A5102717235- Advanced Proteomics Techniques and Applications
- Metabolomics and Mass Spectrometry Studies
- Machine Learning in Bioinformatics
- Mass Spectrometry Techniques and Applications
- Genomics and Phylogenetic Studies
- Bioinformatics and Genomic Networks
- RNA modifications and cancer
- Ubiquitin and proteasome pathways
- Liver Disease Diagnosis and Treatment
- Epigenetics and DNA Methylation
- RNA Research and Splicing
- SARS-CoV-2 and COVID-19 Research
- RNA and protein synthesis mechanisms
- Glycosylation and Glycoproteins Research
- Cancer Genomics and Diagnostics
- Genomics and Chromatin Dynamics
- Molecular Biology Techniques and Applications
- Endoplasmic Reticulum Stress and Disease
- Genetics, Bioinformatics, and Biomedical Research
- Microbial Metabolic Engineering and Bioproduction
- Genetics, Aging, and Longevity in Model Organisms
- Mitochondrial Function and Pathology
- Gene expression and cancer classification
- Animal Virus Infections Studies
- Biomedical Text Mining and Ontologies
Chinese Academy of Medical Sciences & Peking Union Medical College
2009-2023
Beijing Proteome Research Center
2012-2023
Academy of Military Medical Sciences
2022
Academy of Medical Sciences
2021
Chongqing Medical University
2021
Beijing Radiation Center
2003-2014
National Institutes for Food and Drug Control
2012-2013
Institute of Bioinformatics
2013
Victoria University of Wellington
2010
Fudan University
2010
Sharing of research data in public repositories has become best practice academia. With the accumulation massive data, network bandwidth and storage requirements are rapidly increasing. The ProteomeXchange (PX) consortium implements a mode centralized metadata distributed raw management, which promotes effective sharing. To facilitate open access proteome worldwide, we have developed integrated resource iProX (http://www.iprox.org) as platform for collecting sharing analysis results obtained...
The rapid development of proteomics studies has resulted in large volumes experimental data. emergence big data platform provides the opportunity to handle these amounts integrated proteome resource, iProX (https://www.iprox.cn), which was initiated 2017, been greatly improved with an up-to-date implemented 2021. Here, we describe main developments since its first publication Nucleic Acids Research 2019. First, a hyper-converged architecture high scalability supports submission process. A...
Hepatocellular carcinoma (HCC) is a highly malignant tumor, and chronic infection with hepatitis B virus one of its major risk factors. To identify the proteins involved in HCC carcinogenesis, we used two-dimensional fluorescence DIGE to study differentially expressed tumor adjacent nontumor tissue samples. Samples from 12 virus-associated patients were analyzed. A total 61 spots significantly up-regulated (ratio ≥ 2, p ≤ 0.01) samples, whereas 158 down-regulated −2, 0.01). Seventy-one gene...
Abstract Based on the same HUPO reference specimen (C1‐serum) with six proteins of highest abundance depleted by immunoaffinity chromatography, we have compared five proteomics approaches, which were (1) intact protein fractionation anion‐exchange chromatography followed 2‐DE‐MALDI‐TOF‐MS/MS for identification (2‐DE strategy); (2) 2‐D HPLC tryptic digestion each fraction and microcapillary RP‐HPLC/microESI‐MS/MS (protein (3) automated online (strong cation‐exchange (SCX)‐RPC) IT...
Abstract Recently, a new coronavirus was isolated from the lung tissue of autopsy sample and nasal/throat swabs patients with Severe Acute Respiratory Syndrome (SARS) causative association SARS determined. To reveal further characteristics virus to provide insight about molecular mechanism etiology, proteomic strategy utilized identify structural proteins (SARS‐CoV) Vero E6 cells infected BJ‐01 strain virus. At first, Western blotting convalescent sera demonstrated that there were various...
Nonalcoholic fatty liver disease (NAFLD) has emerged as a common public health problem that can progress to end-stage disease. A high-fat diet (HFD) may promote the development of NAFLD through mechanism is poorly understood. We adopted proteomic approach examine effect HFD on proteome during progression NAFLD. Male Sprague-Dawley rats fed an for 4, 12, and 24 weeks replicated human NAFLD: steatosis, nonspecific inflammation, steatohepatitis. Using two-dimensional difference gel...
