• KIISE Transactions on Computing Practices
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• v.22 no.1
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• pp.56-60
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• 2016

Peptide identification in tandem mass spectrometry is usually done by searching the spectra against target databases consisting of reference protein sequences. To control false discovery rates for high-confidence peptide identification, spectra are also searched against decoy databases constructed by permuting reference protein sequences. In this case, a peptide of the same sequence could be included in both the target and the decoy databases or multiple entries of a same peptide could exist in the decoy database. These phenomena make the protein identification problem complicated. Thus, it is important to minimize the number of such redundant peptides for accurate protein identification. In this regard, we examined two popular methods for decoy database generation: 'pseudo-shuffling' and 'pseudo-reversing'. We experimented with target databases of varying sizes and investigated the effect of the maximum number of missed cleavage sites allowed in a peptide (MC), which is one of the parameters for target and decoy database generation. In our experiments, the level of redundancy in decoy databases was proportional to the target database size and the value of MC, due to the increase in the number of short peptides (7 to 10 AA). Moreover, 'pseudo-reversing' always generated decoy databases with lower levels of redundancy compared to 'pseudo-shuffling'.

• Analytical Science and Technology
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• v.24 no.6
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• pp.407-413
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• 2011

Over the last decade sophisticated and powerful microcapillary HPLC for proteomic analysis have been developed increasingly and interfaced with high resolution tandem mass spectrometers. Separation prior to mass spectrometric (MS) analysis removes impurities, and concentrates analytes in the narrow elution peaks, resulting in increased sensitivity of MS analysis. This review will focus on the recent advances of on-line highperformance separation techniques based on microfluidic chips for complex proteomic analysis.

• Journal of KIISE:Software and Applications
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• v.34 no.10
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• pp.889-899
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• 2007

In proteomics, recent advancements In mass spectrometry technology and in protein extraction and separation technology made high-throughput analysis possible. This leads to thousands to hundreds of thousands of MS/MS spectra per single LC-MS/MS experiment. Such a large amount of data creates significant computational challenges and therefore effective data analysis methods that make efficient use of computational resources and, at the same time, provide more peptide identifications are in great need. Here, SIFTER system is designed to avoid inefficient processing of shotgun proteomic data. SIFTER provides software tools that can improve throughput of mass spectrometry-based peptide identification by filtering out poor-quality tandem mass spectra and estimating a Peptide charge state prior to applying analysis algorithms. SIFTER tools characterize and assess spectral features and thus significantly reduce the computation time and false positive rates by localizing spectra that lead to wrong identification prior to full-blown analysis. SIFTER enables fast and in-depth interpretation of tandem mass spectra.

• Journal of The Korean Society of Inherited Metabolic disease
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• v.15 no.2
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• pp.59-64
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• 2015

Purpose: Lactate has two optical isomers, L-lactate and D-lactate. In human L-lactate is the most abundant enantiomer of lactate. As plasma and urinary levels of L-lactate is associated with inherited metabolic disorders in general, D-lactate have been linked to the presence of diabetes and inflammatory bowel disease. Previously developed techniques have shown several limitations to further evaluate D-lactate as a biomarker for this condition. In this paper, we describe a highly sensitive, specific and fast liquid chromatography tandem mass spectrometry (LC-MS/MS) method for the analysis of D-, L-lactate in urine. Methods: D- and L-lactate were quantified using high performance liquid chromatography tandem mass spectrometry (LC-MS/MS) with labelled internal standard. Samples were derivatized with (+)-O,O'-diacety-L-tartaric anhydride (DATAN) and seperated on a Poroshell 120 EC-C18 column. Results: Quantitative analysis of D-, and L-lactate was achieved successfully. Calibration curves were linear (r>0.999) over $0.5-100{\mu}g/mL$. Stabilities for samples were within the 10% varation. Inter- and Intra-day assay variations were below 10%. Conclusion: The presented method proved to be suitable for the quantitation of D- and L-lactate and opens the possibility to explore the use of D-lactate as a biomarker.

