• Journal of Microbiology and Biotechnology
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• v.14 no.3
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• pp.620-627
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• 2004

On the foundation of a database of genome sequences and protein analyses, the ability to clone a gene based on a peptide analysis is becoming more feasible and effective for identifying a specific gene and its protein product of interest. As such, the current study conducted a protein analysis using 2-D PAGE followed by MALDI- TOF and ESI-MS to identify a highly expressed gene product of C. parasitica. A distinctive and highly expressed protein spot with a molecular size of 47.2 kDa was randomly selected and MALDI-TOF MS analysis was conducted. A homology search indicated that the protein appeared to be a fungal enolase (enol). Meanwhile, multiple alignments of fungal enolases revealed a conserved amino acid sequence, from which degenerated primers were designed. A screening of the genomic $\lambda$ library of C. parasitica, using the PCR amplicon as a probe, was conducted to obtain the full-length gene, while RT-PCR was performed for the cDNA. The E. coli-expressed eno 1 exhibited enolase enzymatic activity, indicating that the cloned gene encoded the C. parasitica enolase. Moreover, ESI-MS of two of the separated peptides resolved from the protein spot on 2-D PAGE revealed sequences identical to the deduced sequences, suggesting that the cloned gene indeed encoded the resolved protein spot. Northern blot analysis indicated a consistent accumulation of an eno1 transcript during the cultivation.

• Journal of Microbiology and Biotechnology
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• v.28 no.7
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• pp.1112-1121
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• 2018

Jeotgal is a Korean traditional fermented seafood with a high concentration of salt. In this study, we isolated lactic acid bacteria (LAB) from galchi (Trichiurus lepturus, hairtail) and myeolchi (Engraulis japonicas, anchovy) jeotgal on MRS agar and MRS agar containing 5% NaCl (MRS agar+5% NaCl), and identified them by using 16S rRNA gene sequencing and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) as culture-dependent methods. We also performed polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) as a culture-independent method to identify bacterial communities. Five samples of galchi-jeotgal and seven samples of myeolchi-jeotgal were collected from different regions in Korea. A total of 327 and 395 colonies were isolated from the galchi- and myeolchi-jeotgal samples, respectively. 16S rRNA gene sequencing and MALDI-TOF MS revealed that the genus Pediococcus was predominant on MRS agar, and Tetragenococcus halophilus on MRS agar+5% NaCl. PCR-DGGE revealed that T. halophilus, Tetragenococcus muriaticus, and Lactobacillus sakei were predominant in both types of jeotgal. T. halophilus was detected in all samples. Even though the same species were identified by both culture-dependent and -independent methods, many species identified by the culture-dependent methods were not in the bacterial list identified by the culture-independent methods. The distribution of bacteria in galchi-jeotgal was more diverse than in myeolchi-jeotgal. The diverse LAB in galchi- and myeolchi-jeotgals can be further studied as candidates for starter cultures to produce fermented foods.

• Korean Journal of Agricultural Science
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• v.45 no.4
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• pp.635-643
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• 2018

Bovine milk is widely consumed by humans and is a primary ingredient of dairy foods. Proteomic approaches have the potential to elucidate complex milk proteins and have been used to study milk of various species. Here, we performed a proteomic analysis using 2-dimensional electrophoresis (2-DE) and matrix assisted laser desorption ionization-time of flight mass spectrometer (MALDI-TOF MS) to identify whey proteins in bovine milk obtained soon after parturition (bovine early milk). The major casein proteins were removed, and the whey proteins were analyzed with 2-dimensional polyacrylamide gel electrophoresis (2-D PAGE). The whey proteins (2 mg) were separated by pI and molecular weight across pH ranges of 3.0 - 10.0 and 4.0 - 7.0. The 2-DE gels held about 300 to 700 detectable protein spots. We randomly picked 12 and nine spots that were consistently expressed in the pH 3.0 - 10.0 and pH 4.0 - 7.0 ranges, respectively. Following MALDI-TOF MS analysis, the 21 randomly selected proteins included proteins known to be present in bovine milk, such as albumin, lactoferrin, serum albumin precursor, T cell receptor, polymeric immunoglobulin receptor, pancreatic trypsin inhibitor, aldehyde oxidase and microglobulin. These proteins have major functions in immune responses, metabolism and protein binding. In summary, we herein identified both known and novel whey proteins present in bovine early milk, and our sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) analysis revealed their expression pattern.

