[Show abstract][Hide abstract] ABSTRACT: High-resolution mass spectrometry (HRMS) continues to play an important role in the compositional characterization of larger organic molecules. In the field of polymer characterization, however, the application of HRMS has made only slow progress because of lower compatibility between matrix-assisted laser desorption/ionization (MALDI) and ultrahigh-resolution Fourier transform ion cyclotron resonance mass spectrometry (FT-ICRMS). In this study, a newly developed type of MALDI high-resolution time-of-flight mass spectrometry (TOFMS) with a spiral ion trajectory (MALDI spiral-TOFMS) was applied to the structural and compositional characterization of polymers. To create a graphical distribution of polymer components on a two-dimensional plot converted from complex mass spectra, we adopted a slightly modified Kendrick mass defect (KMD) analysis based on accurate masses determined using spiral-TOFMS. By setting the Kendrick mass scale based on the mass of the repeating units of a given polymer, components with common repeat units lined up in the horizontal direction on the KMD plot, whereas those components with different structures were shifted vertically. This combination of MALDI spiral-TOFMS measurement and KMD analysis enabled the successful discrimination of the polymer components in a blend of poly(alkylene oxide)s, the compositional analysis of poly(ethylene oxide)/poly(propylene oxide) block copolymers, and profiling of the end-group distribution of poly(ε-caprolactone)s synthesized under different conditions.
Journal of the American Society for Mass Spectrometry 05/2014; · 3.59 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: Mycolic acids have been used as important chemotaxonomic markers. In this study, a newly developed matrix-assisted laser desorption/ionization time-of-flight mass spectrometer with a spiral ion trajectory (MALDI spiral-TOFMS) was applied to the characterization of mycolic acids of three type strains of validated species belonging to the genus Dietzia (D. papillomatosis 105045(T), D. kunjamensis NBRC 105042(T) and D. timorensis NBRC 104184(T)), by analysis of total fatty acid methyl ester fractions. In addition, owing to the high mass-resolving power of MALDI spiral-TOFMS, adjacent peaks (0.036 Da mass differences) were successfully separated, and weak peaks corresponding to oxygenated mycolic acids were detected. For all samples, the distributions of carbon-chain lengths were mainly in the range of C30-C42 and the average number of carbon-chain lengths was about 37, which agreed reasonably well with reported results for the genus Dietzia. The number of double bonds and/or cyclopropane rings was 0-2. Relative peak intensities of each mycolic acid methyl ester were used to compare the mycolic acids of the three strains. The mycolic acids of D. papillomatosis and D. kunjamensis were characterized by a high content of mycolic acids with 0-1 double bond or cyclopropane ring and an almost equal content of mycolic acids with odd- and even-numbered carbon-chain lengths. In contrast, mycolic acids of D. timorensis were characterized by a high content of mycolic acids with 1-2 double bonds and/or cyclopropane rings with an even-numbered carbon-chain length. By using MALDI spiral-TOFMS, mycolic acids from three type strains of the genus Dietzia were characterized easily and rapidly.The Journal of Antibiotics advance online publication, 28 August 2013; doi:10.1038/ja.2013.79.
The Journal of Antibiotics 08/2013; · 2.04 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: Matrix-assisted laser-desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) is one of the most widely used mass-based approaches for bacterial identification and classification because of the simple sample preparation and extremely rapid analysis within a few minutes. To establish the accurate MALDI-TOF MS bacterial discrimination method at strain level, the ribosomal subunit proteins coded in the S10-spc-alpha operon, which encodes half of the ribosomal subunit protein and is highly conserved in eubacterial genomes, were selected as reliable biomarkers. This method, named the S10-GERMS method, revealed that the strains of genus Pseudomonas were successfully identified and discriminated at species and strain levels, respectively; therefore, the S10-GERMS method was further applied to discriminate the pathovar of P. syringae. The eight selected biomarkers (L24, L30, S10, S12, S14, S16, S17, and S19) suggested the rapid discrimination of P. syringae at the strain (pathovar) level. The S10-GERMS method appears to be a powerful tool for rapid and reliable bacterial discrimination and successful phylogenetic characterization. In this article, an overview of the utilization of results from the S10-GERMS method is presented, highlighting the characterization of the Lactobacillus casei group and discrimination of the bacteria of genera Bacillus and Sphingopyxis despite only two and one base difference in the 16S rRNA gene sequence, respectively.
