Matrices are necessary materials for ionizing analytes in matrix-assisted laser desorption/ionization-mass spectrometry (MALDI-MS). The choice of a matrix appropriate for each analyte controls the analyses. Thus, in some cases, development or improvement of matrices can become a tool for solving problems. This paper reviews MALDI matrix research that the author has conducted in the recent decade. It describes glycopeptide, carbohydrate, or phosphopeptide analyses using 2,5-dihydroxybenzoic acid (2,5-DHB), 1,1,3,3-tetramethylguanidinium (TMG) salts of p-coumaric acid (CA) (G₃CA), 3-aminoquinoline (3-AQ)/α-cyano-4-hydroxycinnamic acid (CHCA) (3-AQ/CHCA) or 3-AQ/CA and gengeral peptide, peptide containing disulfide bonds or hydrophobic peptide analyses using butylamine salt of CHCA (CHCAB), 1,5-diaminonaphthalene (1,5-DAN), octyl 2,5-dihydroxybenzoate (alkylated dihydroxybenzoate, ADHB), or 1-(2,4,6-trihydroxyphenyl)octan-1-one (alkylated trihydroxyacetophenone, ATHAP).

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In a tutorial paper on the application of free-jet technique for API-MS, John Fenn mentioned that “…for a number of years and a number of reasons, it has been found advantageous in many situations to carry out the ionization process in gas at pressures up to 1000 Torr or more” (Int. J. Mass Spectrom. 200: 459–478, 2000). In fact, the first ESI mass spectrometer constructed by Yamashita and Fenn had a counter-flow curtain gas source at 1050 Torr (ca. 1.4 atm) to sweep away the neutral (J. Phys. Chem. 88: 4451–4459, 1984). For gaseous ionization using electrospray plume, theoretical analysis also shows that “super-atmospheric operation would be more preferable in space-charge-limited situations.”(Int. J. Mass Spectrom. 300: 182–193, 2011). However, electrospray and the corona-based chemical ion source (APCI) in most commercial instrument are basically operated under an atmospheric pressure ambient, perhaps out of the concern of safety, convenience and simplicity in maintenance. Running the ion source at pressure much higher than 1 atm is not so common, but had been done by a number of groups as well as in our laboratory. A brief review on these ion sources will be given in this paper.

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In vivo concentrations of cellular signaling mediators such as inflammatory mediators are normally maintained at very low levels due to their strong ability to induce a biological response. The production, diffusion, and decomposition of such mediators are spatio-temporally regulated. Therefore, in order to understand biochemical basis of disease progression and develop new therapeutic strategies, it is important to understand the spatiotemporal dynamics of the signaling mediators in vivo, during the progression of disorders, e.g., chronic inflammatory diseases; however, the lack of effective imaging technology has made it difficult to determine their localizations in vivo. Such characterization requires technical breakthroughs, including molecular imaging methods that are sensitive enough to detect low levels of metabolites in the heterogeneous tissue regions in diseased organs. We and other groups have attempted to fill this technical gap by developing highly sensitive imaging mass spectrometry (IMS) technologies. To date, we have established two key techniques toward this goal, including (i) a sample preparation procedure that has eliminated the problem of the postmortem degradation of labile metabolites, and (ii) on-tissue derivatization of metabolites, which can enhance analyte ionization efficiency. Here, we review recent progress in the development of these technologies as well as how the highly sensitive IMS technique has contributed to increasing understanding of the biochemical basis of disease mechanisms, discovery of new diagnostic markers, and development of new therapies.

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A dynamic headspace extraction method (DHS) with high-pressure injection is described. This dynamic extraction method has superior sensitivity to solid phase micro extraction, SPME and is capable of extracting the entire gas phase by purging the headspace of a vial. Optimization of the DHS parameters resulted in a highly sensitive volatile profiling system with the ability to detect various volatile components including alcohols at nanogram levels. The average LOD for a standard volatile mixture was 0.50 ng mL⁻¹, and the average LOD for alcohols was 0.66 ng mL⁻¹. This method was used for the analysis of volatile components from biological samples and compared with acute and chronic inflammation models. The method permitted the identification of volatiles with the same profile pattern as in vitro oxidized lipid-derived volatiles. In addition, the concentration of alcohols and aldehydes from the acute inflammation model samples were significantly higher than that for the chronic inflammation model samples. The different profiles between these samples could also be identified by this method. Finally, it was possible to analyze alcohols and low-molecular-weight volatiles that are difficult to analyze by SPME in high sensitivity and to show volatile profiling based on multi-volatile simultaneous analysis.

