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  • P-ISSN2233-4203
  • E-ISSN2093-8950
Search Word: proteomics, Search Result: 21
1
Albert-Baskar Arul(Gachon University) ; Na-Young Han(Gachon University) ; Hookeun Lee(Gachon University) 2013, Vol.4, No.2, pp.25-29 https://doi.org/10.5478/MSL.2013.4.2.25
초록보기
Abstract

Proteomics for biomarker validation needs high throughput instrumentation to analyze huge set of clinical samplesfor quantitative and reproducible analysis at a minimum time without manual experimental errors. Sample preparation, a vitalstep in proteomics plays a major role in identification and quantification of proteins from biological samples. Tryptic digestion amajor check point in sample preparation for mass spectrometry based proteomics needs to be more accurate with rapid processingtime. The present study focuses on establishing a high throughput automated online system for proteolytic digestion anddesalting of proteins from biological samples quantitatively and qualitatively in a reproducible manner. The present study comparesonline protein digestion and desalting of BSA with conventional off-line (in-solution) method and validated for real timesample for reproducibility. Proteins were identified using SEQUEST data base search engine and the data were quantified usingIDEALQ software. The present study shows that the online system capable of handling high throughput samples in 96 well formatscarries out protein digestion and peptide desalting efficiently in a reproducible and quantitative manner. Label free quantificationshowed clear increase of peptide quantities with increase in concentration with much linearity compared to off linemethod. Hence we would like to suggest that inclusion of this online system in proteomic pipeline will be effective in quantificationof proteins in comparative proteomics were the quantification is really very crucial.

2
Heeyoun Hwang(Korea Basic Science Institute) ; Jin Young Kim(Korea Basic Science Institute) ; Jong Shin Yoo(Korea Basic Science Institute) 2021, Vol.12, No.3, pp.60-65 https://doi.org/10.5478/MSL.2021.12.3.60
초록보기
Abstract

As a part of the Chromosome-centric Human Proteome Project (C-HPP), we have developed a few algorithms for accurate identification of missing proteins, alternative splicing variants, single amino acid variants, and characterization of func-tion unannotated proteins. We have found missing proteins, novel and known ASVs, and SAAVs using LC-MS/MS data from human brain and olfactory epithelial tissue, where we validated their existence using synthetic peptides. According to the neXtProt database, the number of missing proteins in chromosome 11 shows a decreasing pattern. The development of genomic and transcriptomic sequencing techniques make the number of protein variants in chromosome 11 tremendously increase. We developed a web solution named as SAAvpedia for identification and function annotation of SAAVs, and the SAAV information is automatically transformed into the neXtProt web page using REST API service. For the 73 uPE1 in hromosome 11, we have studied the function annotaion of CCDC90B (NX_Q9GZT6), SMAP (NX_O00193), and C11orf52 (NX_Q96A22).

3
Sunkyu Choi(Proteomics Core, Weill Cornell Medicine-Qatar) 2020, Vol.11, No.2, pp.25-29 https://doi.org/10.5478/MSL.2020.11.2.25
초록보기
Abstract

Pseudopodia are dynamic actin cytoskeleton-based membrane protrusions of cells that enable directional cell migra-tion. Pseudopodia of cancer cells play key roles in cancer metastasis. Recent studies using pseudopodial subcellular fractionation methodologies combined with mass spectrometry-based proteomic profiling have provided insight into the pseudopodiome that control the protrusions of invasive metastatic cancer cells. This review highlights how to characterize the protein composition of pseudopodia and develop strategies to identify biomarkers or drug candidates that target reduction or prevention of metastatic cancer.

4
Jeong Won Kang(Kyung Hee University) ; Daehee Hwang(Institute for Basic Science) ; Kwang Pyo Kim(Kyung Hee University) 2016, Vol.7, No.4, pp.85-90 https://doi.org/10.5478/MSL.2016.7.4.85
초록보기
Abstract

Post-translational modifications (PTMs) of proteins regulate self-renewal and differentiation in embryonic stem cells (ESCs). Nitration of tyrosine residues of proteins in ESCs modulates their downstream pathways, which can affect self-renewal and differentiation. However, protein tyrosine nitration (PTN) in ESCs has been rarely studied. We reviewed 23 nitrated sites in stem cell proteins. Functional enrichment analysis showed that these nitrated proteins are involved in signal transduction, cell adhesion and migration, and cell proliferation in ESCs. Comparison between the nitrated and known phosphorylated sites revealed that 7 nitrated sites had overlapping phosphorylated sites, indicating functional links of PTNs to their associated signaling pathways in ESCs. Therefore, nitrated proteome provides a basis for understanding potential roles of PTN in self-renewal and differentiation of ESCs.