Journal of the American Society for Mass Spectrometry 05/2013; · 3.59 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: The structural characterization of copolymers by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOFMS) remains a challenging task, since their random comonomer distribution creates very complicated mass spectra. In this study, a high-resolution TOF mass spectrometer with a spiral ion trajectory was applied to the structural and compositional characterization of free radical copolymerized poly(methyl methacrylate-co-tert-butyl methacrylate), poly(MMA-co-tBMA)s in ethyl lactate acting as a chain transfer agent. Virtually complete peak assignments of the isobaric components within the poly(MMA-co-tBMA)s served to identify the end-group combinations and copolymer compositions of individual copolymer components, allowing the distributions of comonomer compositions and six types of end-group combinations to be evaluated.
Mass spectrometry (Tokyo, Japan). 01/2013; 2(1):A0014.
[Show abstract][Hide abstract] ABSTRACT: The taxonomy of the members of the Lactobacillus casei group is complicated because of their phylogenetic similarity and controversial nomenclatural status. In this study, matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) of ribosomal proteins coded in the S10-spc-alpha operon, termed S10-GERMS, was applied in order to classify 33 sample strains belonging to the L. casei group. A total of 14 types of ribosomal protein genes coded in the operon were first sequenced from four type strains of the L. casei group (L. casei JCM 1134(T), L. paracasei subsp. paracasei JCM 8130(T), L. paracasei subsp. tolerans JCM 1171(T), and L. rhamnosus JCM 1136(T)) together with L. casei JCM 11302, which is the former type strain of 'L. zeae'. The theoretical masses of the 14 types of ribosomal proteins used as biomarkers were classified into five types and compiled into a ribosomal protein database. The observed ribosomal proteins of each strain, identified by MALDI-TOF MS, were categorized into types based on their masses, summarized as ribosomal protein profiles, and they were used to construct a phylogenetic tree. The 33 sample strains, together with seven genome-sequenced strains, could be classified into four major clusters, which coincided precisely with the taxa of the (sub)species within the L. casei group. Three "ancient" strains, identified as L. acidophilus and L. casei, were correctly re-identified as L. paracasei subsp. paracasei by S10-GERMS. S10-GERMS would thus appear to be a powerful tool for phylogenetic characterization, with considerable potential for management of culture collections.
Systematic and Applied Microbiology 10/2012; · 3.31 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: Matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) using ribosomal subunit proteins coded in the S10-spc-alpha operon as biomarkers was applied for the classification of the Sphingomonadaceae from the environment. To construct a ribosomal protein database, S10-spc-alpha operon of type strains of the Sphingomonadaceae and their related alkylphenol polyethoxylate (APEO(n) )-degrading bacteria were sequenced using specific primers designed based on nucleotide sequences of genome-sequenced strains. The observed MALDI mass spectra of intact cells were compared with the theoretical mass of the constructed ribosomal protein database. The nine selected biomarkers coded in the S10-spc-alpha operon, L18, L22, L24, L29, L30, S08, S14, S17, and S19, could successfully distinguish the Sphingopyxis terrae NBRC 15098(T) and APEO(n) -degrading bacteria strain BSN20, despite only one base difference in the 16S rRNA gene sequence. This method, named the S10-GERMS (S10-spc-alpha operon gene-encoded ribosomal protein mass spectrum) method, is a significantly useful tool for bacterial discrimination of the Sphingomonadaceae at the strain level and can detect and monitor the main APEO(n) -degrading bacteria in the environment.
[Show abstract][Hide abstract] ABSTRACT: A rapid bacterial identification method by matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) using ribosomal proteins coded in S10 and spc operons as biomarkers, named the S10-GERMS (the S10-spc-alpha operon gene encoded ribosomal protein mass spectrum) method, was applied for the genus Bacillus a Gram-positive bacterium. The S10-GERMS method could successfully distinguish the difference between B. subtilis subsp. subtilis NBRC 13719(T) and B. subtilis subsp. spizizenii NBRC 101239(T) because of the mass difference of 2 ribosomal subunit proteins, despite the difference of only 2 bases in the 16S rRNA gene between them. The 8 selected reliable and reproducible ribosomal subunit proteins without disturbance of S/N level on MALDI-TOF MS analysis, S10, S14, S19, L18, L22, L24, L29, and L30, coded in S10 and spc operons were significantly useful biomarkers for rapid bacterial classification at species and strain levels by the S10-GERMS method of genus Bacillus strains without purification of ribosomal proteins.