• Journal of Life Science
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• v.29 no.2
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• pp.198-201
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• 2019

Recently, it has been reported that Bacillus mojavensis possesses antifungal properties and plant growth-promoting activities, which are similar to the characteristics of siderophore. In this study, the siderophore produced by B. mojavensis was assessed using a solid phase extraction (SPE) cartridge and liquid chromatography quadrupole time-of-flight tandem mass spectrometry (Q-TOF MS/MS). After B. mojavensis was incubated in phenol medium for 16 hr and lyophilized, the sample was dissolved in water and loaded to an SPE cartridge to remove interferences. The cartridge was washed with 5% methanol in water and eluted with 2% formic acid in methanol sequentially. The eluted solution was evaporated under a stream of nitrogen gas and reconstituted in methanol. The reconstituted sample was filtered, and $1{\mu}l$ of the sample was assessed using Q-TOF MS/MS. The mass spectrometer was operated using the positive electrospray ionization mode. Based on the mass spectrum and tandem mass spectrum, the siderophore produced by B. mojavensis was bacillibactin, one of the catechol types of siderophore with a molecular weight of 882.2556. This siderophore analysis could provide a justification for the study of B. mojavensis as a functional food and for pharmaceutical applications.

• Korean Journal of Clinical Laboratory Science
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• v.52 no.2
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• pp.91-97
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• 2020

Standardization of vitamin analysis continues around the world, and much effort has been made to improve the accuracy of the results. This study analyzed the sigma metrics of the vitamin D test using the external quality assessment (EQA) program. Sigma metrics is used for quantitative tests performed in the laboratory, and the test results can be objectively visualized in terms of quality. This analysis was performed based on the accuracy of the College of American Pathologists (CAP) using the results of the 2019 accuracy-based vitamin D (ABVD) survey, and about 300 laboratories participated in the survey. Reference values were obtained by the Center for Disease Control and Prevention (CDC) reference laboratory. At six different concentrations, the sigma metrics were analyzed to be 1.00, 1.85, 2.42, 1.01, 1.54 and 0.78, respectively. An average of 1.43 sigma metrics was determined. In particular, only positive biases for ABVD-16 and 17 were shown in the liquid chromatography tandem-mass spectrometry (LC-MS/MS), which is the standard method for vitamin D determination when compared to the reference values. The causes of the difference can be explained by cross reactivity to various vitamin D metabolites. Laboratories need to improve their overall performance.

• Analytical Science and Technology
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• v.20 no.2
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• pp.138-146
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• 2007

A simple and sensitive method for the determination of paroxetine in canine plasma was developed and validated by liquid-liquid extraction and liquid chromatography-tandem mass spectrometry (LC-/MS/MS). Fluoxetine was used as an internal standard. Paroxetine and internal standard in plasma samples were extracted using TBME (tert-butyl methyl ether). A centrifuged upper layer was then evaporated and reconstituted with mobile phase of 50% acetonitrile adjusted to pH 3 by formic acid. The reconstituted samples were injected into a Capcell Pak UG120 ($2.0{\times}150mm$, $5{\mu}m$) column. Using MS/MS with SRM (selective reaction monitoring) mode, the transitions (precursor to product) monitored were m/z $330{\rightarrow}192$ for paroxetine, and m/z $310{\rightarrow}148$ for internal standard. Linear detection responses were obtained for paroxetine concentration range of 0.02~5 ng/mL. A correlation coefficient of linear regression ($R^2$) was 0.9993. Detection of paroxetine in canine plasma was accurate and precise, with limit of quantification at 0.02 ng/mL. The method has been successfully applied to pharmacokinetic study of paroxetine in healthy beagle dogs.

• Journal of Applied Biological Chemistry
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• v.65 no.3
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• pp.173-181
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• 2022

This study was carried out to investigate the residual characteristics of flubendiamide in kale to establish pre-harvest residue limits (PHRL) and the removal efficiency according to the washing solvent and method. Field tests were conducted at two different greenhouses, field 1 (Anseong-si, Gyeonggi-do) and field 2 (Incheon-si, Gyeonggi-do). According to the safe use guidelines kale was sprayed with flubendiamide twice every 10 days and harvested 0 (after 2 h), 1, 2, 3, 5, 7 and 10 days after the final application. The biological half-live of flubendiamide in kale was calculated based on dissipation curves of the pesticide in samples analyzed by liquid chromatography coupled with tandem mass spectrometry. In the analysis, method limits of quantitation (MLOQ) were 0.01 mg/kg, and recoveries performed with two different fortification levels of 10 MLOQ and maximum residue limit (0.7 mg/kg) were 104.2±3.6 and 101.9±10.2%, respectively. The dissipation rate constant of flubendiamide in kales were 0.2437 at field 1 and 0.1981 at field 2. PHRL calculation equations obtained using the dissipation constants estimated as follows: if the residual concentration of flubendiamide in kale on 10 days before harvest is less than 8.0 mg/kg, the residual concentration on the harvest would be under MRL. The removal of flubendiamide from kale was the greatest when it was washed with vinegar (39.8%), followed by baking soda (31.7%), calcium powder (30.2%), neutral detergent (27.2%), and tap water (15.9%). The results of this study would be useful for both farmers and consumers to produce or consume safe agricultural products.

