• Genomics & Informatics
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• 제4권2호
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• pp.65-70
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• 2006

Peptide mass mapping is the matching of experimentally generated peptides masses with the predicted masses of digested proteins contained in a database. To identify proteins by matching their constituent fragment masses to the theoretical peptide masses generated from a protein database, the peptide mass fingerprinting technique is used for the protein identification. Thus, it is important to know the theoretical mass distribution of the database. However, few researches have reported the peptide mass distribution of a database. We analyzed the peptide mass distribution of non-redundant protein sequence database in the NCBI after digestion with 15 different types of enzymes. In order to characterize the peptide mass distribution with different digestion enzymes, a power law distribution (Zipfs law) was applied to the distribution. After constructing simulated digestion of a protein database, rank-frequency plot of peptide fragments was applied to generalize a Zipfs law curve for all enzymes. As a result, our data appear to fit Zipfs law with statistically significant parameter values.

• 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.

• 한국멀티미디어학회:학술대회논문집
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• 한국멀티미디어학회 2000년도 추계학술발표논문집
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• pp.571-574
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• 2000

오늘날 단백질 정보 분석은 HGP(Human Genome Project)이후 Post-genome 시대를 맞이하면서 매우 중요한 분야로 인식되고 있다. 이 단백질 정보를 이용하는 응용은 Discovery of Protein Structure/Function Relationships, Evolutionary Relationships, 3D Modeling 등 많은 분야에서 활용되어진다. 여러 가지 분야들 중에서 특히 단백질 구조 분석을 위한 많은 다양한 소프트웨어들이 출현되고 있다. 하지만 복잡하게 얽혀 있는 단백질들을 검증하기 위해서 Mass Spectrometry에서 발생되는 Peptide Masses의 정보들을 이용할 수 있다. 이에 본 논문에서는 Mass Spectrometry에서 생성된 Peptide Mass Map을 이용하여 기존의 단백질 Database에 있는 단백질들과 비교하는 자동화 단백질 검증 시스템 설계 및 구현에 관한 연구내용을 담고 있다. 이 시스템은 3-계층 중심으로 개발이 이루어지며 이 기종 시스템과의 원활한 통신 다중 계층의 환경에 있는 각 객체들간에 통신을 위해서 RMI 기반의 미들 웨어를 활용하기로 한다.

• Journal of Pharmaceutical Investigation
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• 제41권2호
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• pp.91-94
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• 2011

The purpose of this study was to investigate the effect of peptide charge on the interaction between peptide and poly(D,L-lactide-co-glycolide) (PLGA) for evaluating mechanism of acylated peptide formation in PLGA matrix. As a model peptide, octreotide, a synthetic somatostatin analogue and active ingredient of commercial PLGA product, was used. The disulfide group of octreotide was reduced with dithiothreitol and the sulfhydryl groups were modified with N-${\beta}$-maleimidopropionic acid (BMPA) to neutralize octreotide with positive charge in physiological conditions. The BMPA-conjugated octreotide was identified by measuring the molecular mass with liquid chromatography-mass spectrometry. In the interaction study with PLGA, native octreotide showed initial adsorption to PLGA and substantial production of acylated peptides (56% of overall peptide), whereas BMPA-conjugated octreotide showed minimal adsorption to PLGA and no acylation products for 42 days. Consequently, the neutralization of octreotide completely inhibited the peptide acylation by preventing interaction of peptide with PLGA. In conclusion, this study demonstrates that the initial polymer interaction of peptide is important step for peptide acylation in PLGA matrix and suggests the modulation of peptide charge as strategy for inhibiting the formation of acylated peptide impurities.

• Mass Spectrometry Letters
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• 제4권4호
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• pp.71-74
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• 2013

In the present study, we report that the charge-directed (assisted) peptide dissociation products, such as b- and y-type peptide backbone fragments, were the major products in MS/MS and $MS^3$ applications of some o-TEMPO-Bz-C(O)-peptide ions, while radical-driven dissociation products, such as a/x and c/z-type fragments, were previously shown to be the major products in the free radical initiated peptide sequencing mass spectrometry (FRIPS MS). Those o-TEMPO-Bz-C(O)-peptides share a common feature in their sequences, that is, the peptides do not include an arginine residue that has the highest proton affinity among free amino acids. The appearance of b- and y-type fragments as major products in FRIPS MS can be understood in terms of the so-called "mobile-proton model". When the proton is highly mobilized by the absence of arginine, the chare-directed peptide dissociation pathways appear to be more competitive than the radical-driven dissociation pathways, in our FRIPS experiments.

• Mass Spectrometry Letters
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• 제10권2호
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• pp.50-55
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• 2019

The fragmentation statistics of ion trap CID (Collision-Induced Dissociation) spectra using 87,661 tandem mass spectra of doubly charged tryptic peptides are analyzed here. In contrast to the usual method of using intensity information, the frequency of occurrence of fragment ions, with respect to the position of the cleavage site and the residues at these sites is studied in this paper. The analysis shows that the frequency of occurrence of fragment ion peaks is more towards the middle of the peptide than its ends. It was noted that amino acid with an aromatic and basic side chain at N- & C- terminal end of the peptide stimulates more peaks at the lower end of the spectrum. The residue pair effect was shown when the amide bond occurs between acidic and basic residues. The fragmentation at these sites (D/E-H/R/K) stimulates the generation of the y-ion peak. Also, the cleavage site H-H/R/K stimulates the generation of b-ions. K-P environment in the peptide sequence has more tendency to generate y-ions than b-ions. Statistical analysis helps in the visualization of the CID fragmentation pattern. Cleavage pattern along the length of the peptide and the residue pair effects, enhance the knowledge of fragmentation behavior, which is useful for the better interpretation of tandem mass spectra.