Journal of Agricultural and Food Chemistry 04/2011; 59(10):5222-30. · 3.11 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: The taxonomic positions of the subspecies of Bifidobacterium longum (B. longum subsp. longum, subsp. infantis, and subsp. suis) have been controversial. A current proposal is that the former two species "B. infantis" and "B. suis" be unified with B. longum and all three reclassified as three subspecies. To test this proposal, ribosomal protein profiling as observed by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) was applied to the classification of 17 strains of B. longum, including three subspecies. Among 41 different kinds of ribosomal proteins selected as biomarkers whose masses were calculated from their amino acid sequences, 31-41 ribosomal proteins were observed in sample strains with the same masses as the references. The high matching rate indicates high conservation of ribosomal proteins within the sample strains, and therefore strongly supports the unification of the former species. However, the masses of some ribosomal proteins varied within species. The phylogenetic tree constructed from the profiles of ribosomal proteins matched the references, showing a clear cluster of the subsp. longum and the subsp. infantis strains. This result supports the proposal to reclassify B. longum into subsp. longum and subsp. infantis. The subsp. suis strains formed an individual sub-cluster within the infantis cluster. However, their ribosomal proteins have both characters of longum and infantis types. This result suggests that the taxonomic position of the subsp. suis should be reconsidered.
Systematic and Applied Microbiology 02/2011; 34(1):76-80. · 3.31 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: We have proposed a rapid phylogenetic classification at the strain level by MALDI-TOF MS using ribosomal protein matching profiling. In this study, the S10-spc-alpha operon, encoding half of the ribosomal subunit proteins and highly conserved in eubacterial genomes, was selected for construction of the ribosomal protein database as biomarkers for bacterial identification by MALDI-TOF MS analysis to establish a more reliable phylogenetic classification. Our method revealed that the 14 reliable and reproducible ribosomal subunit proteins with less than m/z 15,000, except for L14, coded in the S10-spc-alpha operon were significantly useful biomarkers for bacterial classification at species and strain levels by MALDI-TOF MS analysis of genus Pseudomonas strains. The obtained phylogenetic tree was consisted with that based on genetic sequence (gyrB). Since S10-spc-alpha operons of genus Pseudomonas strains were sequenced using specific primers designed based on nucleotide sequences of genome-sequenced strains, the ribosomal subunit proteins encoded in S10-spc-alpha operon were suitable biomarkers for construction and correction of the database. MALDI-TOF MS analysis using these 14 selected ribosomal proteins is a rapid, efficient, and versatile bacterial identification method with the validation procedure for the obtained results.
Journal of Proteome Research 10/2010; 9(12):6722-8. · 5.06 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: Rhodococcus erythropolis strains characterized as antibiotic producers can be classified into three groups according to their antibiotic spectrum and growth compatibility. Due to their high genotypic similarity, the taxonomic relationship of these strains has not been elucidated. In this study, ribosomal protein profiling using matrix-assisted laser desorption ionization-mass spectrometry (MALDI-MS) was employed to classify twenty-one strains of R. erythropolis (15 antibiotic producers and 6 non-antibiotic producers). In the first step in this method, a total of 30 intense peaks observed for purified ribosomal subunit proteins of the type strain (R. erythropolis JCM 3201(T)) were selected as the reference peaks. The mass spectra observed for the cell lysates of each sample strain were then checked as to whether peaks were observed at the same masses of the reference peaks. The results of peak matching were processed by cluster analysis, generating a dendrogram. Four major clusters of the R. erythropolis strains corresponded to three antibiotic groups and the non-antibiotic group. Furthermore, the topology of the dendrogram was highly comparable with the phylogenetic tree based on DNA gyrase subunit B gene (gyrB) sequencing. These results indicate that our proposed ribosomal protein profiling method using MALDI-MS is a potentially reliable and sufficiently high-throughput technique for the taxonomic analysis of closely related bacterial strains without using DNA sequence information.
Journal of Bioscience and Bioengineering 11/2009; 108(4):348-53. · 1.74 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: In surface-assisted laser desorption/ionization mass spectrometry (SALDI-MS), a chemical background signal, arising from organic contaminants such as plasticizers, is frequently observed mainly under m/z ca. 600, which impairs the advantages of the matrix-free approach. Silver salts, which are used for the cationization of aromatic compounds, are also difficult to remove completely after the measurements. In this study, surface cleaning techniques used in semiconductor processing were used to clean our developed silicon-based SALDI substrate on which self-assembled germanium nanodots (GeNDs) had been deposited (termed a GeND chip). An immersion cleaning method using acetone with sonication, and a sulfuric-peroxide mixture (SPM) cleaning method using a mixture of H(2)SO(4)/H(2)O(2)/deionized water, were examined for their effectiveness in removing organic compounds and residual silver salts. Removal of both types of contaminants was successfully performed by SPM cleaning. The limit of detection for glutathione was improved from ca. 5 pmol without cleaning to ca. 50 fmol after the SPM cleaning. Since GeND chips can tolerate acidic cleaning and sonication due to their chemical inertness and rigid nanodot structures, they appear to be an ideal reusable SALDI substrate.