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Mycolic acids (MAs) are characteristic components of bacteria in the suborder Corynebacterineae, such as Mycobacterium. MAs are categorized into subclasses based on their functional bases (cyclopropane ring, methoxy, keto, and epoxy group). Since MAs have heterogeneity among bacterial species, analyzing of MAs are required in the chemotaxonomic field. However, their structural analysis is not easy because of their long carbon-chain lengths and several functional groups. In this study, total fatty acid (FA) methyl ester (ME) fraction of M. tuberculosis H37Rv was analyzed by matrix-assisted laser desorption/ionization (MALDI) time-of-flight mass spectrometry (TOFMS) with a spiral ion trajectory (MALDI spiral-TOFMS). The distributions of carbon-chain length and their relative peak intensities were confirmed with those obtained by analysis of each subclass fraction which was separated from total FA ME fraction using thin-layer chromatography (TLC). The observed major peaks were reliably assigned as MAs owing to the high mass accuracy (error<3 ppm). The types of MA subclasses, their distributions of carbon-chain lengths, their relative peak intensities, and the ratio of even- and odd-numbered carbon-chain MAs for the total FA ME fraction were consistent with those of MA subclass fractions. To visualize whole MAs, contour maps of relative peak intensities for whole MAs were created. The contour maps indicated the MA subclasses and their distributions of carbon-chains with relative peak intensities at a glance. Our proposed method allows simple characterization in a short time and thus enables the analysis of large numbers of samples, and it would contribute to the chemotaxonomy.

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Owing to biotransformation, xenobiotics are often found in conjugated form in biological samples such as urine and plasma. Liquid chromatography coupled with accurate mass spectrometry with multistage collision-induced dissociation provides spectral information concerning these metabolites in complex materials. Unfortunately, compound databases typically do not contain a sufficient number of records for such conjugates. We report here on the development of a novel protocol, referred to as ChemProphet, to annotate compounds, including conjugates, using compound databases such as PubChem and ChemSpider. The annotation of conjugates involves three steps: 1. Recognition of the type and number of conjugates in the sample; 2. Compound search and annotation of the deconjugated form; and 3. In silico evaluation of the candidate conjugate. ChemProphet assigns a spectrum to each candidate by automatically exploring the substructures corresponding to the observed product ion spectrum. When finished, it annotates the candidates assigning a rank for each candidate based on the calculated score that ranks its relative likelihood. We assessed our protocol by annotating a benchmark dataset by including the product ion spectra for 102 compounds, annotating the commercially available standard for quercetin 3-glucuronide, and by conducting a model experiment using urine from mice that had been administered a green tea extract. The results show that by using the ChemProphet approach, it is possible to annotate not only the deconjugated molecules but also the conjugated molecules using an automatic interpretation method based on deconjugation that involves multistage collision-induced dissociation and in silico calculated conjugation.

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We previously reported on the development of a portable mass spectrometer for the onsite screening of illicit drugs, but our previous sampling system could only be used for liquid samples. In this study, we report on an attempt to develop a probe heating method that also permits solid samples to be analyzed using a portable mass spectrometer. An aluminum rod is used as the sampling probe. The powdered sample is affixed to the sampling probe or a droplet of sample solution is placed on the tip of the probe and dried. The probe is then placed on a heater to vaporize the sample. The vapor is then introduced into the portable mass spectrometer and analyzed. With the heater temperature set to 130°C, the developed system detected 1 ng of methamphetamine, 1 ng of amphetamine, 3 ng of 3,4-methylenedioxymethamphetamine, 1 ng of 3,4-methylenedioxyamphetamine, and 0.3 ng of cocaine. Even from mixtures consisting of clove powder and methamphetamine powder, methamphetamine ions were detected by tandem mass spectrometry. The developed probe heating method provides a simple method for the analysis of solid samples. A portable mass spectrometer incorporating this method would thus be useful for the onsite screening of illicit drugs.

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Mass spectrometric proteomics is an effective approach for identifying and quantifying histone post-translational modifications (PTMs) and their binding proteins, especially in the cases of methylation and acetylation. However, another vital PTM, phosphorylation, tends to be poorly quantified because it is easily lost and inefficiently ionized. In addition, PTM binding proteins for phosphorylation are sometimes resistant to identification because of their variable binding affinities. Here, we present our efforts to improve the sensitivity of detection of histone H4 tail peptide phosphorylated at serine 1 (H4S1ph) and our successful identification of an H4S1ph binder candidate by means of a chemical proteomics approach.Our nanoLC-MS/MS system permitted semi-quantitative label-free analysis of histone H4 PTM dynamics of cell cycle-synchronized HeLa S3 cells, including phosphorylation, methylation, and acetylation. We show that H4S1ph abundance on nascent histone H4 unmethylated at lysine 20 (H4K20me0) peaks from late S-phase to M-phase. We also attempted to characterize effects of phosphorylation at H4S1 on protein–protein interactions. Specially synthesized photoaffinity bait peptides specifically captured 14-3-3 proteins as novel H4S1ph binding partners, whose interaction was otherwise undetectable by conventional peptide pull-down experiments.This is the first report that analyzes dynamics of PTM pattern on the whole histone H4 tail during cell cycle and enables the identification of PTM binders with low affinities using high-resolution mass spectrometry and photo-affinity bait peptides.

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Conifer and broadleaf trees emit volatile organic compounds in the summer. The major components of these emissions are volatile monoterpenes. Using solid phase microextraction fiber as the adsorbant, monoterpenes were successfully detected and identified in forest air samples. Gas chromatography/mass chromatogram of monoterpenes in the atmosphere of a conifer forest and that of serum from subjects who were walking in a forest were found to be similar each other. The amounts of α-pinene in the subjects became several folds higher after forest walking. The results indicate that monoterpenes in the atmosphere of conifer forests are transferred to and accumulate in subjects by inhalation while they are exposed to this type of environment.

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