) tissues. Further, AmP as part of α‐CHCA matrix could enhance protein identifications and support MALDI MSI‐based proteomic approaches.     

Charge state distribution shifting of protein ions observed in matrix-assisted laser desorption ionization mass spectrometry

By using a new sample preparation method for matrix-assisted laser desorption ionization, a significant shift to lower mass-to-charge values can be obtained for many protein samples. The sample preparation technique involves the creation of a thin film of protein-doped -cyano-4-hydroxycinnamic acid (CHCA) matrix formed in the presence of glycerol on top of a previously deposited pad of CHCA matrix. The higher charge states were not observed if the laser power was significantly above the threshold needed to produce protein molecular ions. Similar spectra were observed when samples were prepared in the presence of urea. The phenomenon was specific for the CHCA matrix because no effects were observed when sinapinic acid (3,5-dimethoxy-4-hydroxy-trans-cinnamic acid) and 2-(4-hydroxyphenylazo) benzoic acid matrices were used with the new sample preparation method.     

Degree of Ionization in MALDI of Peptides: Thermal Explanation for the Gas-Phase Ion Formation

Degree of ionization (DI) in matrix-assisted laser desorption ionization (MALDI) was measured for five peptides using α-cyano-4-hydroxycinnanmic acid (CHCA) as the matrix. DIs were low 10(-4) for peptides and 10(-7) for CHCA. Total number of ions (i.e., peptide plus matrix) was the same regardless of peptides and their concentration, setting the number of gas-phase ions generated from a pure matrix as the upper limit to that of peptide ions. Positively charged cluster ions were too weak to support the ion formation via such ions. The total number of gas-phase ions generated by MALDI, and that from pure CHCA, was unaffected by the laser pulse energy, invalidating laser-induced ionization of matrix molecules as the mechanism for the primary ion formation. Instead, the excitation of matrix by laser is simply a way of supplying thermal energy to the sample. Accepting strong Coulomb attraction felt by cations in a solid sample, we propose three hypotheses for gas-phase peptide ion formation. In Hypothesis 1, they originate from the dielectrically screened peptide ions in the sample. In Hypothesis 2, the preformed peptide ions are released as part of neutral ion pairs, which generate gas-phase peptide ions via reaction with matrix-derived cations. In Hypothesis 3, neutral peptides released by ablation get protonated via reaction with matrix-derived cations.     

Combination of two matrices results in improved performance of MALDI MS for peptide mass mapping and protein analysis

A new sample preparation method for MALDI based on the use of a mixture of the two commonly used matrices, DHB and CHCA, is described. The matrix mixture preparation results in increased sequence coverage and spot-to-spot reproducibility for peptide mass mapping compared to the use of the single matrix components. This results in more reliable protein identification in proteomics studies and facilitates automated data acquisition. This method shows better tolerance towards salts and impurities, eliminating the need for pre-purification of the samples. It has also been found to be advantageous for the analysis of intact proteins, and especially for glycoproteins. The mixture allows the presence of rather high concentrations of urea in the sample solutions.     

Protein extraction for 2-DE from the lamina of Ecklonia kurome (laminariales): recalcitrant tissue containing high levels of viscous polysaccharides

Extraction of proteins from the tissues of laminarialean algae, i.e. kelp, is difficult due to high levels of nonprotein interfering compounds, mainly viscous polysaccharides. To establish proteomic analysis of kelp species, an ethanol/phenol extraction method was developed and compared to other popular methods. Proteins were extracted with phenol from crude protein powder, obtained by homogenizing the kelp tissues in ice-cold ethanol. The ethanol/phenol method produced high-quality proteins of the highest purity from the lamina of Ecklonia kurome, one of the Japanese dominant laminarialean algae. This method gave well-resolved 1-D SDS-PAGE or 2-DE images with low background and the highest number of bands or spots. In particular, proteins with neutral to basic pI's were efficiently extracted. Furthermore, 27 spots on the 2-DE gel were extensively identified by MALDI-TOF/TOF analysis. To the best of our knowledge, this is the first report of a protocol for protein extraction from kelp tissues that gives satisfactory 2-D protein profiles. It is expected that the protocol can be applied to other algae tissues or other recalcitrant plant tissues containing high levels of nonprotein interfering compounds.     

ATR/FTIR characterization of Steinernema glaseri and Heterorhabditis indica

The use of Fourier transform mid-infrared spectroscopy with attenuated total reflection for characterizing entomopathogenic nematodes is evaluated for the first time. The resulting spectra of Steinernema glaseri and Heterorhabditis indica were compared with the spectrum of Caenorhabditis elegans. In the absorption spectra generated by the nematodes samples, the absorption bands were assigned to the molecular species and some important components were identified including triglycerides, trehalose, glycogen and collagen. Also, the use of star diagrams for the fingerprint section of nematode spectra for separating genera is discussed.     

Optimization of a MALDI TOF-TOF mass spectrometer for intact protein analysis

A MALDI TOF-TOF instrument was optimized and evaluated for intact protein analysis by tandem mass spectrometry. Ion source voltages and delay times were adjusted to affect an up to a 10-fold improvement in fragment ion yield compared to data obtained using default settings employed in peptide analysis. For large peptides (3-4.5 kDa), up to 90% of all possible b- and y-fragment ions were observed, which provides sufficient information for de novo sequencing and unambiguous protein identification. Product ion signals associated with preferential cleavages C-terminal to aspartic acid and glutamic acid residues and N-terminal to proline residues became dominant with increased protein molecular weight. Matrix effects were also evaluated and, among the eight matrices examined, alpha-cyano-4-hydroxycinnamic acid (CHCA) was found to produce the best intact protein tandem mass spectra for proteins up to 12 kDa. Optimized performance yielded detection limits of 50-125 fmol for proteins of 4 and 12 kDa, respectively. This improved performance has yielded an instrument with potential to be a useful tool in proteomic investigations via analysis of intact proteins.