Direct surface analysis of fungal species by matrix-assisted laser desorption/ionization mass spectrometry

In this study various methods of sample preparation and matrices were investigated to determine optimum collection and analysis criteria for fungal analysis by matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS). Intact spores and/or hyphae of Aspergillus niger, Rhizopus oryzae, Trichoderma reesei and Phanerochaete chrysosporium were analyzed by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOFMS). The fungal samples were applied to the MALDI sample target as untreated, sonicated, or acid/heat treated samples, or blotted directly from the fungal culture with double-stick tape. Ferulic acid or sinapinic acid matrix solution was layered over the dried samples and analyzed by MALDI-MS. Statistical analysis showed that simply using double-stick tape to collect and transfer to a MALDI sample plate typically worked as well as the other preparation methods, and required the least sample handling.     

Electrospray and matrix-assisted laser desorption/ionization mass spectral characterization of linear single nylon-6 oligomers

Synthetic nylon-6 single molecular mass oligomers were studied by matrix-assisted laser desorption/ionization (MALDI) and electrospray ionization (ESI) mass spectrometry. These oligomers, considered as model compounds for the study of nylon-6 polymers, gave good mass spectrometric results using both MALDI and ESI. In spite of the gentle nature of both techniques, the MALDI and ESI spectra showed evidence of end-group cleavage from the oligomer chains. MALDI-MS was found to give similar fragmentation patterns for all of the oligomer samples. An increase in doubly charged ion signals with increasing oligomer mass was observed in the ESI mass spectra, as was end-group fragmentation. Signals from oligomer clusters were observed in ESI-MS for the dimer, tetramer and hexamer, most likely due to non-covalent bonding among the low-mass oligomer molecules.     

Importance of matrix: Analyte ratio for buffer tolerance using 2,5-dihydroxybenzoic acid as a matrix in matrix-assisted laser desorption/ionization-fourier transform mass spectrometry and matrix-assisted laser desorption/ionization-time of flight

Many biological samples destined for matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) contain buffers. The presence of these buffers often inhibits the ability to obtain spectra. Here, the results of a study of the effects of six different buffers on spectra of three representative small proteins are reported utilizing 2,5-dihydroxybenzoic acid as matrix. These proteins, bovine insulin, cytochrome c, and bovine albumin have masses from ～5000 to 66,000 Da. Three different sample preparation techniques were investigated: aerospray, dried-drop, and acetone redeposition. Both MALDI Fourier transform and time-of-flight mass spectrometry results show that buffer tolerance of MALDI-MS samples depends upon several factors, including the relative amount of the buffer in the MALDI matrix, as well as the identity of the specific buffer. Furthermore, the rate at which buffer tolerance decreases as buffer concentration is increased varies from buffer to buffer. The current results reveal that, at very high matrix:analyte ratios, buffer tolerance of MALDI is dramatically greater than concluded in previous literature reports.     

Desorption/ionization mass spectrometry on nanocrystalline titania sol-gel-deposited films

This paper describes a matrix-free method for performing desorption/ionization directly from mesoporous nanocrystalline titania sol-gel thin films, which have good absorption capacity in the ultraviolet (UV) range and can act as assisting materials during UV matrix-assisted laser desorption/ionization mass spectrometric (MALDI-MS) analysis. A high concentration of citrate buffer was added into this system to provide the proton source and to reduce the presence of alkali cation adducts of the analytes. The analyte signals appear uniformly over the whole sample deposition area. Protonated molecules (MH(+) ions) of analytes dominate the titania MALDI mass spectra. Surfactants, peptides, tryptic digest products, and small proteins with molecular weights below ca. 24 000 Da, are observed in the titania MALDI mass spectra. Detection limits for insulin are as low as ca. 2 fmol with mass resolution of ca. 660.     

