Proteomic Analysis of the Vitreous Body in Proliferative and Non-Proliferative Diabetic Retinopathy

Duong, Van-An; Ahn, Jeeyun; Han, Na; Park, Jong; Lee, Hookeun; Kim, Tae Wan; Lee, Hookeun

doi:10.2174/1570164617666200302101442

Cited by 5 publications

(2 citation statements)

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“…If samples containing proteins are culture media, exosomes, or body fluids such as serum, plasma, saliva, tears, nasal fluids, urine, or aqueous humor, they do not require lysis pretreatment. In these cases, an appropriate amount of buffer is added to favor subsequent enzymatic digestion steps [63,64]. If samples are cells, a lysis step is applied to break the cell membrane.…”

Section: Sampling and Sample Pretreatmentmentioning

confidence: 99%

Proteomics in Forensic Analysis: Applications for Human Samples

et al. 2021

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Proteomics, the large-scale study of all proteins of an organism or system, is a powerful tool for studying biological systems. It can provide a holistic view of the physiological and biochemical states of given samples through identification and quantification of large numbers of peptides and proteins. In forensic science, proteomics can be used as a confirmatory and orthogonal technique for well-built genomic analyses. Proteomics is highly valuable in cases where nucleic acids are absent or degraded, such as hair and bone samples. It can be used to identify body fluids, ethnic group, gender, individual, and estimate post-mortem interval using bone, muscle, and decomposition fluid samples. Compared to genomic analysis, proteomics can provide a better global picture of a sample. It has been used in forensic science for a wide range of sample types and applications. In this review, we briefly introduce proteomic methods, including sample preparation techniques, data acquisition using liquid chromatography-tandem mass spectrometry, and data analysis using database search, spectral library search, and de novo sequencing. We also summarize recent applications in the past decade of proteomics in forensic science with a special focus on human samples, including hair, bone, body fluids, fingernail, muscle, brain, and fingermark, and address the challenges, considerations, and future developments of forensic proteomics.

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Section: Sampling and Sample Pretreatmentmentioning

confidence: 99%

Proteomics in Forensic Analysis: Applications for Human Samples

et al. 2021

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“…Various approaches have attempted to achieve complete proteome coverage of complex samples, and yet reducing sample complexity remains a bottleneck against reaching a fundamental goal in proteomics [17]. In proteomic studies, separations in protein or peptide levels are frequently used to reduce sample complexity prior to mass spectrometric analysis [18][19][20][21]. Many separation techniques have been widely used in proteomic studies, including two-dimensional electrophoresis (2-DE) [22], reversed-phase liquid chromatography (RPLC) [23], isoelectric focusing [24], and capillary zone electrophoresis (CZE) [25].…”

Section: Introductionmentioning

confidence: 99%

Proteomic Profiling of Emiliania huxleyi Using a Three-Dimensional Separation Method Combined with Tandem Mass Spectrometry

et al. 2020

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Emiliania huxleyi is one of the most abundant marine planktons, and it has a crucial feature in the carbon cycle. However, proteomic analyses of Emiliania huxleyi have not been done extensively. In this study, a three-dimensional liquid chromatography (3D-LC) system consisting of strong cation exchange, high- and low-pH reversed-phase liquid chromatography was established for in-depth proteomic profiling of Emiliania huxleyi. From tryptic proteome digest, 70 fractions were generated and analyzed using liquid chromatography-tandem mass spectrometry. In total, more than 84,000 unique peptides and 10,000 proteins groups were identified with a false discovery rate of ≤0.01. The physicochemical properties of the identified peptides were evaluated. Using ClueGO, approximately 700 gene ontology terms and 15 pathways were defined from the identified protein groups with p-value ≤0.05, covering a wide range of biological processes, cellular components, and molecular functions. Many biological processes associated with CO2 fixation, photosynthesis, biosynthesis, and metabolic process were identified. Various molecular functions relating to protein binding and enzyme activities were also found. The 3D-LC strategy is a powerful approach for comparative proteomic studies on Emiliania huxleyi to reveal changes in its protein level and related mechanism.

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