Direct tissue analysis using matrix-assisted laser desorption/ionization mass spectrometry: practical aspects of sample preparation

Practical guidelines for the preparation of tissue sections for direct analysis by matrix-assisted laser desorption/ionization (MALDI) mass spectrometry are presented. Techniques for proper sample handling including tissue storage, sectioning and mounting are described. Emphasis is placed on optimizing matrix parameters such as the type of matrix molecule used, matrix concentration, and solvent composition. Several different techniques for matrix application are illustrated. Optimal instrument parameters and the necessity for advanced data analysis approaches with regards to direct tissue analysis are also discussed.     

Direct analysis of alkaloid profiling in plant tissue by using matrix-assisted laser desorption/ionization mass spectrometry

A method for the direct determination of alkaloid profiling in plant tissues by using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOFMS) was developed. The alkaloid profiles of the herbs were obtained without the need for complicated sample preparation. Experimental results demonstrated that the direct MALDI-TOFMS analysis allowed rapid and reliable characterization of the components in plant tissues. Four commonly used Chinese medicinal herbs were studied, including Aconitum Carmichaeli Debx. (Fuzi in Chinese) and Processed Fuzi, for herb differentiation and explanation of the significant difference in their toxicities. The direct analysis method proved valuable for the preliminary study of plant component profiles. The rapid collection of information from the direct analysis on plant tissues could be valuable for supporting the discovery of new compounds and for the quality control of medicinal herbs.     

Characterization of polyethylenimine by electrospray ionization and matrix-assisted laser desorption/ionization

Branched polyethylenimines (PEIs) with lower average molecular weights (600, 1200 and 1800 Da) have been studied by Electrospray Ionization (ESI) and Matrix‐Assisted Laser Desorption/Ionization (MALDI) mass spectrometry. In both, ESI and MALDI mass spectra, the main distribution arises from protonated PEI oligomers with NH₂ end groups, [PEI + H]⁺, which are observed at m/z 43n + 18. A trace of sodium contamination in the PEI samples results in the presence of a series that appears at m/z 43n + 40 [PEI + Na]⁺. However, only the MALDI mass spectra show a [PEI + K]⁺ series at m/z 43n + 56, because of matrix contamination with potassium, and a series generated by condensation of the matrix with PEI at m/z 43n + 30. Collisionally activated dissociation tandem mass spectrometry (CAD (MS/MS)) of protonated PEI oligomers is shown to yield three fragment ion series b_n, and K_n. The experiments have demonstrated the capabilities of these mass spectrometry techniques, along with CAD MS/MS to detect and characterize such polar synthetic polymers. Copyright © 2011 John Wiley & Sons, Ltd.     

Direct laser desorption/ionization time-of-flight mass spectrometry of conjugated polymers

Two conjugated polymers (CPs), poly(9,9-dioctylfluorene) (PF) and poly(3-octylthiophene) (PT) were analyzed by direct laser desorption/ionization time-of-flight mass spectrometry (LDI-ToF MS). Because of their strong absorption near the wavelength of the laser (337 nm), easy and transient energy transfer properties and sufficient thermal stability, CPs can be desorbed and ionized directly without a matrix. For comparison, these two polymers were also analyzed using matrix-assisted laser desorption/ionization (MALDI)-ToF MS in the positive reflectron mode. The results revealed that they are very similar in terms of quality and resolution. All results demonstrate that LDI-ToF MS is an alternative method for the mass characterization of some conjugated systems, thereby simplifying the process of sample preparation and result analysis.     

Miniaturizing sample spots for matrix-assisted laser desorption/ionization mass spectrometry

The trend of miniaturization in bioanalytical chemistry is shifting from technical development to practical application. In matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS), progress in miniaturizing sample spots has been driven by the needs to increase sensitivity and speed, to interface with other analytical microtechnologies, and to develop miniaturized instrumentation.We review recent developments in miniaturizing sample spots for MALDI-MS. We cover both target modification and microdispensing technologies, and we emphasize the benefits with respect to sensitivity, throughput and automation.We hope that this review will encourage further method development and application of miniaturized sample spots for MALDI-MS, so as to expand applications in analytical chemistry, protein science and molecular biology.     

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.     

On-tissue chemical derivatization of volatile metabolites for matrix-assisted laser desorption/ionization mass spectrometry imaging

Mass spectrometry imaging (MSI) of volatile metabolites is challenging, especially in matrix-assisted laser desorption/ionization (MALDI). Most MALDI ion sources operate in vacuum, which leads to the vaporization of volatile metabolites during analysis. In addition, tissue samples are often dried during sample preparation, leading to the loss of volatile metabolites even for other MSI techniques. On-tissue chemical derivatization can dramatically reduce the volatility of analytes. Herein, a derivatization method is proposed utilizing N,N,N-trimethyl-2-(piperazin-1-yl)ethan-1-aminium iodide to chemically modify short-chain fatty acids in chicken cecum, ileum, and jejunum tissue sections before sample preparation for MSI visualization.     