• Bulletin of the Korean Chemical Society
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• 제20권11호
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• pp.1299-1302
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• 1999

Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS) was used to demonstrate cross-linking of peptides induced by transglutaminase. The presence of ε-( Υ-glutamyl)lysine isopeptide cross-link in the acid hydrolysate of the cross-linking reaction mixture was also demonstrated by MALDI-TOF-MS without prior separation. MALDI-TOF-MS quickly provided peptide mass maps after pronase digestion of the cross-linked peptide adduct, which enabled us to monitor the hydrolytic sequence. Pronase appears to preferentially hydrolyze peptide bonds distant from the cross-link before hydrolyzing peptide bonds around the cross-link. The results suggest that pronase digestion followed by MALDI-TOF-MS could be used for determination of amino acid sequence around a modification site.

• Mass Spectrometry Letters
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• 제12권4호
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• pp.137-145
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• 2021

Herein we report multiple ion mobility (IM) peaks in electrospray ionization IM mass spectrometry (ESI-IM-MS) produced by glutamine residue in peptide. The mobility features of 147 peptides were investigated using ESI-IM-MS combined with liquid chromatography. Of these peptides, 66 presented multiple IM peaks, and analysis of their sequence using collision induced dissociation (CID) revealed that glutamine (Gln), as well as proline (Pro), plays a critical role in generating multiple IM peaks. Mutant-based investigations using Gln-containing peptides indicate that the side chain of Gln promotes intermolecular interactions, inducing multiple structures of the peptide ions in the gas phase. Consequently, the present study demonstrates that the distinct ion mobility signatures identified herein can potentially be used to characterize glutamine-containing peptide ions.

• Mass Spectrometry Letters
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• 제9권1호
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• pp.17-23
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• 2018

Studies on the interactions of amyloidogenic proteins with trace metals, such as copper, have indicated that the metal ions perform a critical function in the early oligomerization process. Herein, we investigate the effects of Cu(II) ions on the active sequence regions of amyloidogenic proteins using electrospray ionization mass spectrometry (ESI-MS) and collision induced dissociation tandem MS (CID-MS/MS). We chose three amyloidogenic peptides NNQQNY, LYQLEN, and VQIVYK from yeast prion like protein Sup35, insulin chain A, and tau protein, respectively. [Cu-peptide] complexes for all three peptides were observed in the mass spectra. The mass spectra also show that increasing Cu(II) concentrations decrease the population of existing peptide oligomers. The tandem mass spectrum of NNQQNY shows preferential binding for the N-terminal region. All three peptides are likely to appear to be in a Cu-monomer-monomer (Cu-M-M) structure instead of a monomer-Cu-monomer (M-Cu-M) structure.

• Journal of Microbiology and Biotechnology
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• 제15권5호
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• pp.1054-1059
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• 2005

An extracellular protease was identified from Bacillus subtilis KCCM 10257 by N-terminal sequencing and mass spectral analysis. The molecular mass of the extracellular protease was estimated to be 28 kDa by SDS-PAGE. Sequencing of the N-terminal of the protease revealed the sequence of A(G,S,R)QXVPYG(A)V(P,L)SQ. The N-terminal sequence exhibited close similarity to the sequence of other proteases from Bacillus sp. A mass list of the monoisotopic peaks in the MALDI-TOF spectrum was searched after peptide fragmentation of the protease. Six peptide sequences exhibiting monoisotopic masses of 1,276.61, 1,513.67, 1,652.81, 1,661.83, 1,252.61, and 1,033.46 were observed from the fragmented protease. These monisotopic masses corresponded to the lytic enzyme L27 from Bacillus subtilis 168, and the Mowse score was found to be 75. A doubly charged Top product (MS) at a m/z of 517.3 exhibiting a molecular mass of 1034.6 was further analyzed by de novo sequencing using a PE Sciex QSTAR Hybrid Quadropole-TOF (MS/MS) mass spectrometer. MS/MS spectra of the Top product (MS) at a m/z of 517.3 obtained from the fragmented peptide mixture of protease with Q-star contained the b-ion series of 114.2, 171.2, 286.2, 357.2, 504.2, 667.4, 830.1, and 887.1 and y-ion series of 147.5, 204.2, 367.2, 530.3, 677.4, 748.4, 863.4, and 920.5. The sequence of analyzed peptide ion was identified as LGDAFYYG from the b- and y-ion series by de novo sequencing and corresponded to the results from the MALDI-TOF spectrum. From these results the extracellular protease from Bacillus subtilis KCCM 10257 was successfully identified with the lytic enzyme L27 from Bacillus subtilis 168.