Thermal proteome profiling (TPP) is a combination of cellular thermal shift assay (CETSA) and quantitative mass spectrometry (MS), also termed as MS-CETSA. TPP determines the stability of the entire proteome by measuring the content of soluble proteins in cells or cell lysates at different heating temperatures. Proteins can change their thermostability when interacting with small molecules (e.g., drugs or metabolites), nucleic acids, or other proteins or posttranslational modification, while TPP can identify target proteins based on the difference in thermostability with or without ligand-binding. At present, TPP has been applied to identify the targets and off-targets of drugs and interrogate protein-metabolite and protein-protein interactions. Due to limited understanding of this technology, this review introduced the principles, methods, applications, advantages and limitations of TPP.
Proteome ; Mass Spectrometry

The Korean Bioinformation Center (KOBIC) is a national bioinformatics research center in Korea. We developed many bioinformatics algorithms and applications to facilitate the biological interpretation of OMICS data. Here we present an introduction to major bioinformatics resources of databases and tools developed at KOBIC. These resources are classified into three main fields: genome, proteome, and literature. In the genomic resources, we constructed several pipelines for next generation sequencing (NGS) data processing and developed analysis algorithms and web-based database servers including miRGator, ESTpass, and CleanEST. We also built integrated databases and servers for microarray expression data such as MDCDP. As for the proteome data, VnD database, WDAC, Localizome, and CHARMM_HM web servers are available for various purposes. We constructed IntoPub server and Patome database in the literature field. We continue constructing and maintaining the bioinformatics infrastructure and developing algorithms.
Computational Biology ; Genome ; Korea ; Proteome

Protein ubiquitination is one of the most important and widely exist protein post-translational modifications in eukaryotic cells, which takes the ubiquitin and ubiquitin chains as signal molecules to covalently modify other protein substrates. It plays an important roles in the control of almost all of the life processes, including gene transcription and translation, signal transduction and cell-cycle progression, besides classical 26S protesome degradation pathway. Varied modification sites in the same substrates as well as different types of ubiquitin linkages in the same modification sites contain different structural information, which conduct different signal or even determine the fate of the protein substrates in the cell. Any abnormalities in ubiquitin chain formation or its modification process may cause severe problem in maintaining the balance of intracellular environment and finally result in serious health problem of human being. In this review, we discussed the discovery, genetic characteristics and the crystal structure of the ubiquitin. We also emphasized the recent progresses of the assembly processes, structure and their biological function of ubiquitin chains. The relationship between the disregulation and related human diseases has also been discussed. These progress will shed light on the complexity of proteome, which may also provide tools in the new drug research and development processes.
Humans ; Proteome ; Ubiquitin ; chemistry ; Ubiquitination

PURPOSE: To evaluation of the safety and the usefulness of our "You's bottle" that we have invented for sampling vitreous. METHODS: We performed the vitreous sampling with our collection bottle in 13 patients who had undergone vitrectomy for diabetic retinopathy. We observed the usefulness and complications after sampling. Collected vitreous was used for analysis of protein components. RESULTS: There was no complication associated with collection bottle. The analysis of proteome was successful. CONCLUSIONS: Our study showed that "You's bottle" might be a useful tool for the research of vitreous.
Biopsy* ; Diabetic Retinopathy ; Humans ; Proteome ; Vitrectomy

The advances in mass spectrometry-based proteomics technologies have enabled the generation of global proteome data from tissue or body fluid samples collected from a broad spectrum of human diseases. Comparative proteomic analysis of global proteome data identifies and prioritizes the proteins showing altered abundances, called differentially expressed proteins (DEPs), in disease samples, compared to control samples. Protein biomarker candidates that can serve as indicators of disease states are then selected as key molecules among these proteins. Recently, it has been addressed that cellular pathways can provide better indications of disease states than individual molecules and also network analysis of the DEPs enables effective identification of cellular pathways altered in disease conditions and key molecules representing the altered cellular pathways. Accordingly, a number of network-based approaches to identify disease-related pathways and representative molecules of such pathways have been developed. In this review, we summarize analytical platforms for network-based protein biomarker discovery and key components in the platforms.
Body Fluids ; Humans ; Proteome ; Proteomics ; Biomarkers