Rapid Communications in Mass Spectrometry 03/2009; 23(5):603-10. · 2.64 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: A search of streptomycin-resistant bacteria was carried out using ten creek water samples collected in Saga prefecture by spreading the sample water on an R2A medium containing 10 microg/ml of streptomycin. It was clarified that such streptomycin-resistant bacteria as Bacillus, Novosphigobium, Sphingopyxis and Oceanobacillus were distributed in the creek water. Further, 60% of the isolates didn't form an inhibitory zone by the application of 700 microg/ml streptomycin solution in the cup method assay. Further, the effectiveness of the MALDI-TOF MS analysis for the grouping of the isolates was examined. The discriminating ability of MALDI-TOF MS analysis was higher than that of RFLP analysis and it was almost equal to that of sequence analysis using 16S rDNA. Considering the high-throughput ability of the MALDI-TOF MS instrument, MALDI-TOF mass spectral identification of bacteria will be a powerful method in the construction of a MALDI-TOF mass spectra database.
[Show abstract][Hide abstract] ABSTRACT: A new method for phylogenetic classification of bacterial strains using matrix-assisted laser desorption/ionization-mass spectrometry (MALDI-MS) is proposed. This method was developed using a bioinformatics-based approach to the rapid identification of bacteria as previously proposed by Demirev and co-workers, which uses ribosomal proteins composed of approximately 50 subunit proteins as biomarkers. Although the amino acid sequences of ribosomal proteins are highly conserved, slight sequence variations can occur at the strain level. Since ribosomal subunit proteins are a complex of housekeeping proteins that have different phylogenetic evolution rates, sequence variation detected as mass differences by MALDI-MS may be useful for the phylogenetic classification of bacteria at strain level. In our proposed method, the first step is the selection of reliable biomarkers through characterization of the expressed ribosomal subunit proteins of a reference strain (usually a genome-sequenced strain) by MALDI-MS. The observed masses in the MALDI mass spectra of cell lysates of sample strains are then compared with the biomarker masses of the reference strain. The biomarkers for each sample strain were designated as present or absent at the reference masses, indicated by 1 or 0, respectively, which were summarized in a table. This table is processed by cluster analysis, generating a phylogenetic tree. In this study, the success of this approach was confirmed by classification of Pseudomonas putida strains because its classification is much more complicated than that of other bacterial strains. Forty-three reliable biomarkers were selected from ribosomal sub-unit proteins of a genome-sequenced strain, P. putida KT2440. The numbers and kinds of biomarkers observed for 16 strains of P. putida, including different biovars, were markedly different, reflecting the variety of the strains. The classification results by the proposed method were highly comparable to those based on the DNA gyrase subunit B gene (gyrB) sequence analysis, suggesting our proposed method would be a useful high-throughput method for phylogenetic classification of newly isolated bacteria.
[Show abstract][Hide abstract] ABSTRACT: Rapid identification of bacteria by a bioinformatics-based approach, which processes the mass spectra observed by matrix-assisted laser desorption/ionization-mass spectrometry (MALDI-MS), relies on the calculated masses of ribosomal subunit proteins as biomarkers predicted from amino acid sequences found in protein sequence databases. To verify the actual state of the registered sequence information, a simple intact protein analysis by MALDI-MS using cell lysates as samples was applied to the characterization of ribosomal proteins from genome-sequenced Streptococcus thermophilus and Lactobacillus delbrueckii subsp. bulgaricus strains. This method avoided the risk of loss of some subunit proteins and the formation of disulfide bonds during the purification of ribosomal proteins. By comparing this with the MALDI mass spectra of different strains and carrying out manual inspection of sequence information, a total of five errors in N-terminal amino acid sequences were identified. After sequence correction, approximately 40 out of 53 subunit proteins could be assigned, considering N-terminal methionine loss only as a post-translational modification. These show promise for use as practical biomarkers for the rapid identification of S. thermophilus and L. bulgaricus. After verification of these amino acid sequences, mass differences relative to those of genome-sequenced strains have the potential for distinguishing bacteria at the strain level.
