Keisuke Shima

A simple and highly successful C‐terminal sequence analysis of proteins by mass spectrometry

A simple and efficient method for C‐terminal sequencing of proteins has long been pursued because it would provide substantial information for identifying the covalent structure, including post‐translational modifications. However, there are still significant impediments to both direct sequencing from C termini of proteins and specific isolation of C‐terminal peptides from proteins. We describe here a highly successful, de novo C‐terminal sequencing method of proteins by employing succinimidyloxycarbonylmethyl tris (2,4,6‐trimethoxyphenyl) phosphonium bromide and mass spectrometry.

Heat-shock protein 27 (Hsp27) as a target of methylglyoxal in gastrointestinal cancer

The molecular mechanisms underlying the posttranslational modification of proteins in gastrointestinal cancer are still unknown. Here, we investigated the role of methylglyoxal modifications in gastrointestinal tumors. Methylglyoxal is a reactive dicarbonyl compound produced from cellular glycolytic intermediates that reacts non-enzymatically with proteins. By using a monoclonal antibody to methylglyoxal-modified proteins, we found that murine heat-shock protein 25 and human heat-shock protein 27 were the major adducted proteins in rat gastric carcinoma mucosal cell line and human colon cancer cell line, respectively. Furthermore, we found that heat-shock protein 27 was modified by methylglyoxal in ascending colon and rectum of patients with cancer. However, methylglyoxal-modified heat-shock protein 25/heat-shock protein 27 was not detected in non cancerous cell lines or in normal subject. Matrix-associated laser desorption/ionization mass spectrometry/mass spectrometry analysis of peptide fragments identified Arg-75, Arg-79, Arg-89, Arg-94, Arg-127, Arg-136, Arg-140, Arg-188, and Lys-123 as methylglyoxal modification sites in heat-shock protein 27 and in phosphorylated heat-shock protein 27. The transfer of methylglyoxal-modified heat-shock protein 27 into rat intestinal epithelial cell line RIE was even more effective in preventing apoptotic cell death than that of native control heat-shock protein 27. Furthermore, methylglyoxal modification of heat-shock protein 27 protected the cells against both the hydrogen peroxide- and cytochrome c-mediated caspase activation, and the hydrogen peroxide-induced production of intracellular reactive oxygen species. The levels of lactate converted from methylglyoxal were increased in carcinoma mucosal cell lines. Our results suggest that posttranslational modification of heat-shock protein 27 by methylglyoxal may have important implications for epithelial cell injury in gastrointestinal cancer.

Selective isolation of N-terminal peptides from proteins and their de novo sequencing by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry without regard to unblocking or blocking of N-terminal amino acids

We have developed a new method to determine the N-terminal amino acid sequences of proteins, regardless of whether their N-termini are modified. This method consists of the following five steps: (1) reduction, S-alkylation and guanidination for targeted proteins; (2) coupling of sulfo-NHS-SS-biotin to N(alpha)-amino groups of proteins; (3) digestion of the modified proteins by an appropriate protease followed by oxidation with performic acid; (4) specific isolation of N-terminal peptides from digests using DITC resins; (5) de novo sequence analysis of the N-terminal peptides by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) using the CAF (chemically assisted fragmentation) method or tandem mass spectrometric (MS/MS) analysis according to unblocked or blocked peptides, respectively. By employing DITC resins instead of avidin resins used in our previous method (Yamaguchi et al., Rapid Commun. Mass Spectrom. 2007; 21: 3329), it has been possible to isolate selectively N-terminal peptides from proteins regardless of modification of N-terminal amino acids. Here we propose a universal method for N-terminal sequence analysis of proteins.

An improved method for de novo sequencing of arginine-containing, Nα-tris(2,4,6-trimethoxyphenyl)phosphonium-acetylated peptides

An improved method for de novo sequencing of arginine-containing peptides modified with succinimidyloxycarbonylmethyl tris(2,4,6-trimethoxyphenyl)phosphonium bromide (TMPP-Ac-OSu) is reported. A tagging reagent, TMPP-Ac-OSu, was introduced to improve the sequence analysis of peptides owing to the simplified fragmentation pattern. However, peptides containing arginine residues did not fragment efficiently even after TMPP-Ac modification at their N-termini. This report describes how fragmentation efficiency of TMPP-Ac-modified arginine-containing peptides was significantly improved by modifying the guanidino group on the side chain of arginine with acetylacetone.

