• 정보과학회 컴퓨팅의 실제 논문지
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• 제22권1호
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• pp.56-60
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• 2016

탠덤 질량 분석에서는 신뢰도 높은 펩타이드 동정을 위해 목표 데이터베이스의 참조 단백질 순서를 재배치한 디코이 데이터베이스가 주로 이용된다. 한편 목표 데이터베이스와 디코이 데이터베이스 사이 혹은 디코이 데이터베이스 내부에 서열이 동일한 중복 펩타이드가 존재할 수 있으며, 이는 단백질 동정을 어렵게 하는 요인이 된다. 따라서 디코이 데이터베이스의 중복성을 최소화하는 것은 중요한 문제이다. 본 논문에서는 디코이 데이터베이스 생성에 널리 사용되는 의사셔플(pseudo-shuffling)과 의사역순(pseudo-reversing) 방법이 디코이 데이터베이스의 중복성에 미치는 영향을 조사하였다. 실험 결과, 목표 데이터베이스 크기와 데이터베이스 생성 시 허용되는 'missed cleavage site'의 최대 개수는 중복성을 증가시킴을 확인하였다. 또한 동일한 조건에서는 의사역순 방법이 의사셔플보다 항상 낮은 수준의 중복성을 가지는 디코이 데이터베이스를 생성하였다.

• Mass Spectrometry Letters
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• 제7권4호
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• pp.96-101
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• 2016

To determine the influence of the cationization agent on the collision activated dissociation (CAD) fragmentation behavior of oligosaccharides, the CAD spectra of the singly protonated, sodiated oligosaccharides and singly sodiated and dibenzo-18-crown-6 ether conjugated oligosaccharides were carefully compared. Each of these three different species showed quite different fragmentation spectra. The comparison of singly protonated and sodiated oligosaccharide CAD spectra revealed that different cationization agents affected the cationization agent adduction sites as well as the fragmentation sites within the oligosaccharides. When the mobility of $Na^+$ was limited by the dibenzo-18-crown-6 ether encapsulation agent, the examined linear oligosaccharides showed fragmentation patterns quite different from the unmodified ones. For the dibenzo-18-crown-6 ether conjugated oligosaccharides, the charge-remote fragmentation pathways were more likely to be activated than the chargedirected pathways. This work demonstrates that dibenzo-18-crown-6 ether conjugation can potentially provide a route to selectively activate the charge-remote fragmentation pathways, albeit to a limited extent, in tandem mass spectrometry studies.

• Bulletin of the Korean Chemical Society
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• 제26권5호
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• pp.740-746
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• 2005

In this article, we report the tandem mass spectrometry investigations for the electron capture efficiencies of the protons belonging to the different locations (generations) in a poly(propylene imine) dendrimer with three layers of a repeat unit (named as the third generation dendrimer). The employed tandem mass spectrometry methods include SORI-CAD (sustained off-resonance irradiation collisional activation dissociation) and ECD(electron capture dissociation) mass spectrometry. We obtained SORI-CAD spectra for the dendrimer ions in the different charge states, ranging from 2+ to 4+. The analysis of fragmentation sites provides the information as to where the protons are distributed among various generations of the dendrimer. Based upon this, a new strategy to study the electron capture efficiencies of the protons is utilized to examine a new type of triplycharged ions by SORI-CAD, i.e., the 3+ ions generated from the charge reduction of the native 4+ ions by ECD: (M+4H)$^{4+}\;+\;e^-\;{\rightarrow}$ (M+4H)$^{3+\bullet}$ ${\rightarrow}\;({H^{\bullet}}_{ejected}$) + (M+3H)$^{3+}\;\rightarrow$ CAD. Interestingly, comparison of these four SORICAD spectra indicates that the proton distribution in the charge-reduced 3+ ions is very close to that in the native 4+ ions. It further suggests that in this synthetic polymer ($\sim$1.7 kDa) with an artificial architecture, the electron capture efficiencies of the protons are actually insensitive to where they are located in the molecule. This is somewhat contradictory to common expectations that the protons in the inner generations may not be well exposed to the incoming electron irradiation as much as the outer ones are, thus may be less efficient for electron capture. This finding may carry some implications for the case of medium sized peptide ions with similar masses, which are known to show no obvious site-specific fragmentations in ECD MS.