• KSBB Journal
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• v.31 no.4
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• pp.263-269
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• 2016

For decades, the microorganisms in arctic soils have been newly discovered according to the climate change and global warming. In this study, the chemical structure of a lipid A molecule from Pseudomonas sp. strain PAMC 28615 which was newly discovered from arctic soils was characterized by mass spectrometric approaches such as matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) and MALDI multi-stage tandem mass spectrometry (MS). First, lipopolysaccharide (LPS) from Pseudomonas sp. strain PAMC 28615 was extracted and subsequently hydrolyzed to obtain the lipid A. The parent ion peak at m/z 1632 was determined by MALDI-TOF MS, which also can validate our lipid A purification method. For detailed structural determination, we performed the multiple-stage tandem mass analysis ($MS^4$) of the parent ion, and subsequently the abundant fragment ions in each MS stage are tested. The fragment ions in each MS stage were produced from the loss of phosphate groups and fatty acyl groups, which could be used to confirm the composition or the position of the lipid A components. Consequently, the mass spectrometry-based lipid A profiling method could provide the detail chemical structure of lipid A from the Pseudomonas sp. strain PAMC 28615 as an arctic bacterium from the frozen arctic soil.

• Mass Spectrometry Letters
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• v.5 no.4
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• pp.110-114
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• 2014

The method of direct mass spectrometry profiling is reliable and reproducible for the rapid identification of clinical isolates of bacteria and fungi. This is the first study evaluating the approach of MALDI-TOF mass spectrometry profiling for rapid identification of carbapenemase-resistant enterobacteriaceae (CRE). Proof of concept was achieved by the discrimination of CRE using MALDI Biotyper MS based on the protein. This profiling appears promising by the visual observation of consistent unique peaks, albeit low intensity, that could be picked up from the mean spectra (MSP) method. The Biotyper MSP creation and identification methods needed to be optimized to provide significantly improved differences in scores to allow for subspecies identification with and without carbapenemases. These spectra were subjected to visual peak picking and in all cases; there were pertinent differences in the presence or absence of potential biomarker peaks to differentiate isolates. We also evaluated this method for potential discrimination between different carbapenemases bacteria, utilizing the same strategy. Based on our data and pending further investigation in other CREs, MALDI-TOF MS has potential as a diagnostic tool for the rapid identification of even closely related carbapenemases but would require a paradigm shift in which Biotyper suppliers enable more flexible software control of mass spectral profiling methods.

• Bulletin of the Korean Chemical Society
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• v.34 no.6
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• pp.1708-1714
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• 2013

Polyhexamethylene guanidine (PHMG) polymers used as an active ingredient in an antibacterial humidifier disinfectant were reported to cause harm to the human health when inhaled, although physical contact with this material was known to present low toxicity to humans. It is therefore necessary to develop an optimal analysis method which enables detection and analysis of PHMG polymers. MALDI-TOF investigations of PHMG are performed with a variety of matrices, and it is found that CHCA and 2,5-DHB are excellent matrices which well reflects the polymer population even at high mass. For the provided PHMG sample, the number-average ($M_n$) and weight-average ($M_w$) molecular masses were determined to be 744.8 and 810.7, respectively, when the CHCA was used as a matrix. The rank of the matrices in terms of averaged molecular weight was CHCA ~2,5-DHB > 5-NSA > DHAP, THAP > ATT > IAA ~ super-DHB ~ HABA. In addition, PSD of the PHMG oligomer ions exhibited a few unique fragmenation characteristics. The formation of a- and c-type fragments was the major fragmentation pathway, and the 25-Da loss peaks generally accompanied a- and c-type fragments.

