Jeongkwon Kim

Enrichment of phosphopeptides using bare magnetic particles.

Magnetic iron(II, III) oxide (magnetite, Fe(3)O(4)) nanoparticles were used to selectively enrich phosphopeptides from tryptic digests of bovine beta-casein and from tryptic digest mixtures containing bovine beta-casein, cytochrome c, bovine serum albumin, and horse heart myoglobin. The magnetic property of the particles permits an easy and speedy enrichment process. No enrichment of phosphopeptides was observed from ferric magnetic iron(III) oxide (Fe(2)O(3)) nanoparticles. These data collectively demonstrate that the enrichment of phosphopeptides using magnetic iron(II, III) oxide nanoparticles is a practical method for the selective analysis of phosphopeptides and could be helpful in isolating and analyzing phosphorylated peptides from complex biological samples.

Analysis of explosives using corona discharge ionization combined with ion mobility spectrometry-mass spectrometry.

Corona discharge ionization combined with ion mobility spectrometry-mass spectrometry (IMS-MS) was utilized to investigate five common explosives: cyclonite (RDX), trinitrotoluene (TNT), pentaerythritol tetranitrate (PETN), cyclotetramethylenetetranitramine (HMX), and 2,4-dinitrotoluene (DNT). The MS scan and the selected ion IMS analyses confirmed the identities of the existing ion species and their drift times. The ions observed were RDX·NO3(-), TNT(-), PETN·NO3(-), HMX·NO3(-), and DNT(-), with average drift times of 6.93 ms, 10.20 ms, 9.15 ms, 12.24 ms, 11.30 ms, and 8.89 ms, respectively. The reduced ion mobility values, determined from a standard curve calculated by linear regression of (normalized drift times)(-1) versus literature K0 values, were 2.09, 1.38, 1.55, 1.15, 1.25, and 1.60 cm(2) V(-1) s(-1), respectively. The detection limits were found to be 0.1 ng for RDX, 10 ng for TNT, 0.5 ng for PETN, 5.0 ng for HMX, and 10 ng for DNT. Simplified chromatograms were observed when nitrogen, as opposed to air, was used as the drift gas, but the detection limits were approximately 10 times worse (i.e., less sensitivity of detection).

Development of isotope dilution-liquid chromatography tandem mass spectrometry for the accurate determination of fluoroquinolones in animal meat products: Optimization of chromatographic separation for eliminating matrix effects on isotope ratio measurements

Isotope dilution-liquid chromatography/tandem mass spectrometry (ID-LC-MS/MS) has been established as a candidate reference method for the accurate determination of three representative fluoroquinolone antibiotics (enrofloxacin, ciprofloxacin, and norfloxacin) in meat products. Enrofloxacin-d₅, ciprofloxacin-¹³C₃¹⁵N, and norfloxacin-d₅ were used as internal standards. After extraction and SPE clean-up, samples were analyzed by using LC-MS/MS in positive ion mode. We observed that the deuterium-labeled internal standards have slightly different LC retention time from their native analogues, which reduces the benefits of using isotope dilution techniques as ion suppression/enhancement effects caused by co-eluting matrix interferences are not completely compensated. In this study, LC conditions were optimized to minimize matrix effects causing different ionization efficiency between the target analytes and their isotope analogues by separating them from significant matrix interferences. The analytical method was validated by measuring samples (chicken breast, bovine muscle, and porcine muscle) gravimetrically fortified in various levels with the target analytes. The method provided accurate analytical results of the target analytes in the range of 5-50 μg/kg with the relative expanded uncertainty of 1-5%.

Targeted label-free quantitative analysis of secretory proteins from adipocytes in response to oxidative stress

Adipocytes are well known to release regulation factors associated with metabolic disorders. In particular, increased oxidative stress in adipocytes contributes to dysregulation of adipokine production. In this study, we applied relative quantitative proteomic analysis based on label-free multiple reaction monitoring (MRM) to discover biological changes of adipokines under oxidative stress. Among a total of 194 identified proteins, 8 proteins were selected and quantified between control and hydrogen peroxide (H(2)O(2))-treated groups by label-free MRM quantification. The secretion levels of matrix metalloproteinase-2 (MMP-2), stromal cell-derived factor-1 (SDF-1, CXCL12), resistin, and complement factor D (CFD, adipsin) decreased, whereas the secretion levels of tissue inhibitor of metalloproteinase-2 (TIMP-2) and aldolase A increased. Here we suggest that our study with label-free quantitative analysis will contribute to the efficient quantitative analysis of targeted proteins in complex mixtures and specifically to a better understanding of changes of adipokines under oxidative stress.

An optimised method for the accurate determination of zeranol and diethylstilbestrol in animal tissues using isotope dilution-liquid chromatography/mass spectrometry.

Isotope dilution-liquid chromatography/mass spectrometry (ID-LC/MS) has been established as a candidate reference method for the accurate determination of growth promoters (zeranol, taleranol, and diethylstilbesterol) in raw meat samples. Sample preparation processes including an enzymatic hydrolysis, extraction, and SPE clean-up were optimised. The sensitivity difference of trans- and cis-diethylstilbestrol (isomerizing in sample preparation processes) by the LC/MS was measured by running a trans/cis mixture (ratio measured by a quantitative NMR) with and without sample matrices, and applied for the determination of total diethylstilbestrol. Validity, repeatability, and reproducibility of the analytical method were tested by measuring gravimetrically fortified samples (chicken breast, bovine muscles, and porcine muscle) in a number of different time periods. Measurement results agreed with the fortified values within their uncertainties. The method provided accurate results of the target analytes in the range of 0.05-15 μg/kg with the relative expanded uncertainty of 2-15%.

