• Mass Spectrometry Letters
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• v.5 no.1
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• pp.16-23
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• 2014

Liquid chromatography based mass spectrometry (LC-MS) is a key technology for analyzing highly complex and dynamic proteome samples. With highly accurate and sensitive LC-MS analysis of complex proteome samples, efficient data processing is another critical issue to obtain more information from LC-MS data. A typical proteomic data processing starts with protein database search engine which assigns peptide sequences to MS/MS spectra and finds proteins. Although several search engines, such as SEQUEST and MASCOT, have been widely used, there is no unique standard way to interpret MS/MS spectra of peptides. Each search engine has pros and cons depending on types of mass spectrometers and physicochemical properties of peptides. In this study, we describe a novel data process pipeline which identifies more peptides and proteins by correcting precursor ion mass numbers and unifying multi search engines results. The pipeline utilizes two open-source software, iPE-MMR for mass number correction, and iProphet to combine several search results. The integrated pipeline identified 25% more proteins in mouse epididymal adipose tissue compared with the conventional method. Also the pipeline was validated using control and colitis induced colon tissue. The results of the present study shows that the integrated pipeline can efficiently identify increased number of proteins compared to the conventional method which can be a breakthrough in identification of a potential biomarker candidate.

• Interdisciplinary Bio Central
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• v.1 no.3
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• pp.9.1-9.6
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• 2009

Introduction: In the mass spectrometry-based proteomics, biological samples are analyzed to identify proteins by mass spectrometer and database search. Database search is the process to select the best matches to the experimental mass spectra among the amino acid sequence database and we identify the protein as the matched sequence. The match score is defined to find the matches from the database and declare the highest scored hit as the most probable protein. According to the score definition, search result varies. In this study, the difference among search results of different search engines or different databases was investigated, in order to suggest a better way to identify more proteins with higher reliability. Materials and Methods: The protein extract of human mesenchymal stem cell was separated by several bands by one-dimensional electrophorysis. One-dimensional gel was excised one by one, digested by trypsin and analyzed by a mass spectrometer, FT LTQ. The tandem mass (MS/MS) spectra of peptide ions were applied to the database search of X!Tandem, Mascot and Sequest search engines with IPI human database and SwissProt database. The search result was filtered by several threshold probability values of the Trans-Proteomic Pipeline (TPP) of the Institute for Systems Biology. The analysis of the output which was generated from TPP was performed. Results and Discussion: For each MS/MS spectrum, the peptide sequences which were identified from different conditions such as search engines, threshold probability, and sequence database were compared. The main difference of peptide identification at high threshold probability was caused by not the difference of sequence database but the difference of the score. As the threshold probability decreases, the missed peptides appeared. Conversely, in the extremely high threshold level, we missed many true assignments. Conclusion and Prospects: The different identification result of the search engines was mainly caused by the different scoring algorithms. Usually in proteomics high-scored peptides are selected and low-scored peptides are discarded. Many of them are true negatives. By integrating the search results from different parameter and different search engines, the protein identification process can be improved.

• Analytical Science and Technology
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• v.21 no.4
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• pp.245-258
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• 2008

Five triterpenic acids as marker compounds were extracted and isolated from Prunellae Spica by column chromatography and reversed-phase high-performance liquid chromatography (HPLC), and their purity was determinated by HPLC (purity ${\geq}90%$). Molecular weight and elemental compositions of the five marker compounds were determined by fast atom bombardment high-resolution mass spectrometry (FAB-HRMS). The structural determination of the five marker compounds was carried out fast atom bombardment collision-induced dissociation tandem mass spectrometry (FAB-CID-MS/MS). The collision-induced dissociation (CID) of protonated molecules $[M+H]^+$ and deprotonated molecules $[M-H]^-$ produced diverse product ions due mainly to retro Diels-Alder reaction (RDA), dehydration and decarboxylation. Moreover, the CID-MS/MS spectra of the $[M-H]^-$ ions were observed charge-remote fragmentation (CRF) patterns. On the basis of interpretation of CID-MS/MS spectra, structural elucidation of triterpenic acids isolated from Prunellae Spica was clearly performed.