• Bulletin of the Korean Chemical Society
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• v.34 no.9
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• pp.2635-2639
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• 2013

The rapid and accurate identification of biological agents is a critical step in the case of bio-terror and biological warfare attacks. Recently, matrix-assisted laser desorption/ionization time-of-flight mass spectrometry has been widely used for the identification of microorganisms. In this study, we describe a method for the rapid and accurate discrimination of Bacillus anthracis spores using MALDI-TOF MS. Our direct in-situ analysis of MALDI-TOF MS does not involve subsequent high-resolution mass analyses and sample preparation steps. This method allowed the detection of species-specific biomarkers from each Bacillus spores. Especially, B. anthracis spores had specific biomarker peaks at 2503, 3089, 3376, 6684, 6698, 6753, and 6840 m/z. Cluster and PCA analyses of the mass spectra of Bacillus spores revealed distinctively separated clusters and within-groups similarity. Therefore, we believe that this method is effective in the real-time identification of biological warfare agents such as B. anthracis as well as other microorganisms in the field.

• Environmental Mutagens and Carcinogens
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• v.26 no.1
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• pp.20-24
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• 2006

An antimicrobial substance was purified from the giant snail body extract (Achatina fulica) using solid-phase extraction and separation on HPLC reversed-phase chromatography. The primary structure were determined by a combination of an automated amino acid sequence and MALDI-TOF Mass. Its molecular mass was found to be 1392.64 Da. This result was in excellent agrement with the theoretical molecular mass calculated from the amino acid sequence. purified peptide showed antimicrobial activity in vitro against Escherichia coli D31. This result indicate that giant snail whole body was potentially antimicrobial.

• Journal of fish pathology
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• v.28 no.3
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• pp.133-143
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• 2015

The antigenic proteins of Lymphocystis disease virus (LCDV) from tumors of olive flounder, Paralichthys olivaceus, are described following characterization by mass spectrometry. In SDS-PAGE, predominant protein bands were observed at 114, 88, 70, 54, 52, 47, 42 and 24 kDa. Western blot analysis showed that antisera reacted strongly at molecular weights of 114, 67 and 54 kDa, and reacted weakly at molecular weights of 74, 70, 36, 24 and 22 kDa. In the identification of LCDV antigenic proteins by matrix-assisted laser desorption ionization (MALDI) TOF mass spectrometry, 10 of 14 excised bands consisted mostly of proteins with amino acid sequences that matched LCDV-C (lymphocystis disease virus isolate China) ORFs. Strong antigens with molecular weights of 114, 67 and 54 kDa were identified as LDVICp236 (chromosome segregation ATPase), LDVICp033 (membrane bound metallopeptidase) and LDVICp157 (hypothetical protein), respectively. Minor antigens with molecular weights of 70, 36, 24 and 22 kDa proteins were identified as LDVICp160 (acetyl-coA hydrolase), LDVICp213 (hypothetical protein), LDVICp039 (hypothetical protein) and LDVICp213 (hypothetical protein). However, the major capsid protein (LDVICp043) did not react with the polyclonal antibody.

• Bulletin of the Korean Chemical Society
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• v.28 no.12
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• pp.2359-2362
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• 2007

MALDI-TOF-MS technique was applied to obtain structural and compositional information of synthetic polyamides, Nylon6 and Nylon66. Mass spectra of both the original and the hydrolyzed polyamide samples were analyzed using the self calibration method as well as the internal calibration method with the standard materials of known masses. The MALDI-TOF mass spectra of Nylon6 samples showed the presence of protonated, sodiated, and potassiated ions that were assigned to cyclic and NH2/COOH terminated linear oligomers. From the MALDI-TOF mass spectra of Nylon66 samples, the potassiated linear oligomers with three different end groups are identified as well as the cyclic oligomers, i.e., NH2/COOH terminated oligomers, NH2/NH2 terminated oligomers, and COOH/COOH terminated oligomers. Full characterization of the molecular species and end groups present in the polyamide samples has been achieved, and also the changes in mass spectral patterns after the hydrolysis of the samples are presented.