Effects of temperature on ultrasound-assisted tryptic protein digestion

The effects of temperature on ultrasound-assisted tryptic protein digestion were comprehensively investigated using matrix-assisted laser desorption/ionization (MALDI) time-of-flight mass spectrometry. Three standard proteins, cytochrome c, myoglobin, and bovine serum albumin, were digested at 4°C (ice), room temperature (20-25), 37, and 55°C for 0 s, 30s, 1 min, and 5 min, in an ultrasonic bath. We found that the number of identified peptides generally increased with increasing temperature or digestion time. Compared with conventional overnight digestion at 37°C without ultrasonication, digestions performed under ultrasonication generally produced more peptides under most of the above listed conditions, mainly due to miscleaved peptides. Tryptic digestions were also performed under all the conditions evaluated without using ultrasound, where the most significant improvement with the application of ultrasound in terms of sequence coverage and the number of identified peptides was observed at 4°C, followed by room temperature, and 37°C, while no improvement was observed at 55°C with the application of ultrasound, which may be due to the fact that the current experiments were performed in an ultrasonic bath.

Pressure‐assisted tryptic digestion using a syringe

A simple and effective digestion method was developed using a syringe. A 3 mL syringe was used to apply a pressure of 6 atm to expedite tryptic digestion. Application of a pressure of 6 atm during digestion resulted in better digestion efficiency than digestion under atmospheric pressure. The protein peaks in the matrix-assisted laser desorption/ionization mass spectra of three model proteins (cytochrome c, horse heart myoglobin, and bovine serum albumin (BSA)) completely disappeared within 30 min at 37 degrees C under a pressure of 6 atm, with greater numbers of peptides observed in 30 min pressure-assisted digestion than in overnight atmospheric pressure digestion. This is mostly due to the miscleaved peptides. Similar sequence coverages were obtained for 30 min pressure-assisted digestion and overnight atmospheric pressure digestion of the three model proteins (92% vs. 88% for cytochrome c, 100% vs. 97% for horse heart myoglobin, and 53% vs. 53% for BSA).

Comparative proteome analysis using amine-reactive isobaric tagging reagents coupled with 2D LC/MS/MS in 3T3-L1 adipocytes following hypoxia or normoxia.

Hypoxia during the expansion of adipocytes is known to contribute both to the secretion of multiple inflammation-related adipokines as well as to obesity. We therefore investigated the nature of protein changes occurring in adipocytes during hypoxia by observation of the intracellular proteins that are expressed in 3T3-L1 adipocytes. Lysates were utilized for quantitative proteome analysis using isobaric tags for relative and absolute quantitation (iTRAQ) combined with peptide separation by multi-dimensional liquid chromatography. Antioxidants and elongation factors, as well as glycolytic enzymes were increased in hypoxic adipocytes. These changes were supported by similar changes suggested by real-time PCR. The proteins showing changes are all potential targets for revering the mechanism behind the phenomenon of induction of obese adipocytes by hypoxia. This study can therefore aid in defining the proteomic changes that occur in adipocytes in response to oxygen stress, and can further characterize adipocyte metabolism and adaptation to low oxygen conditions.

Analysis of oligosaccharides in beer using MALDI-TOF-MS.

Oligosaccharides in four different brands of beer (Cass, Hite, Budweiser, Miller) were systematically analysed with three different dihydroxybenzoic acid (DHB) isomer matrices (2,4-DHB, 2,5-DHB, and 2,6-DHB) using matrix-assisted laser desorption/ionisation time-of-flight mass spectrometry (MALDI-TOF-MS). Different experimental conditions, such as dilution (up to 1000-fold) and cationisation agents (sodium chloride or sodium trifluoroacetate) were analysed. No ionised peaks of oligosaccharides were observed with 2,4-DHB matrix. 2,6-DHB was more effective than 2,5-DHB in most of the investigated concentration ranges. 2,6-DHB with 4-fold dilution was the most effective. In certain cases, a cationisation agent was necessary to detect the signals of the oligosaccharides, and sodium chloride provided greater ionisation than sodium trifluoroacetate.

Analysis of cancer cell lipids using matrix‐assisted laser desorption/ionization 15‐T Fourier transform ion cyclotron resonance mass spectrometry

A combination of methodologies using the extremely high mass accuracy and resolution of 15-T Fourier transform ion cyclotron resonance (FT-ICR) mass spectrometry (MS) was introduced for the identification of intact cancer cell phospholipids. Lipids from a malignant glioma cell line were initially analyzed at a resolution of >200,000 and identified by setting the mass tolerance to ±1 mDa using matrix-assisted laser desorption/ionization (MALDI) 15-T FT-ICR MS in positive ion mode. In most cases, a database search of potential lipid candidates using the exact masses of the lipids yielded only one possible chemical composition. Extremely high mass accuracy (<0.1 ppm) was then attained by using previously identified lipids as internal standards. This, combined with an extremely high resolution (>800,000), yielded well-resolved isotopic fine structures allowing for the identification of lipids by MALDI 15-T FT-ICR MS without using tandem mass spectrometric (MS/MS) analysis. Using this method, a total of 38 unique lipids were successfully identified.