• Journal of Food Hygiene and Safety
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• v.14 no.2
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• pp.140-145
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• 1999

Analytical method for preservatives in food was developed using gas chromatography/mass spectrometry (GC/MS). Propionic acid, sorbic acid, benzoic acid, ethyl salicylate, ethyl p-hydroxy benzoate, iso-propyl p-hydroxy benzoate, n-propyl p-hydroxy benzoate, iso-butyl p-hydroxy benzoate, n-butyl p-hydroxy benzoate, p-hydroxy benzoic acid and dehydro acetic acid were extracted from cooling beverage with diethyl ether. The polar hydroxyl and carboxyl groups of food preservatives were derivatized with N-methyl-N-tert-butyldimethylisilyl-trifluoroscetamide (MTBSTFA) to form the corresponding tert-bytyldimethyl-silylated derivatives, and submitted to GC/MS analysis. The mass spectra of the derivatives were investigated for the selection of monitoring ions for multi-residue analysis of 11 preservatives by GC/MS. The macro program was also developed for the qualitative analysis of these preservatives in food.

• Mass Spectrometry Letters
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• v.4 no.4
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• pp.75-78
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• 2013

A gas chromatography/mass spectrometric (GC/MS) method was developed as a candidate reference method for the accurate determination of essential fatty acids (linoleic acid, ${\alpha}$- and ${\gamma}$-linolenic acids) in food supplemental oil products. Samples were spiked with three internal standards (stearic acid-$d_{35}$, $^{13}C_{18}$-linoleic acid, and $^{13}C_{18}$-${\alpha}$-linolenic acid). Samples were then subject to saponification, derivatization for methylation, and extraction by organic solvent. For GC/MS measurement, an Agilent HP-88 column, designed for the separation of fatty acid methyl esters, was selected after comparing with other columns as it provided better separation for target analytes. Target analytes and internal standards were detected by selected ion monitoring of molecular ions of their methyl ester forms. The GC/MS method was applied for the measurement of three botanical oils in NIST SRM 3274 (borage oil, evening primrose oil, and flax oil), and measurement results agreed with the certified values. Measurement results for target analytes which have corresponding isotope-labeled analogues as internal standard were calculated based on isotope dilution mass spectrometry (IDMS) approach, and compared with results calculated by using the other two internal standards. Results from the IDMS approach and the typical internal standard approach were in good agreement within their measurement uncertainties. It proves that the developed GC/MS method can provide similar metrological quality with IDMS methods for the measurement of fatty acids in natural oil samples if a proper fatty acid is used as an internal standard.

• Mass Spectrometry Letters
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• v.10 no.2
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• pp.61-65
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• 2019

Korean ginseng (Panax ginseng Meyer) is a traditional herb used across the world to treat various diseases. Although, red ginseng is this herb's most famous product and has demonstrated diverse pharmacological activities, white ginseng (WG) is another ginseng product that is made fresh and individually regulated in Eastern Asia. Red and white ginseng show different characteristics due to distinct processing steps despite originating from the same plant, and the drug interactions induced by WG have not been well documented. Selegiline is a selective monoamine oxidase (MAO) inhibitor used as an antidyskinetic and antiparkinsonian agent. Here we developed a quantification method for selegiline in mouse plasma using a C8 stationary phase in triple quadrupole-mass spectrometry (LC-MS/MS) with multiple reaction monitoring (MRM). The validated LC-MS/MS method was successfully applied to determine the potential interaction with WG extract (0.1 g/kg/day) pre-administered for 4 weeks. The $AUC_{0-240min}$ of selegiline was altered due to a decrease in the absorption of selegiline with repeated administration of WG extract.

• Mass Spectrometry Letters
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• v.11 no.4
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• pp.108-112
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• 2020

A certified reference material (CRM) for the analysis of nutrient elements in an edible mushroom (Ganoderma lyceum) powder has been developed (KRISS CRM 108-10-011). The mass fractions of calcium (Ca), iron (Fe), and zinc (Zn) were measured by isotope dilution inductively coupled plasma mass spectrometry (ID ICP/MS). To dissolve the fungi cell wall of mushroom consisted of chitin fibers, sample preparation method by single reaction chamber type microwave-assisted acid digestion with acid mixtures was optimized. The mean measurement results obtained from 12 sample bottles were used to assign as the certified values for the CRM and the between-bottle homogeneities were evaluated from the relative standard deviations. The certified values were metrologically traceable to the definition of the kilogram in the International System of Units (SI). This CRM is expected to be used for validation of analytical methods or quality control of measurement results in analytical laboratories when they determine the mass fractions of elements in mushroom or other similar samples.