基质辅助激光解吸电离质谱和电喷雾电离质谱在辣根过氧化物酶糖肽结构分析中的应用

糖链结构的质谱解析是今后糖蛋白分析中的重要研究内容,其中完整糖肽的分析,由于可以同时获得糖基化位点和对应糖链的结构信息,更具有重要意义和研究前景。本工作对质谱软电离技术在完整糖肽分析中的应用进行了研究,其中包括了基质辅助激光解吸电离(matrix-assisted laser desorption ionization, MALDI)和电喷雾电离(electrospray ionization, ESI)技术。通过平行使用两种串联质谱(tandem mass spectrometry, MS/MS)分析策略: MALDI-MS/MS和ESI-MS/MS对目标糖蛋白——辣根过氧化物酶进行分析,并讨论了其互补性。结果表明,MALDI和ESI技术各有优劣,结合串联质谱分析,可获得糖肽的糖链结构信息;两条路线互补使用,在揭示蛋白质糖基化修饰(位点和结构)的研究中十分必要。     

Direct analysis of cellulose in poplar stem by matrix-assisted laser desorption/ionization imaging mass spectrometry

Matrix-assisted laser desorption/ionization imaging mass spectrometry (MALDI-IMS) was applied to the analysis of the spatial distribution of cellulose on a cross-section of juvenile poplar (Populus deltoids) stems. Microcrystalline cellulose (MCC) was used to optimize matrix (2,5-dihydroxybenzoic acid) application and instrument parameters for the detection of low hexose oligomers, which originated from cellulose in the solid phase. A section of poplar cellulose isolated from juvenile poplar stem which consisted primarily of glucose (～95%) and minor components such as xylose and lignin was used for the MALDI-IMS studies. The mass spectrum of poplar cellulose consisted of a series of evenly spaced signals having a difference of 162 m/z units, which was similar to that of MCC in linear and reflectron positive ion modes. MS images of cellulose compounds with sodium ion adducts were generated and illustrated the distribution of cellulose on the surface of the poplar stem.     

Investigations with O-linked protein glycosylations by matrix-assisted laser desorption/ionization Fourier transform ion cyclotron resonance mass spectrometry

Posttranslational modifications such as glycosylation can play a fundamental role in signaling pathways that transform an ordinary cell into a malignant one. The development of a protocol to detect these changes in the preliminary stages of disease can lead to a sensitive and specific diagnostic for the early detection of malignancies such as ovarian cancer in which differential glycan patterns are linked to etiology and progression. Small variations in instrument parameters and sample preparation techniques are known to have significant influence on the outcome of an experiment. For an experiment to be effective and reproducible, these parameters must be optimized for the analyte(s) under study. We present a detailed examination of sample preparation and matrix-assisted laser desorption/ionization Fourier transform ion cyclotron resonance mass spectrometry (MALDI-FT-ICR-MS) analysis of O-linked glycans globally cleaved from mucin glycoproteins. Experiments with stable isotope-labeled biomolecules allowed for the establishment of appropriate acquisition times and excitation voltages for MALDI-FT-ICR-MS of oligosaccharides. Quadrupole ion guide optimization studies with mucin glycans identified conditions for the comprehensive analysis of the entire mass range of O-linked carbohydrates in this glycoprotein. Separately optimized experimental parameters were integrated in a method that allowed for the effective study of O-linked glycans. Copyright (c) 2008 John Wiley & Sons, Ltd.     

Structural characterization of carcinogen-modified oligodeoxynucleotide adducts using matrix-assisted laser desorption/ionization mass spectrometry