Serum protein profiling by miniaturized solid-phase extraction and matrix-assisted laser desorption/ionization mass spectrometry

Serum profiling by matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) holds promise as a clinical tool for early diagnosis of cancer and other human diseases. Sample preparation is key to achieving reproducible and well-resolved signals in MALDI-MS; a prerequisite for translation of MALDI-MS based diagnostic methods to clinical applications. We have investigated a number of MALDI matrices and several miniaturized solid-phase extraction (SPE) methods for serum protein concentration and desalting with the aim of generating reproducible, high-quality protein profiles by MALDI-MS. We developed a simple protocol for serum profiling that combines a matrix mixture of 2,5-dihydroxybenzoic acid and alpha-cyano-4-hydroxycinnamic acid with miniaturized SPE and MALDI-MS. Functionalized membrane discs with hydrophobic, ion-exchange or chelating properties allowed reproducible MALDI mass spectra (m/z 1000-12,000) to be obtained from serum. In a proof-of-principle application, SPE with chelating material and MALDI-MS identified protein peaks in serum that had been previously reported for distinguishing a person diagnosed with breast cancer from a control. These preliminary results indicate that this simple SPE/MALDI-MS method for serum profiling provides a versatile and scalable platform for clinical proteomics.     

Serum protein profiles of patients with pancreatic cancer and chronic pancreatitis: searching for a diagnostic protein pattern.

In this study, 13 sera from patients with pancreatic cancer, 9 from chronic pancreatitis and 10 from healthy subjects were analyzed by matrix-assisted laser desorption/ionization (MALDI) mass spectrometry. The MALDI mass spectra revealed the presence of several low molecular weight peptides, among which some were detected only in the sera from both pathological conditions. On the other hand many peptides were observed only in control sera, and were absent in the sera from the two diseases. Therefore, MALDI analysis of the low molecular weight fraction (<10 000 Da) of sera from patients with pancreatic diseases enabled us to identify the presence of some disease-related signals and also some signals characteristic of normal subjects.     

PSMA@Ag复合微球的制备及其在MALDI-MS分析小分子化合物中的应用研究

基质辅助激光解吸电离质谱(MALDI-MS)作为一种有力的分析手段,在生物分子分析中有着广泛的应用,但很难应用于分子量小于500的待测物的分析。该文利用聚多巴胺修饰还原法制备了核壳结构的聚苯乙烯-马来酸酐共聚物@银纳米壳层(PSMA@Ag)复合微球。采用傅立叶红外光谱法验证了聚多巴胺(PDA)的成功修饰。结合扫描电子显微镜(SEM)和紫外-可见光谱(UV-Vis)分析结果,发现Ag纳米壳层成功地包覆在PSMA微球的表面。将制备的PSMA@Ag复合微球作为辅助基质直接应用于MALDI-MS,成功地从0.5μL待测物样品中检测到2 pmol脯氨酸(M_w=115)和1 pmol丝氨酸(M_w=105)。研究结果证明PSMA@Ag微球对MALDI的离子化过程有促进作用,为解决MALDI-MS在分析小分子待测物时背景噪声过大,信号无法分辨的问题提供了一个有效途径。     

Halohydrination of epoxy resins using sodium halides as cationizing agents in MALDI-MS and DIOS-MS

Halohydrination of epoxy resins using sodium halides as cationizing agents in matrix-assisted laser desorption/ionization (MALDI) and desorption ionization on porous silicon mass spectrometry (DIOS-MS) were investigated. Different mass spectra were observed when NaClO(4) and NaI were used as the cationizing agents at the highest concentration of 10.0 mM, which is much higher than that normally used in MALDI-MS. MALDI mass spectra of epoxy resins using NaI revealed iodohydrination to occur as epoxy functions of the polymers. The halohydrination also occurred using NaBr, but not NaCl, due to the differences in their nucleophilicities. On the basis of the results of experiments using deuterated CD(3)OD as the solvent, the hydrogen atom source was probably ambient water or residual solvent, rather than being derived from matrices. Halohydrination also occurred with DIOS-MS in which no organic matrix was used; in addition, reduction of epoxy functions was observed with DIOS. NaI is a useful cationizing agent for changing the chemical form of epoxy resins due to iodohydrination and, thus, for identifying the presence of epoxy functions.     