Seed quality plays an important role in the agricultural and animal husbandry production, the effective utilization of genetic resources, the conservation of biodiversity and the restoration and reconstruction of plant communities. Seed aging is a common physiological phenomenon during storage. It is a natural irreversible process that occurs and develops along with the extension of seed storage time. It is not only related to the growth, yield and quality of seed and seedling establishment, but also has an important effect on the conservation, utilization and development of plant germplasm resources. The physiological mechanisms of seed aging are complex and diverse. Most studies focus on conventional physiological characterization, while systematic and comprehensive in-depth studies are lacking. Here we review the recent advances in understanding the physiology of seed aging process, including the methods of seed aging, the effect of aging on seed germination, and the physiological and molecular mechanisms of seed aging. The change of multiple physiological parameters, including seed vigor, electrical conductivity, malondialdehyde content and storage material in the seed, antioxidant enzyme activity and mitochondrial structure, were summarized. Moreover, insights into the mechanism of seed aging from the aspects of transcriptome, proteome and aging related gene function were summarized. This study may facilitate the research of seed biology and the conservation and utilization of germplasm resources.
Germination ; Plants ; Proteome ; Seedlings ; Seeds/genetics*

The mechanism of methamphetamine toxicity and addiction is the key research direction of forensic toxicology, and the development of omics technology provides a new platform for further study of this direction. METH toxic damage and addiction are reflected differently in genes, ribonucleic acid (RNA) transcription, protein and metabolism. This article summarizes the achievements and shortcomings of multi-omics technologies such as genome, transcriptome, metabolome and proteome in the study of METH damage and addiction, and discusses the strategies and advantages of multi-omics combined analysis in the study of METH toxic damage and addiction mechanism, in order to provide more useful reference information for forensic toxicology of METH.
Metabolome ; Metabolomics ; Methamphetamine/toxicity* ; Proteome ; Proteomics

The abundance of proteins in human urine is low and easily to be masked by high-abundance proteins during mass spectrometry analysis. Development of efficient and highly selective enrichment methods is therefore a prerequisite for achieving deep coverage of urine protein markers. Notably, different experimental methods would affect the urine protein enrichment efficacy and the coverage of urine proteome. In this study, ultrafiltration, nitrocellulose membrane enrichment and saturated ammonium sulfate precipitation were used to process 10 mL urine samples from five healthy volunteers and five bladder cancer patients. The urine proteins were enriched and separate by SDS-PAGE to compare the purification efficiency of different methods. Moreover, the peptide identification effects of different purification methods were analyzed by mass spectrometry to determine the best method for enriching urine protein histones. Saturated ammonium sulfate precipitation method outperformed the ultrafiltration and the nitrocellulose membrane enrichment methods in terms of the protein enrichment efficacy and quality. The interference of highly abundant albumin was reduced, whereas the amount of low-abundance protein was increased, and the sensitivity of mass spectrometry identification was increased. The saturated ammonium sulfate precipitation method may be applied for large-scale urine processing for screening clinical diagnostic markers through proteomics.
Histones ; Humans ; Mass Spectrometry ; Proteome ; Proteomics ; Urinalysis

Penicillin is a kind of β-lactam drug which has been applied in the clinical treatment firstly in the world, and it has still been widely used at present. The synthesis and regulation mechanism of Penicillium chrysogenum, which is used to produce penicillin, has been studied quite maturely, but its proteomics research started relatively late and fewer reports were published. This paper reviews the synthesis and application of penicillin, transformation of Penicillium chrysogenum, and the research progress of its proteomics. On this basis, the study highlights the advantages of proteomics in the research of protein expression.
Penicillins ; biosynthesis ; Penicillium chrysogenum ; metabolism ; Proteome ; Proteomics

Biofilms ; Dental Caries ; microbiology ; Humans ; Proteome ; metabolism