5
Sang-Yeop Lee(Korea Basic Science Institute) ; Sung Ho Yun(Korea Basic Science Institute) ; Geul Bang(Korea Basic Science Institute) ; Chang-Seop Lee(Chonbuk National University Medical School) ; Seung Il Kim(Korea Basic Science Institute) 2021, Vol.12, No.3, pp.76-80 https://doi.org/10.5478/MSL.2021.12.3.76
초록보기
Abstract

Scrub typhus is an acute febrile disease caused by the pathogenic bacterium Orientia tsutsugamushi, belonging to the Rickettsiaceae family. The shotgun proteomic analysis was performed using the sera of scrub typhus patients to identify the pro-teins having their origin in O. tsutsugamushi. Three different databases approaches were used for the identification of the pro-teomes. We identified the RsmD, an RNA methyltransferase as the commonly detected protein from all three approaches. This protein was not detected in the sera of healthy negative controls. We believe that this protein is a potential biomarker of Orientia tsutsugamushi present in the sera of scrub typhus patients.

6
Kun Cho(Korea Basic Science Institute, Sogang University) ; Gun Wook Park(Korea Basic Science Institute, Chungnam National University) ; Jin Young Kim(Korea Basic Science Institute) ; Sang Kwang Lee(Korea Basic Science Institute) ; Han Bin Oh(Sogang University) ; Jong Shin Yoo(Korea Basic Science Institute, Chungnam National University) 2010, Vol.1, No.1, pp.25-28 https://doi.org/10.5478/MSL.2010.1.1.025
초록보기
Abstract

The high-throughput identification and accurate quantification of proteins are essential strategies for exploring cellularfunctions and processes in quantitative proteomics. Stable isotope tagging is a key technique in quantitative proteomicresearch, accompanied by automated tandem mass spectrometry. For the differential proteome analysis of mouse neuronal celllines, we used a multiplexed isobaric tagging method, in which a four-plex set of amine-reactive isobaric tags are available forpeptide derivatization. Using the four-plex set of isobaric tag for relative and absolute quantitation (iTRAQ) reagents, we analyzedthe differential proteome in several stroke time pathways (0, 4, and 8 h) after the mouse neuronal cells have been stressed usinga glutamate oxidant. In order to obtain a list of the differentially expressed proteins, we selected those proteins which had apparentlychanged significantly during the stress test. With 95% of the peptides showing only a small variation in quantity before andafter the test, we obtained a list of eight up-regulated and four down-regulated proteins for the stroke time pathways. To validatethe iTRAQ approach, we studied the use of oxidant stresses for mouse neuronal cell samples that have shown differential proteome inseveral stroke time pathways (0, 4, and 8 h). Results suggest that histone H1 might be the key protein in the oxidative injurycaused by glutamate-induced cytotoxicity in HT22 cells.

7
Donggeun Oh(University of Science & Technology) ; Sun Young Lee(Korea Research Institute of Standard and Science) ; Meehyang Kwon(Korea Research Institute of Standard and Science) ; Sook-Kyung Kim(Korea Research Institute of Standard and Science) ; Myeong Hee Moon(Yonsei University) ; Dukjin Kang(Korea Research Institute of Standard and Science) 2014, Vol.5, No.3, pp.63-69 https://doi.org/10.5478/MSL.2014.5.3.63
초록보기
Abstract