• Mass Spectrometry Letters
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• 제4권4호
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• pp.67-70
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• 2013

The Cu-binding site in the $[Cu{\cdot}dCMP{\cdot}dCMP-H]^{1-}$ complex was investigated. The tandem mass (MS/MS) spectra of the [$[Cu{\cdot}dCMP{\cdot}dCMP-H]^{1-}$ parent ion showed $[dCMP{\cdot}Cu{\cdot}H_2PO_4+CONH]^{1-}$ fragment ions. Therefore, we propose that the Cu cation is simultaneously coordinated to the phosphate site and cytosine moiety in the stable geometry of the $[Cu{\cdot}dCMP{\cdot}dCMP-H]^{1-}$ complex. Three geometries for the complex were considered in an attempt to optimize the structure of the $[Cu{\cdot}dCMP{\cdot}dCMP-H]^{1-}$ complex. The ab initio calculations were performed at the $B3LYP/6-311G^{**}$ level.

• Mass Spectrometry Letters
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• 제5권3호
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• pp.89-93
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• 2014

Lincomycin is one of the major species among the Pharmaceuticals and Personal Care Products (PPCPs) detected from the four major rivers in Korea. The structure characterization was performed of six degradation products of lincomycin formed under the irradiation of electron beam, and the degradation efficiency as a function of the various irradiation dose and sample concentration was investigated. Electron beam (10 MeV, 0.5 mA and 5 kW) experiments for the structural characterization of degradation products that are fortified with lincomycin, were performed at the dose of 10 kGy. The separation of degradation products and lincomycin was carried out using a C18 column ($2.1{\times}100$ mm, $3.5{\mu}m$), using gradient elution with 20 mM ammonium acetate and acetonitrile. The structures of six degradation products of lincomycin were proposed by interpretation of mass spectra and chromatograms by LC-MS/MS. The mass fragmentation pathways of mass spectra in tandem mass spectrometry were also proposed. Experiments were performed of the degradation efficiency as a function of the irradiation dose intensity and the initial concentration of lincomycin in an aqueous environment. In addition, increased degradation efficiency was observed with a higher dose of electron beam and lower concentration.

• 분석과학
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• 제30권2호
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• pp.102-111
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• 2017

Here we reported a methodology for identification of triacylglycerols (TAGs) and diacylglycerols (DAGs) in coix seed by preparative thin layer chromatography (prep-TLC) and non-aqueous reversed-phase liquid chromatography (NARP LC)-atmospheric pressure chemical ionization (APCI) tandem mass spectrometry (MS/MS). Lipid components were extracted from coix seed by reflux extraction using n-hexane for 3 hr. TAGs and DAGs in coix seed extract were effectively purified and isolated from matrix interferences by prep-TLC and then analyzed by LC-APCI-MS and MS/MS for identification. TAGs were effectively identified taking into consideration of their LC retention behavior, APCI-MS spectra patterns, and MS/MS spectra of $[DAG]^+$ ions. In MS/MS spectra of TAGs, diacylglycerol-like fragment $[DAG]^+$ ions were useful to identify TAGs with isobaric fragment ions. Based on an established method, 27 TAGs and 8 DAGs were identified in coix seed extract. Among them, 15 TAGs and 8 DAGs were for the first time observed in coix seed. Interestingly, some of TAGs isolated by prep-TLC were partly converted into DAGs through probably photolysis process during storing in room temperature. Thus, degradation phenomenon of TAGs should be considered in the quality evaluation and nutritional property of coix seed. LC-APCI-MS/MS combined with prep-TLC will be practical method for precise TAG and DAG analysis of other herbal plants.

• Mass Spectrometry Letters
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• 제10권1호
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• pp.32-37
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• 2019

The ${\pi}-{\pi}$ interactions of the peptide-dimer and peptide-trimer complexes were investigated in the (VQIVYK + LYQLEN) and (VQIVYK + NNQQNY) mixing solutions. The results showed that tyrosine (Y) residues were critical in the formation of hetero peptide-dimers and -trimers during the early oligomerization process. We used collision-induced dissociation (CID) along with electrospray ionization mass spectroscopy (ESI-MS) to obtain the structural information of the hetero-dimers and -trimers. We chose three amyloidogenic peptides-VQIVYK, NNQQNY, and LYQLEN-from tau protein, yeast prion-like protein Sup35, and insulin chain A, respectively. Hetero-dimer, -trimer, -tetramer, and -pentamer complexes were observed in the mass spectra. The tandem mass spectrum of the hetero-dimer and hetero-trimer showed two different fragmentation patterns (covalent and non-covalent bond dissociation). Y-Y interaction structures were also proposed for the hetero-dimer and -trimer complexes.