The aim of this study was to determine the chemical structure of in vitro 2-amino-1-methyl-6-phenylimidazo[4,5-b]pyridine (PhIP)-modified oligodeoxynucleotides (ODNs) by exonuclease digestion and matrix-assisted laser desorption/ionization mass spectrometry. A single-stranded 11-mer ODN, 5'-d(CCATCGCTACC), was reacted with N-acetoxy-PhIP, resulting in the formation of one major and eight minor PhIP-ODN adducts. A 10 min treatment of the major and one minor PhIP-ODN adduct with a 3'-exonuclease, bovine intestinal mucosa phosphodiesterase (BIMP), and a 5'-exonuclease, bovine spleen phosphodiesterase, results in inhibition of the primary exonuclease activity at deoxyguanosine (dG) producing 5'-d(CCATCG(PhIP)) and 5'-d(G(PhIP)CTACC) product ions, respectively. Post-source decay (PSD) of these enzymatic end products identifies dG as the sole modification site in two 11-mer ODN-PhIP adducts. PSD of the minor PhIP-ODN adduct digestion end product, 5'-d(CCATCG(PhIP)), also reveals that the PhIP adducted guanine moiety is in an oxidized form. Prolonged treatment of the PhIP-ODN adducts at 37 degrees C with BIMP induces a non-specific, or endonuclease, enzymatic activity culminating in the formation of deoxyguanosine 5'-monophosphate-PhIP (5'-dGMP-PhIP). The PSD fragmentation pattern of the 5'-dGMP-PhIP [M + H](+) ion of the major adduct confirms PhIP binds to the C-8 position of dG. For the minor adduct, PSD results suggest that PhIP binds to the C-8 position of an oxidized guanine, supporting the hypothesis that this adduct arises from oxidative degradation, resulting in a spirobisguanidino structure.     

Determination of neutral oligosaccharides in vegetables by matrix-assisted laser desorption/ionization mass spectrometry

In this work, matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI–TOF–MS) was used for characterization of oligosaccharides in some vegetable samples (Jerusalem artichoke, red onion, glucose syrup from potatoes). The selection of suitable matrix has critical importance for quality of MALDI–TOF spectra. Therefore six selected matrices (2,5-dihydroxybenzoic acid, 2,4,6-trihydroxyacetophenone, -cyano-4-hydroxycinnamic acid, 2-(4-hydroxyphenylazo)benzoic acid, 3-aminoquinoline and sinapinic acid) were tested. The optimization of experimental conditions was carried out for two model carbohydrates that are important in food chemistry—inulin and starch. The experiments were performed in both positive linear and reflectron mode. The signals of the standard samples in reflectron mode were weak and repeatability of the measurements was lower than in linear mode. 2,4,6-Trihydroxyacetophenone for inulin and 2,5-dihydroxybenzoic acid for starch were found as the best matrices. Therefore, the real samples were analyzed with these two matrices in linear mode. The distribution of oligosaccharides from Jerusalem artichoke showed the degree of polymerization (DP) of the oligosaccharides in the range from 2 to 25. Red onion contained the saccharides with DP from 1 to 14. Glucose syrup from potatoes had DP from 2 to 48. MALDI–TOF–MS was found more sensitive for detection of oligosaccharides than the chromatographic methods used for the some purpose.     

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.     

Chromophore effect in photodissociation at 266 nm of protonated peptides generated by matrix-assisted laser desorption ionization (MALDI)

Chromophore effect in the photodissociation of protonated peptides at 266 nm was investigated using synthetic peptides with the sequence RGGXGGGGGR where X was a phenylalanyl(F), tyrosyl(Y), cysteinyl(C), glycyl(G), seryl(S), or histidyl(H) residue. The peptides with an F or Y residue dissociated efficiently. Fragment ions due to cleavages at either end of the chromophore were especially prominent just as for the peptide with a tryptophanyl residue reported previously.1Photodissociation was observed even for the peptides without any noticeable chromophore at 266 nm. Here, dissociation at all the peptide bonds was almost equally prominent. Photodissociation of the protonated angiotensin I was investigated using the spectral correlation rules observed in the model systems. Role of the chromophores and the plausible mechanisms involved are discussed.     

Direct analysis of laser capture microdissected endometrial carcinoma and epithelium by matrix-assisted laser desorption/ionization mass spectrometry

Direct analysis of laser capture microdissected malignant and normal endometrial epithelium using matrix-assisted laser desorption/ionization (MALDI) time-of-flight mass spectrometry (MS) was able to detect a number of proteins that are overexpressed in malignant epithelial cells. A total of 16 physiologic and malignant endometrial samples were laser capture microdissected, including four proliferative and four secretory endometria, and eight endometrioid adenocarcinomas. Two of these proteins, at 10,834 and 10,843 Da, likely correspond to calgranulin A and chaperonin 10, two proteins that had previously been identified in endometrioid adenocarcinoma in whole tissue homogenate by MS analysis. Direct analysis by MALDI-MS not only confirms that these proteins are overexpressed in endometrial carcinoma, but also localizes them to the epithelial cells, the expected cancer site.     