Journal of Proteome Research 11/2007; 6(10):3899-907. · 5.00 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: A novel ionization platform for matrix-free laser desorption/ionization-mass spectrometry (LDI-MS) was developed using self-assembled germanium nanodots (GeNDs) of uniform size (approximately 150 - 200-nm width and approximately 50-nm height) grown on a silicon wafer produced by molecular beam epitaxy. The performance of LDI-MS using GeNDs (GeND-MS) was investigated through measurements of a broad range of analytes, including peptides, proteins, synthetic oligomers, and polymer additives. Mass spectra of tryptic digests were clearly observed even for the mass range lower than m/z 800 without obstructive peaks. A detection limit of subfemtomole level was achieved for angiotensin-I. The upper limit of detectable mass range was approximately 17 kDa (myoglobin). GeND-MS also has potential for application to the characterization of industrial compounds. Almost accurate molecular weight distribution was obtained for a nonionic surfactant (Triton X-100) and for poly(ethylene glycol) oligomer. Furthermore, a brominated flame retardant, tetrabromobisphenol-A bis(2,3-dibromopropyl ether), was successfully ionized with less fragmentation, a result not obtainable by matrix-assisted laser desorption/ionization-mass spectrometry or desorption/ionization on porous silicon-mass spectrometry.
[Show abstract][Hide abstract] ABSTRACT: Nylon 6-clay hybrid (NCH) was characterized by temperature-programmed pyrolysis (TPPy) techniques such as TPPy-mass spectrometry and TPPy-gas chromatography mainly focusing on the interaction between nylon 6 molecule and the surface of silicate monolayers in the NCH samples, which leads to the superior properties of the hybrid nanomateirals. Pyrolysis profile of nylon 6 matrix in the NCH samples was gradually shifted to lower temperature region with increase in the clay content. The yields of main pyrolysis products such as ϵ-caprolactam from the NCH samples decreased with increase in the clay content, whereas those of the nitrile compounds significantly increased. These results suggested that the clay surface accelerate cis-elimination reaction of nylon 6 matrix in the NCH samples to form the nitrile compounds rather than intramolecular amide exchange to ϵ-caprolactam. Based on the changes in pyrolysis behaviors of nylon 6 matrix in the NCH samples, the interaction between positively charged NH proton of nylon 6 molecules and negatively charged clay surface was proposed which would stabilize the six-membered transition state during pyrolysis.Keywords: Nylon 6-clay Hybrid, Polymer-silicate Interaction, Nanocomposite, Pyrolysis, Gas Chromatography, Mass Spectrometry
[Show abstract][Hide abstract] ABSTRACT: For rapid identification of bacteria by matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS), a bioinformatics approach using ribosomal subunit proteins as biomarkers has been proposed. This method compares the observed masses for biomarkers with calculated masses as predicted from the amino acid sequences registered on protein databases. To evaluate this approach, the expressed ribosomal proteins of a genome-sequenced bacterium, Lactobacillus plantarum NCIMB 8826, were characterized as a model sample. The protein expression of 42 ribosomal subunit proteins, together with 10 ribosome-associated proteins in the isolated ribosome fraction, was confirmed through two-dimensional gel electrophoresis combined with peptide mass fingerprinting. The observed masses of the proteins in the isolated ribosome fraction were then determined by MALDI-MS. We preliminarily selected 44 biomarkers whose observed masses were matched with the calculated masses predicted from the amino acid sequence registered in the protein databases by considering N-terminal methionine loss only. Of these, the finally selected reliable biomarkers were 34 proteins including 31 ribosomal subunit proteins and 3 ribosome-associated proteins that could be observed in the MALDI mass spectra of the cell lysate sample. These biomarkers were usable in MALDI-MS characterization of two industrial L. plantarum cultures.
Rapid Communications in Mass Spectrometry 02/2006; 20(24):3789-98. · 2.64 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: Copolymer composition of a biodegradable aliphatic copolyester, poly(3-hydroxybutyrate-co-3-hydroxyvalerate) (P(3HB-co-3HV)) with a wide range of 3HV contents (ca. 4–23mol%) was determined by pyrolysis-gas chromatography (Py-GC) in the presence of tetramethylammonium hydroxide (TMAH). Nine major peaks of methylated products, five of which were attributed to the products from 3HV unit and the other four from 3HB unit, were commonly observed in the pyrograms. The copolymer compositions of P(3HB-co-3HV) samples estimated based on the relative intensities of these peaks were consistent with those by 1H NMR. These results demonstrated that Py-GC in the presence of TMAH can be applied to the accurate and highly sensitive compositional analysis of P(3HB-co-3HV) using trace amounts (ca. 0.1mg or less) of the samples. Furthermore, the fact that a small amount (ca. 1%) of the pyrolyzate from 3HV unit was also observed on the pyrogram of a commercially available poly(3-hydroxybutyrate), PHB, suggested that the given PHB might be actually a copolymer containing minor amount of 3HV unit.
Journal of Analytical and Applied Pyrolysis 08/2005; 74(1):193-199. · 3.07 Impact Factor