• Toxicological Research
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• v.29 no.3
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• pp.203-209
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• 2013

A simple and rapid liquid chromatography-tandem mass spectrometry (LC-MS/MS) method was developed and validated for the quantification of ${\varepsilon}$-acetamidocaproic acid (AACA), the primary metabolite of zinc acexamate (ZAC), in rat plasma by using normetanephrine as an internal standard. Sample preparation involved protein precipitation using methanol. Separation was achieved on a Gemini-NX $C_{18}$ column ($150mm{\times}2.0mm$, i.d., 3 ${\mu}m$ particle size) using a mixture of 0.1% formic acid-water : acetonitrile (80 : 20, v/v) as the mobile phase at a flow rate of 200 ${\mu}l/min$. Quantification was performed on a triple quadrupole mass spectrometer employing electrospray ionization and operating in multiple reaction monitoring (MRM) and positive ion mode. The total chromatographic run time was 4.0 min, and the calibration curves of AACA were linear over the concentration range of 20~5000 ng/ml in rat plasma. The coefficient of variation and relative error at four QC levels were ranged from 1.0% to 5.8% and from -8.4% to 6.6%, respectively. The present method was successfully applied for estimating the pharmacokinetic parameters of AACA following intravenous or oral administration of ZAC to rats.

• Mass Spectrometry Letters
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• v.13 no.4
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• pp.158-165
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• 2022

Many therapeutic class drugs such as beta-blocker, corticosteroids, NSAIDs, etc are prohibited substances in the horse racing industry. Liquid chromatography-tandem mass spectrometry (LC-MS/MS) technology makes it possible to isolate drugs from interference, enables various drug analyses in complex biological samples due to its sensitive sensitivity, and has been successfully applied to doping control. In this paper, we describe a rapid and sensitive method based on solid-phase extraction (SPE) using solid phase cartridge and LC-MS/MS to screen for different class's 35 drug targets in equine plasma. Plasma samples were pretreated by SPE with the NEXUS cartridge consisted non-polar carbon resin and minimum buffer solvent. Chromatographic separation of the analytes was performed on ACQUITY HSS C18 column (2.1 × 150 mm, 1.8 ㎛). The elution gradient was conducted with 5 mM ammonium formate (pH 3.0) in distilled water and 0.1% formic acid in acetonitrile at a flow rate of 0.25 mL/min. The selected reaction monitoring (SRM) mode was used for drug screening with multiple transitions in the positive ionization mode. The specificity, limit of detection, recovery, and stability was evaluated for validation. The method was found to be sensitive and reproducible for drug screening. The method was applied to plasma sample analysis for the proficiency test from the Association of Racing Chemist.

• Bulletin of the Korean Chemical Society
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• v.33 no.10
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• pp.3233-3240
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• 2012

We demonstrated the combined applications of online protein digestion using trypsin immobilized enzyme reactor (IMER) and dual tandem mass spectrometry with collisionally activated dissociation (CAD) and electron transfer dissociation (ETD) for tryptic peptides eluted through the trypsin-IMER. For the trypsin-IMER, the organic and inorganic hybrid monolithic material was used. By employing the trypsin-IMER, the long digestion time could be saved with little or no sacrifice of the digestion efficiency, which was demonstrated for standard protein samples. For three model proteins (cytochrome c, carbonic anhydrase, and bovine serum albumin), the tryptic peptides digested by the IMER were analyzed using LC-MS/MS with the dual application of CAD and ETD. As previously shown by others, the dual application of CAD and ETD increased the sequence coverage in comparison with CAD application only. In particular, ETD was very useful for the analysis of highly-protontated peptide cations, e.g., ${\geq}3+$. The combination approach provided the advantages of both trypsin-IMER and CAD/ETD dual tandem mass spectrometry applications, which are rapid digestion (i.e., 10 min), good digestion efficiency, online coupling of trypsin-IMER and liquid chromatography, and high sequence coverage.