Copper(I) chloride: a simple salt for enhancement of polystyrene cationization in matrix-assisted laser desorption/ionization mass spectrometry

The possibility of using copper(I) chloride as a doping salt to enhance the cationization of polystyrene in matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) was investigated. It was shown that copper(I) chloride possesses sufficient solubility in tetrahydrofuran. The parameters of the MALDI mass spectra of different polystyrene samples, such as the number-average (M(n)) and mass-average (M(w)) molecular mass values, obtained by copper(I) cationization were compared with those obtained by means of silver(I) cationization, and good agreement was found. It was also shown that application of copper(I) chloride as a doping salt, and dithranol as a matrix, ensured good MALDI mass spectra of the sample spots even after storage for 1 month.     

Matrix-assisted laser desorption/ionization mass spectrometry of polysaccharides with 2',4',6'-trihydroxyacetophenone as matrix

So far, there have been only a few matrices reported for detection of polysaccharides with molecular weight higher than 3000 Daltons by matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS). In this work, we found that 2',4',6'-trihydroxyacetophenone (THAP) is a good matrix for MALDI time-of-flight MS analysis of polysaccharides with broad mass range. Large polysaccharides, dextrans, glycoproteins and polysialic acids have been successfully detected by MALDI-MS with THAP as matrix.     

Detection of inorganic species by chemical reaction laser desorption ionization mass spectrometry

The oxidation numbers of metals in inorganic compounds were identified by matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) by using their acetylacetonates, which are soluble in acetone. For the MALDI analysis of inorganic species insoluble in common solvents used for matrices, such as acetone, methanol, water, etc., a suspension method of sample preparation was developed. Turbid suspensions of inorganic species in the solvent were spotted on the sample holder with chelating reagents, as in the conventional sample preparation for MALDI-MS. Chemical reaction between the inorganic species and the chelating reagents occurred in the plume after irradiation by laser light. Metal oxides were also analyzed by this method, and samples with different oxidation numbers gave different mass spectra. These results suggest that many other metal oxides with different oxidation numbers could be identified if suitable chelating reagents are chosen for sample preparation for MALDI-MS.     

Diagnostic protein discovery using proteolytic peptide targeting and identification

Plasma protein profiling with mass spectrometry is currently being evaluated as a diagnostic tool for cancer and other diseases. These experiments consist of three steps: plasma protein fractionation, analysis with matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOFMS), and comparisons of the MALDI profiles to develop diagnostic fingerprints using bioinformatic techniques. While preliminary results appear promising in small sample groups, the method is limited by the sensitivity of MALDI-MS for intact proteins, the limited mass range of MALDI-MS, and difficulties associated with isolating individual proteins for identification to validate the diagnostic fingerprint. Here we present an alternative and improved method directed toward diagnostic protein discovery, which incorporates proteolytic peptide profiling, bioinformatic targeting of ion signals, and MALDI tandem mass spectrometry (MS/MS) peptide sequencing, rather than fingerprinting. Pancreatic cancer patients, pancreatitis patients, and controls are used as the model system. Profiling peptides after enzymatic digestion improves sensitivity and extends the accessible protein molecular weight range when compared to intact protein profiling. The first step is to extract and fractionate the proteins from plasma. Each fraction is digested with trypsin and subsequently analyzed by MALDI-MS. Rather than using bioinformatic analysis as a pattern-matching technique, peptides are targeted based on the disease to control peak intensity ratios measured in the averages of all mass spectra in each group and t-tests of the intensity of each individual peak. The targeted peptide ion signals are subsequently identified using MALDI-MS/MS in quadrupole-TOF and tandem-TOF instruments. This study found not only the proteins targeted and identified by a previous protein profiling experiment, but also detected additional proteins. These initial results are consistent with the known biology of pancreatic cancer or pancreatitis, but are not specific to those diseases.     