• 분석과학
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• 제21권4호
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• pp.245-258
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• 2008

본 연구에서는 하고초의 지표성분인 triterpenic acids 5종을 컬럼 크로마토그래피와 역상 HPLC를 이용하여 추출 및 분리했고, 이들 성분의 순도는 90% 이상임을 HPLC를 이용하여 확인했다. 고속원자충돌 이온화법-고분해능 질량분석기(FAB-HRMS)를 사용하여 지표성분의 분자량 및 원소조성을 결정했으며, 지표성분의 구조 분석은 FAB-MS/MS 의해 음이온 및 양이온 모드에서 수행하였다. Triterpenic acid류의 충돌유발분해(collision-induced dissociation, CID) 탄뎀질량분석(MS/MS) 스펙트럼에서 protonated molecule인 $[M+H]^+$ 및 deprotonated molecule인 $[M-H]^-$ 이온의 CID는 주로 retro Diels-Alder (RDA), 탈수 (dehydration) 및 탈탄산(decarboxylation) 반응에 의한 다양한 생성이온들이 나타났다. 특히, $[M-H]^-$이온의 CID-MS/MS 스펙트럼에서는 charge-remote fragmentation (CRF) 현상에 의한 이온들도 특성이온으로 나타났다. 이들 CID-MS/MS 스펙트럼의 해석을 통하여 하고초의 지표성분인 triterpenic acids의 구조 규명을 수행하였다.

• 대한화학회지
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• 제42권3호
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• pp.297-301
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• 1998

올리고당의 구조중 연결위치(linkage position)는 충돌 탄뎀 질량분석법(FAB CAD MS/MS: Fast Atom Bombardment Collision Activated Dissociation Mass Spectrometry/Mass Spectrometry)을 이용하여 알 수 있다. 연결위치-이성질체 올리고당을 아세틸화시키면 자유올리고당보다 연결위치의 구별이 쉽고 독특한 분절이온 패턴을 얻을 수 있다. 그 이유는 연결위치에 따라 각 올리고당이 충돌에너지(collision energy)를 흡수하여 glycosidic 결합 주위를 회전하는 회전운동의 자유도가 달라지기 때문이다.

• KSBB Journal
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• 제22권4호
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• pp.234-238
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• 2007

본 연구에서는 전극분무 이온화-이온 포획 질량 분석기를 이용하여 인체 IgG의 N-연결 글라이칸 중 이중촉각 구조를 가지면서 비환원 말단의 갈락토오즈 개수가 0, 1, 2 개인 서로 다른 세 가지 글라이칸의 단일 쪼개짐 (MS/MS) 및 다중 쪼개짐 현상을 관찰하고 이를 구조 분석에 이용하였다. MS/MS 분석에서는 퓨코오즈가 결합된 환원 말단의 N-아세틸 글루코사민의 0,2-고리 쪼개짐으로 파생되는 조각 피크가 가장 높은 세기로 나타나는 것을 관찰할 수 있었고, 전구체 피크와 별개로 연속적인 당 단위체의 쪼개짐이 일어나는 것을 알 수 있었다. 또한 G1 글라이칸의 경우에서만 비환원 말단의 갈락토오즈와 N-아세틸글루코사민이 결합된 채 쪼개지는 현상이 일어나는 것을 관찰할 수 있었다. 다중 쪼개짐 질량 분석 기법을 이용하여 MS/MS 스펙트럼에서 나타나는 조각 피크들의 구조를 재확인할 수 있었고, 이를 트리 구조로 정리할 수 있었다. 또한 추가적인 2,4-고리 쪼개짐 현상이 환원 말단 하나 바깥쪽의 N-아세틸 글루코사민에서 공통적으로 일어나는 것을 관찰할 수 있었다. 이와 같은 다중 쪼개짐 질량 분석기법을 이용하여 보다 복잡한 구조의 글라이칸 구조 분석에 이용될 수 있을 것으로 기대된다.