• Journal of The Korean Society of Inherited Metabolic disease
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• v.14 no.2
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• pp.135-141
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• 2014

Objectives: Fabry disease (FD) is a lysosomal storage disease caused by the inappropriate accumulation of globotriaosylceramide (Gb3) in tissues due to a deficiency in the enzyme ${\alpha}$-galactosidase A. Hypertrophic cardiomyopathy is one of the chronic complications of FD. We tried to evaluate the prevalence of Fabry disease in the Korean patients with left ventricular hypertrophy (LVH). Methods: A total of 257 patients with LVH were recruited and they were 172 males (mean 56 years, range 30-81 years) and 84 females (mean 66 years, range 45-85 years). Urinary Gb3 was used to screen FD by high performance liquid chromatography-tandem mass spectrometry. Confirmatory tests were done by alpha-galactosidaseA activity using fluorometric assay and by GLA mutation analysis using sequencing. Results: Four patients were screening positive by urinary Gb3 analysis (cutoff, 25 ug/mmol creatinine). But, one female patient was diagnosed with FD confirmed by enzyme analysis in leukocytes as well as by genetic analysis (1/257 patients, 0.4%). She showed 54.3 ug/mmoL creatinine of Gb3 and 15.5 nmole/hr/mg protein (reference range, $55.2{\pm}12.7nmole/hr/mg$ protein) of alphagalactosidase A activity. And she had a heterozygous GLA mutation of c.796G>A (p.D266N). Her daughter was found to be a carrier for FD confirmed by GLA mutation analysis. Asymptomatic carrier showed 25.5ug/mmol creatinine of Gb3 and 42.5 nmole/hr/mg protein (reference range, $55.2{\pm}12.7nmole/hr/mg$ protein) of alpha-galactosidase A activity. Conclusions: The prevalence of FD in Koran patients with LVH was detected as 0.4%. Although the prevalence seems to be low, screening studies are of great importance for detecting hidden cases as well as for identifying other effected family members.

• Journal of The Korean Society of Inherited Metabolic disease
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• v.18 no.2
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• pp.35-42
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• 2018

Purpose: To follow up Korean patients with metabolic and endocrine disorders ascertained by Korea Genetics Research Center, and assess the long-term effectiveness of extended newborn screening program in Korea. Methods: From January 2000 to December 2017, tandem mass spectrometry and fluoroimmunoassay were employed in extended newborn screening (NBS). The NBS program obtained dried blood spots from 283,626 babies, 48 hours after birth, and screened for galactosemia, congenital hypothyroidism (CH), congenital adrenal hyperplasia (CAH), and 50 preventable inborn errors of amino acid, fatty acid, and organic acid metabolism. Results: 28 cases of amino acid disorders, 75 cases of organic acid disorders, 27 cases of fatty acid disorders, 51 cases of urea cycle disorders, 127 cases of CH, 14 cases of CAH, and 15 cases of galactosemia were ascertained through NBS and subsequent confirmatory laboratory tests. Patients with amino acid metabolic disorders, galactosemia, CH, or CAH were more likely to have a better long-term outcome if detected early. Early management of MSUD led to much better outcome in over 90%. Despite early intervention, 32% of other organic acidemia cases still resulted in developmental delay and neurological problems. Fatty acid disorders showed varied results; those with EMA and MCAD had a good outcome, but those with VLCAD had serious neurological problems and considerably higher mortality. 75% with UCD experienced serious neurological complications and higher mortality. Conclusion: The nation-wide NBS program must be accompanied by comprehensive long-term management and physician and family education of inborn errors of metabolism for a better outcome.