Improved analysis of membrane protein by PVDF-aided, matrix-assisted laser desorption/ionization mass spectrometry

Characterization of membrane proteins remains an analytical challenge because of difficulties associated with tedious isolation and purification. This study presents the utility of the polyvinylidene difluoride (PVDF) membrane for direct sub-proteome profiling and membrane protein characterization by matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS). The hydrophobic adsorption of protein, particularly membrane proteins, on the PVDF surface enables efficient on-PVDF washing to remove high concentrations of detergents and salts, such as up to 5% sodium dodecyl sulfate (SDS). The enhanced spectrum quality for MALDI detection is particularly notable for high molecular weight proteins. By using on-PVDF washing prior to MALDI detection, we obtained protein profiles of the detergent-containing and detergent-insoluble membrane fractions from Methylococcus capsulatus (Bath). Similar improvements of signal-to-noise ratios were shown on the MALDI spectra for proteins electroblotted from SDS-polyacrylamide gel electrophoresis (SDS-PAGE) onto the PVDF membrane. We have applied this strategy to obtain intact molecular weights of the particulate methane monooxygenase (pMMO) composed of three intrinsic membrane-bound proteins, PmoA, PmoB, and PmoC. Together with peptide sequencing by tandem mass spectrometry, post-translational modifications including N-terminal acetylation of PmoA and PmoC and alternative C-terminal truncation of PmoB were identified. The above results show that PVDF-aided MALDI-MS can be an effective approach for profiling and characterization of membrane proteins.     

Extraction and characterization of adenovirus

A new methodology for the extraction and characterization of proteins from Coomassie-stained sodium dodecylsulfate polyacrylamide gel electrophoresis using matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) has been described. The utility of this methodology was demonstrated in the characterization of adenovirus proteins. The key steps in the extraction and destaining process involve washing the excised band with a combination of solvents that include 10% acetic acid, acetonitrile, methanol, and formic acid:water:isopropanol mixture. By using this procedure, we determined adenovirus proteins with molecular weights ranging from 10,000 to 110,000 Da by MALDI-MS, obtaining a detection limit of approximately 6 pmol. Parallel experiments were successfully carried out to analyze adenovirus proteins from Cu-stained gels. It was observed that increase in laser intensity resulted in significant improvements in the quality of MALDI mass spectra for the analysis of inefficiently destained proteins from Cu-stained gels.     

Solid sampling technique for direct detection of condensed tannins in bark by matrix-assisted laser desorption/ionization mass spectrometry

A novel method for the direct analysis of condensed tannin components in bark was developed on the basis of matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) combined with a simple solid sampling technique. The MALDI mass spectra obtained from the wood (bark) powder sample clearly showed a series of peaks corresponding to the sodium ion adducts of condensed tannin oligomers up to around m/z 3000. The results indicate that the condensed tannins in the bark sample used in this work mostly consist of combinations of flavan-3-ol units such as profisetinidin (PF), prorobinetinidin (PR) and prodelphinidin (PD), at least up to 10-mers (m/z approximately 3000).     

Matrix-assisted laser desorption/ionization mass spectrometry for the characterization of ionic liquids and the analysis of amino acids, peptides and proteins in ionic liquids

Ionic liquids are interesting solvents for a number of applications in chemistry and biotechnology. We characterized five different ionic liquids by laser desorption/ionization (LDI) and by matrix-assisted laser desorption/ionization (MALDI) mass spectrometry (MS) and studied the analysis of amino acids, peptides and proteins dissolved in these solvents. Signals of both anions and cations of the ionic liquids could be observed both in LDI- and in MALDI-MS. In the latter case, adduct formation between anions and cations of the analytes was observed. Amino acids, peptides and proteins could be analyzed in ionic liquids after addition of matrix substances. Sodium and potassium adducts were not observed in any analysis involving ionic liquids. Low molecular mass compounds and peptides could be analyzed best in the presence of water-immiscible ionic liquids, whereas proteins gave the best results in water-miscible ionic liquids. Optimal analysis conditions such as molar matrix-to-analyte and ionic liquid-to-matrix ratios were determined. Homogeneity of samples in the presence of ionic liquids was reduced compared with classical MALDI preparations. Relative quantitation of amino acids was possible using isotope-labeled internal standards. MALDI-MS thus can be used for the analysis of chemical reactions and the screening of enzyme-catalyzed reactions in ionic liquids and for the analysis of the biocatalysts dissolved in these solvents. Theoretical aspects of ion formation in the presence of ionic liquids both in LDI and MALDI analysis are discussed.     

