• 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'.

• Journal of Periodontal and Implant Science
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• v.33 no.3
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• pp.331-340
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• 2003

본 연구의 목적은 인간의 동맥경화증에서 Porphyromonas gingivalis (P. gingivalis)와 인체 열충격단백 60의 T-세포 및 교차성 B-세포 epitope를 규명하고 수립된 T-세포주의 T-세포 주요조직적합체 양상을 파악하려는 데 있다. P. gingivalis 열충격단백-반응성 T 세포주와 환자의 혈청을 이용하여 P. gingivalis 열충격단백60 분자를 구성하는 104개의 중복성 합성 펩타이드의 T-세포 epitope과 B-세포 epitope을 규명하였다. 인체 열충격단백60에 대한 B-세포 epitope도 같은 방법으로 파악하였다. P. gingivalis, P. gingivalis 열충격단백60 또는 인체 열충격단백60에 대한 IgG 항체는 모든 동맥경화증 환자에서 상승하였다. P. gingivalis 열충격단백60의 3, 15, 24, 33, 45, 53, 64, 84, 88, 99번 펩타이드가 주요한 T-세포 epitope였고 이것들은 T-세포 및 B-세포 공동 epitope이기도 했다. 또한 인체 열충격단백60 교차반응 B-세포 epitope은 15, 29, 53, 56, 69, 74번 펩타이드로 판명되었다. 대부분 환자의 주요조직적합체는 $HLA-DRB1^{\ast}1504$와 $HLA-DZB1^{\ast}0603$으로 나타났다. 결론적으로 P. gingivalis 열충격단백60은 제 2급 주요조직적합제-제한적으로 분해되고 전달되었으며 이 단백질이 공통적인 T-세포 및 B-세포 epitope를 가지면서 동시에 인체 열충격단백60과 교차성 B-세포 epitope을 가지면서 동맥경화증의 면역조절기능에 관여한다고 볼 수 있다.

• Analytical Science and Technology
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• v.30 no.6
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• pp.348-354
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• 2017

In this study, patterns of proteome expression were monitored and specifically expressed proteins in human milk were detected in collected human milk after 1 week, 3 weeks, and 6 weeks from delivery. A quantitative shotgun proteomic approach was used to identify human milk proteins and reveal their relative expression amounts. For each sample, two independent human milk samples from two mothers were pooled, and then three replicated shotgun proteomic analyses were carried out. Casein, which is a highly abundant protein in human milk, was removed, and then trypsin was treated to produce a digested peptide mixture. The peptides were loaded in the home-made reversed-phase C18 fused-silica capillary column, and then the eluted peptides were analyzed by using a linear ion-trap mass spectrometer. The relative quantitation of proteins was performed by the normalized spectral count method. For each sample, 81-109 non-redundant proteins were identified. The identified proteins consisted of glycoproteins, metabolic enzyme, and chaperon enzymes such as lactoferrin, carboxylic ester hydrolase, and clusterin. The comparative analysis for the 63 proteins, which were reproducibly identified in all three replications, revealed that 25 proteins were statically significant differentially expressed. Among the differentially expressed proteins, Ig lambda-7 chain C region and tenascin drastically decreased with the delivery time.