Evaluation of a novel system for analyzing hydrophilic blood metabolites

Metabolomics has recently been developed, and there have been a considerable number of metabolomics-based biomarker studies in the medical research field. Therefore, as a first step toward the practical use of metabolite biomarkers, a simple and quick sample preparation method involving metabolite extraction, metabolite measurement, and data analysis needs to be developed. In this study, we evaluated whether the use of simpler metabolite extraction methods would facilitate the stable analysis of hydrophilic blood metabolites during liquid chromatography/triple quadrupole mass spectrometry (LC/QqQMS)-based metabolome analysis. As a result, the anion and cation metabolites in plasma were stably analyzed via a methanol-based extraction procedure followed by ultrafiltration, and it was also confirmed that a lyophilization step was not necessary. When extraction was performed without a lyophilization step, approximately >50% and >80% of the detected metabolites had relative standard deviation values of <20% during LC/QqQMS-based anion and cation analyses, respectively. In addition, the plasma levels of l-valine, l-leucine, l-isoleucine, l-tyrosine, and l-phenylalanine were quantitatively measured using the corresponding stable isotopes; the SCLAM-2000, a fully automatic pre-treatment system for LC/MS that can be connected online to an LC/MS device; and an extraction procedure based on the simple procedure that we developed. Our findings suggest that simpler pretreatment procedures can be employed during LC/QqQMS-based metabolomics and might aid searches for metabolite biomarker candidates, the validation of metabolite biomarker candidates, and the practical use of metabolite biomarkers.

Application of proteotyping Strain Solution™ ver. 2 software and theoretically calculated mass database in MALDI-TOF MS typing of Salmonella serotype

Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS)-based microbial identification is a popular analytical method. Strain Solution proteotyping software available for MALDI-TOF MS has great potential for the precise and detailed discrimination of microorganisms at serotype- or strain-level, beyond the conventional mass fingerprinting approaches. Here, we constructed a theoretically calculated mass database of Salmonella enterica subspecies enterica consisting of 12 biomarker proteins: ribosomal proteins S8, L15, L17, L21, L25, and S7, Mn-cofactor-containing superoxide dismutase (SodA), peptidyl-prolyl cis-trans isomerase C (PPIase C), and protein Gns, and uncharacterized proteins YibT, YaiA, and YciF, that can allow serotyping of Salmonella. Strain Solution ver. 2 software with the novel database constructed in this study demonstrated that 109 strains (94%), including the major outbreak-associated serotypes, Enteritidis, Typhimurium, and Infantis, could be correctly identified from others by colony-directed MALDI-TOF MS using 116 strains belonging to 23 kinds of typed and untyped serotypes of S. enterica from culture collections, patients, and foods. We conclude that Strain Solution ver. 2 software integrated with the accurate mass database will be useful for the bacterial proteotyping by MALDI-TOF MS-based microbial classification in the clinical and food safety fields.

Region of Interest analysis using mass spectrometry imaging of mitochondrial and sarcomeric proteins in acute cardiac infarction tissue

Matrix-assisted laser desorption ionization image mass spectrometry (MALDI-IMS) has been developed for the identification of peptides in various tissues. The MALDI-IMS signal distribution patterns and quantification of the signal intensities of the regions of interest (ROI) with healthy regions were compared for identification of the disease specific biomarkers. We performed a new ROI analysis using the conventional t-test and data number independent Cohen’s d-value analysis. Using these techniques, we analysed heart tissues after acute myocardial infarction (AMI). As a result, IMS signals of mitochondrial adenosine triphosphate synthase alpha subunit (ATP5A), myosin-6/7(MYH6/7), aortic actin, and the myosin light chain 3 (MYL3) were identified in the infarcted region. In particular, the signals of MYH7 are significantly greater in the infarcted region using ROI analysis. ROI analysis using MALDI-IMS may be a promising technique for the identification of biomarkers for pathological studies that involve the comparison of diseased and control areas.