Coupling of nanoflow liquid chromatography to matrix-assisted laser desorption/ionization mass spectrometry: real-time liquid chromatography run mapping on a MALDI plate

The major obstacle in the use of matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) instruments in the analysis of complex proteome samples is the lack of a direct coupling of a highly resolving separation technique with the mass spectrometer itself. To overcome this drawback, a spotting device for capillary and nanoflow liquid chromatography (LC) with a special liquid deposition principle for lowest volumes was developed. The instrument is able to perform MALDI spotting in real time in order to deposit the LC run on the MALDI plate, and therefore couples the high resolution power of nano-RP-HPLC separation directly with MALDI-MS. This work describes the development and optimization of a method for spotting with online matrix addition, and illustrates its use in the analysis of a complex proteome sample.     

A fast atom bombardment and matrix-assisted laser desorption/ionization mass spectrometry study of doubly charged porphyrins

In this mass spectrometry (MS) study of doubly charged porphyrin salts, fast atom bombardment (FAB) and matrix-assisted laser desorption/ionization (MALDI) MS techniques are utilized to examine several unique ionic species. The predominant transformation of preformed doubly charged ions in the desorption/ionization mechanism of FAB and MALDI is the result of deprotonation reactions to form singly charged ions of the type [M(2+) - H(+)](+) and of one-electron reductions to form radical cations [M(2+) + e(-)](+.). The dependence of this phenomenon and the formation of a number of additional ionic species on the different matrices and the FAB-matrix additive benzoquinone is examined. The significant analogous behavior of doubly charged porphyrins in FAB- and MALDI-MS leads to the conclusion that one-electron reductions are of distinct relevance in the desorption/ionization mechanism of MALDI.     

The nature of collision-induced dissociation processes of doubly protonated peptides: comparative study for the future use of matrix-assisted laser desorption/ionization on a hybrid quadrupole time-of-flight mass spectrometer in proteomics.

Comparative MS/MS studies of singly and doubly charged electrospray ionization (ESI) and matrix-assisted laser desorption/ionization (MALDI) precursor peptide ions are described. The spectra from these experiments have been evaluated with particular emphasis on the data quality for subsequent data processing and protein/amino acid sequence identification. It is shown that, once peptide ions are formed by ESI or MALDI, their charge state, as well as the collision energy, is the main parameter determining the quality of collision-induced dissociation (CID) MS/MS fragmentation spectra of a given peptide. CID-MS/MS spectra of singly charged peptides obtained on a hybrid quadrupole orthogonal time-of-flight mass spectrometer resemble very closely spectra obtained by matrix-assisted laser desorption/ionization post-source decay time-of-flight mass spectrometry (MALDI-PSD-TOFMS). On the other hand, comparison of CID-MS/MS spectra of either singly or doubly charged ion species shows no dependence on whether ions have been formed by ESI or MALDI. This observation confirms that, at the time of precursor ion selection, further mass analysis is effectively decoupled from the desorption/ionization event. Since MALDI ions are predominantly formed as singly charged species and ESI ions as doubly charged, the associated difference in the spectral quality of MS/MS spectra as described here imposes direct consequences on data processing, database searching using ion fragmentation data, and de novo sequencing when ionization techniques are changed.     

Multivariate analysis approach to the plasma protein profile of patients with advanced colorectal cancer

The aim of the present study was to identify the pattern of plasma protein species of interest as markers of colorectal cancer (CRC). Using matrix-assisted laser desorption/ionization-mass spectrometry (MALDI-MS), the plasma protein profile was determined in nine stage IV CRC patients (study group) and nine clean-colon healthy subjects (control group). Multivariate analysis methods were employed to identify distinctive disease patterns at protein spectrum. In the study and control groups, cluster analysis (CA) on the complete MALDI-MS spectra plasma protein profile showed a distinction between CRC patients and healthy subjects, thus allowing the identification of the most discriminating ionic species. Principal component analysis (PCA) and linear discriminant analysis (LDA) yielded similar grouping results. LDA with leave-one-out cross validation achieved a correct classification rate of 89% in both the patients and the healthy subjects.