In this study, we present a new isotope-coded carbamidomethylation (iCCM)-based quantitative proteomics, as acomplementary strategy for conventional isotope labeling strategies, with providing the simplicity, ease of use, and robustness. In iCCM-based quantification, two proteome samples can be separately isotope-labeled by means of covalently reaction of allcysteinyl residues in proteins with iodoacetamide (IAA) and its isotope (IAA-13C2, D2), denoted as CM and iCCM, respectively,leading to a mass shift of all cysteinyl residues to be + 4 Da. To evaluate iCCM-based isotope labeling in proteomic quantification,6 protein standards (i.e., bovine serum albumin, serotransferrin, lysozyme, beta-lactoglobulin, beta-galactosidase, andalpha-lactalbumin) isotopically labeled with IAA and its isotope, mixed equally, and followed by proteolytic digestion. Theresulting CM-/iCCM-labeled peptide mixtures were analyzed using a nLC-ESI-FT orbitrap-MS/MS. From our experimentalresults, we found that the efficiency of iCCM-based quantification is more superior to that of mTRAQ, as a conventional nonisobariclabeling method, in which both of a number of identified peptides from 6 protein standards and the less quantitative variationsin the relative abundance ratios of heavy-/light-labeled corresponding peptide pairs. Finally, we applied the developediCCM-based quantitative method to lung cancer serum proteome in order to evaluate the potential in biomarker discovery study

8
Sangeetha Ramachandran(Cochin University of Science and technology) ; Tessamma Thomas(Cochin University of Science and technology) 2019, Vol.10, No.2, pp.50-55 https://doi.org/10.5478/MSL.2019.10.2.50
초록보기
Abstract

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 stud-ied 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 gen-erate 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.

9
Sunil S. Adav(Nanyang Technological University) ; Siu Kwan Sze(Nanyang Technological University) 2013, Vol.4, No.1, pp.1-9 https://doi.org/10.5478/MSL.2013.4.1.1
초록보기
Abstract

Fungal biotechnology has been well established in food and healthcare sector, and now being explored for lignocellulosic biorefinery due to their great potential to produce a wide array of extracellular enzymes for nutrient recycling. Due to global warming, environmental pollution, green house gases emission and depleting fossil fuel, fungal enzymes for lignocellulosic biomass refinery become a major focus for utilizing renewal bioresources. Proteomic technologies tender better biological understanding and exposition of cellular mechanism of cell or microbes under particular physiological condition and are very useful in characterizing fungal secretome. Hence, in addition to traditional colorimetric enzyme assay, mass-spectrometry-based quantification methods for profiling lignocellulolytic enzymes have gained increasing popularity over the past five years. Majority of these methods include two dimensional gel electrophoresis coupled to mass spectrometry, differential stable isotope labeling and label free quantitation. Therefore, in this review, we reviewed more commonly used different proteomic techniques for profiling fungal secretome with a major focus on two dimensional gel electrophoresis, liquid chromatography-based quantitative mass spectrometry for global protein identification and quantification. We also discussed weaknesses and strengths of these methodologies for comprehensive identification and quantification of extracellular proteome.

10
Ha Ra Cho(Dankook University) ; Sung Giu Jin(Dankook University) ; Jun Seo Park(Dankook University) ; Han Sol Kim(Dankook University) ; Yong Seok Choi(Dankook University) 2017, Vol.8, No.4, pp.114-118 https://doi.org/10.5478/MSL.2017.8.4.114
초록보기
Abstract

While saliva can be considered as good biological fluid for monitoring biomarkers due to many advantages including its communication with blood and the non-invasive nature during its sampling, its applications to that purpose is still limited. As a part of efforts to expand the applications of saliva to the protein biomarker research, we carried out global absolute quantitation of proteins in human whole saliva (WS) by bottom-up proteomics techniques mainly based on nLC-Q-IMS-TOF employing MSE. From the analyses of a pooled WS sample collected from 22 healthy Korean volunteers, 93 proteins ranging from 5.89×101 ng/mL (immunoglobulin heavy chain) to 1.59×104 ng/mL (α-amylase 1) were confirmed. For the validation of the present results, human serum albumin in the same sample was quantitated by ELISA and its result was compared with that from the nLC-Q-IMS-TOF study. As a result, there was no significant difference between two results from individual approaches (1.18×104 ± 0.03×104 ng/mL from nLC-Q-IMS-TOF experiments vs. 1.23×104 ± 0.07×104 ng/mL from ELISA experiments, n=3, p=0.309). To our knowledge, this is the first global absolute quantitation of proteins in human whole saliva and information from the present study can be widely used as the first level reference for the discovery

Mass Spectrometry Letters