Intact protein analysis by matrix-assisted laser desorption/ionization tandem time-of-flight mass spectrometry

Direct tandem mass spectrometric (MS/MS) analysis of small, singly charged protein ions by tandem time-of-flight mass spectrometry (TOFMS) is demonstrated for proteins up to a molecular mass of 12 kDa. The MALDI-generated singly charged precursor ions predominantly yield product ions resulting from metastable fragmentation at aspartyl and prolyl residues. Additional series of C-terminal sequence ions provide in some cases sufficient information for protein identification. The amount of sample required to obtain good quality spectra is in the high femtomolar to low picomolar range. Within this range, MALDI-MS/MS using TOF/TOF trade mark ion optics now provides the opportunity for direct protein identification and partial characterization without prior enzymatic hydrolysis.     

Identification of formylglycine in sulfatases by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry

C(alpha)-Formylglycine, the catalytic amino acid residue in the active site of sulfatases, is generated by post-translational modification of a cysteine or serine residue. We describe a highly sensitive procedure for the detection of C(alpha)-formylglycine-containing peptides in tryptic digests of sulfatase proteins. The protocol is based on the formation of hydrazone derivatives of C(alpha)-formylglycine-containing peptides when using dinitrophenylhydrazine as a matrix for matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOFMS). The hydrazone derivatives desorb and ionize with high efficiency and can be detected in the sub-femtomole range. The presence of C(alpha)-formylglycine is indicated by a mass increment of 180.13 u, corresponding to the hydrazone moiety, and also by a unique C-terminal fragment ion, characteristic of sulfatases, that becomes prominent in MALDI post-source decay mass spectra of the hydrazone derivatives.     

Regional phospholipid analysis of porcine lens membranes by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry

The applicability of matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOFMS) to the qualitative and quantitative analysis of most mammalian phospholipid (PL) classes was demonstrated in a crude extract of porcine lens membranes. When 2,5-dihydroxybenzoic acid (DHB) was used as the matrix, positive-ion spectra allowed the accurate quantification of phosphatidylcholines (PCs) and sphingomyelins (SMs). Other PLs such as phosphatidylethanolamines (PEs), phosphatidylethanolamine plasmalogens (PEps), phosphatidylethanolamine ethers (PEes) and phosphatidylserines (PSs), could also be detected, but their lower ionization efficiency led to negative errors in their quantification. Despite this limitation, it was possible to determine relative changes among PLs extracted from cortical and nuclear regions. Negative-ion spectra were acquired with the use of p-nitroaniline (PNA) as the matrix. Because neither PCs nor SMs produce negative ions, other PL classes can be analyzed selectively. The absolute quantification of the various PL classes detectable in negative-ion spectra was also affected by differences in ionization efficiencies. However, the trends in compositional changes between cortical and nuclear-fiber PLs were in agreement with those obtained by (31)P NMR spectroscopy. MALDI-TOFMS also offers the possibility of studying variations in the acyl-chain distribution of the various species comprising each PL class. For porcine lenses, PCs, PEs and phosphatidylinositols (PIs) exhibited the greatest depletions in going from cortical to nuclear membranes. Among their individual species, those with two or more sites of unsaturation suffered the most significant reduction.     

Decomposition of protein nitrosothiolsin matrix-assisted laser desorption/ionization and electrospray ionization mass spectrometry

The S-nitrosylation of proteins is involved in the trafficking of nitric oxide (NO) in intra- and extracellular milieus. To establish a mass spectrometric method for identifying this post-translational modification of proteins, a synthetic peptide and transthyretin were S-nitrosylated in vitro and analyzed by electrospray ionization (ESI) and matrix-assisted laser desorption/ionization (MALDI) mass spectrometry. The intact molecular ion species of nitrosylated compounds was identified in the ESI mass spectrum without elimination of the NO group. However, the labile nature of the S-NO bond was evident when the in-source fragmentation efficiently generated [M + H - 30](+) ions. The decomposition was prominent for multiply charged transthyretin ions with high charge states under ordinary ESI conditions, indicating that the application of minimum nozzle potentials was essential for delineating the stoichiometry of nitrosylation in proteins. With MALDI, the S-NO bond cleavage occurred during the ionization process, and the subsequent reduction generated [M + H - 29](+) ions.     

On-line atmospheric pressure matrix-assisted laser desorption/ionization mass spectrometry

A new technique is presented for the coupling of atmospheric pressure matrix-assisted laser desorption/ionization (AP-MALDI) mass spectrometry with liquid delivery systems. Mass measurements of polymers and peptides are demonstrated using a co-dissolved matrix, e.g. alpha-cyano-4-hydroxycinnamic acid (HCCA). Improvements in terms of sensitivity are achieved by optimizing the shape und control of the exit capillary and by using a laser (355 nm) at a 1 kHz repetition rate. Two calibration experiments promise a good applicability of the presented coupling method for quantitative measurements. The limit of detection achieved so far is 500 nM for peptides in methanol solution containing 25 mM HCCA.