• 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.

• Journal of the Korean Vacuum Society
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• v.6 no.2
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• pp.159-164
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• 1997

We have studied initial oxidation of the alkali metal(AM)/Si(111) surface using X-ray photoelectron spectroscopy(XPS) and reflection high energy electron diffraction(RHEED) at room temperature(RT) and high temperature(HT)(300~50$0^{\circ}C$). The oxidation of the Si(111)7$\times$7 surface was promoted by the adsorption of 1 momolayer(ML) AM, whereas no promotion occurred for submonolayer(<0.5 ML) adsorbed Si(111)7$\times$7 surface at RT. O Is core level spectra were measured with increasing oxygen exposure. It was found that the oxygen adsorbed on the Si(111)7$\times$7-AM surface have two different bond configuration, Si-O and Am-O, respectively. From these results, we discussed the role of AM-O bonding in the promoted oxidation. At HT(300~50$0^{\circ}C$), the AM-adsorbed surface became very inactive with the structural transformation to the 3$\times$1-AM. We present the results of the oxidation of the Si(111)3$\times$1-AM(Na, K, Cs) surface.

• Journal of the Korean Institute of Electrical and Electronic Material Engineers
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• v.18 no.2
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• pp.125-129
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• 2005

Two kinds of physical treatments were examined for the analysis both of intrinsic surface and interior nature of CuInS $e_2$[CIS] and CuGaS $e_2$[CGS] films grown in separated systems. For the first method, a selenium protection layer which was immediately deposited after the growth of the CIS was investigated. The Se cap layer protects CISe surface from oxidation and contamination during the transport under ambient atmosphere. The Se cap was removed by thermal annealing at temperature above 15$0^{\circ}C$. After the decapping treatment at 2$25^{\circ}C$ for 60 min, ultraviolet photoemission and inverse photoemission measurements of the CIS film showed that its valence band maximum(VBM) and conduction band minimum (CBM) are located at 0.58 eV below and 0.52 eV above the Fermi level $E_{F}$, respectively. For the second treatment, an Ar ion beam etching was exploited. The etching with ion kinetic energy $E_{k}$ above 500 eV resulted in broadening of photoemission spectra of core signals and occasional development of metallic feature around $E_{F}$. These degradations were successfully suppressed by decreasing $E_{k}$ below 400 eV. CGS films etched with the beam of $E_{k}$ = 400 eV showed a band gap of 1.7 eV where $E_{F}$ was almost centered.st centered.

• Proceedings of the Korean Vacuum Society Conference
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• 2013.08a
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• pp.283.2-283.2
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• 2013

The variation of chemical and interfacial state during the growth of Ta2O5 films on the Si substrate by atomic layer deposition (ALD) was investigated using in-situ synchrotron radiation photoemission spectroscopy. A newly synthesized liquid precursor Ta(NtBu)(dmamp)2Me was used as the metal precursor, with Ar as a purging gas and H2O as the oxidant source. The core-level spectra of Si 2p, Ta 4f, and O 1s revealed that Ta suboxide and Si dioxide were formed at the initial stages of Ta2O5 growth. However, the Ta suboxide states almost disappeared as the ALD cycles progressed. Consequently, the Ta5+ state, which corresponds with the stoichiometric Ta2O5, only appeared after 4.0 cycles. Additionally, tantalum silicate was not detected at the interfacial states between Ta2O5 and Si. The measured valence band offset value between Ta2O5 and the Si substrate was 3.08 eV after 2.5 cycles.

• Proceedings of the Korean Vacuum Society Conference
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• 2014.02a
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• pp.362-362
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• 2014

Atomic layer deposition (ALD) can be regarded as a special variation of the chemical vapor deposition method for reducing film thickness. ALD is based on sequential self-limiting reactions from the gas phase to produce thin films and over-layers in the nanometer scale with perfect conformality and process controllability. These characteristics make ALD an important film deposition technique for nanoelectronics. Tantalum pentoxide ($Ta_2O_5$) has a number of applications in optics and electronics due to its superior properties, such as thermal and chemical stability, high refractive index (>2.0), low absorption in near-UV to IR regions, and high-k. In particular, the dielectric constant of amorphous $Ta_2O_5$ is typically close to 25. Accordingly, $Ta_2O_5$ has been extensively studied in various electronics such as metal oxide semiconductor field-effect transistors (FET), organic FET, dynamic random access memories (RAM), resistance RAM, etc. In this experiment, the variations of chemical and interfacial state during the growth of $Ta_2O_5$ films on the Si substrate by ALD was investigated using in-situ synchrotron radiation photoemission spectroscopy. A newly synthesized liquid precursor $Ta(N^tBu)(dmamp)_2$ Me was used as the metal precursor, with Ar as a purging gas and $H_2O$ as the oxidant source. The core-level spectra of Si 2p, Ta 4f, and O 1s revealed that Ta suboxide and Si dioxide were formed at the initial stages of $Ta_2O_5$ growth. However, the Ta suboxide states almost disappeared as the ALD cycles progressed. Consequently, the $Ta^{5+}$ state, which corresponds with the stoichiometric $Ta_2O_5$, only appeared after 4.0 cycles. Additionally, tantalum silicide was not detected at the interfacial states between $Ta_2O_5$ and Si. The measured valence band offset value between $Ta_2O_5$ and the Si substrate was 3.08 eV after 2.5 cycles.