To estimate the potential of state-of-the-art proteomics technologies on full coverage encoding gene products, Chinese Human Chromosome Proteome Consortium (CCPC) applied a multiomics strategy to systematically analyze transciptome, translatome, and proteome same cultured hepatoma cells with varied metastatic qualitatively quantitatively. The results provide global view expression profiles. 9064 identified high confident proteins covered 50.2% all products in translatome. Those function...
BioLadder (https://www.bioladder.cn/) is an online data analysis platform designed for proteomics research, which includes three classes of experimental modules and four common modules. It allows a variety analyses to be conducted easily efficiently. Additionally, most can also utilized the other omics data. To facilitate user experience, we have carefully different kinds functions customers quickly accurately utilize relevant In recent years, vigorous development multiomics research has...
Investigations of missing proteins (MPs) are being endorsed by many bioanalytical strategies. We proposed that proteogenomics testis tissue was a feasible approach to identify more MPs because tissues have higher gene expression levels. Here we combined proteomics and transcriptomics survey in human from three post-mortem individuals. Proteins were extracted separated with glycine- tricine-SDS-PAGE. A total 9597 protein groups identified; these, 166 listed as MPs, including 138 (83.1%)...
Physicochemical properties of proteins/peptides are often used to separate from complex biological samples in proteomics research, which is necessary for the further identification.So, analyses these very important design proteomic experiments and identified results.Current available web-based tools difficult analyze large-scale datasets.Here we provide a standalone software ProPAS (Protein Properties Analyses Software) calculate local computers.ProPAS could be several physicochemical...
A high throughput process including subcellular fractionation and multiple protein separation identification technology allowed us to establish the expression profile of human fetal liver, which was composed at least 2,495 distinct proteins 568 non-isoform groups identified from 64,960 peptides 24,454 peptides. In addition basic mentioned above, MS data were used for complementary novel mining. By doing analysis with integrated protein, expressed sequence tag, genome datasets, 223 15...
Abstract High‐throughput screens have begun to reveal protein interaction networks in several organisms. To understand the general properties of these networks, a systematic analysis topological structure and robustness was performed on Saccharomyces cerevisiae , Caenorhabditis elegans Drosophila melanogaster . It shows that three scale‐free high‐degree clustering nature as consequence their hierarchical organization. also they small‐world property with similar diameter at 4–5. Evaluation...
Abstract In this study, a liquid‐based shotgun strategy was used to comprehensively identify the expression of human liver proteome. Proteins were extracted from tissue and digested in‐solution. The tryptic digest mixture desalted separated by off‐line strong cation exchange (SCX) chromatography with 60‐min elution. MS/MS spectra acquired in data‐dependent mode after an RP chromatographic separation combined linear IT MS analysis. To obtain most comprehensive proteome, each SCX fraction run...
Fetal liver intriguingly consists of hepatic parenchymal cells and hematopoietic stem/progenitor cells. Human fetal aged 22 wk gestation (HFL22w) corresponds to the turning point between immigration emigration system. To gain further molecular insight into its developmental functional characteristics, HFL22w was studied by generating expressed sequence tags (ESTs) analyzing compiled expression profiles at different stages. A total 13,077 ESTs were sequenced from a 3′-directed cDNA library...
Multi-modality of pI distribution is a common feature in different whole proteomes. Some researchers considered it relate to the proteins with subcellular locations, indicating result natural selection. We explored predicted proteomes (including animals, plants, bacterium, archaeans) and random proteome [random protein sequences constructed according special amino acid composition molecular weight (MW) human proteome]. Our results suggest that multi-modality discrete pK(R) values for acids....
Tissue interstitial fluid (TIF) forms the interface between circulating body fluids and intracellular fluid. Pathological alterations of liver cells could be reflected in TIF, making it a promising source disease biomarkers. Mouse TIF was extracted, separated by SDS-PAGE, analyzed linear ion trap mass spectrometer, 1450 proteins were identified. These may secreted, shed from membrane vesicles, or represent cellular breakdown products. They show different profiling patterns, quantities,...
In this study, we presented a quality control tool named PepDistiller to facilitate the validation of MASCOT search results. By including number tryptic termini, and integrating refined false discovery rate (FDR) calculation method, demonstrated improved sensitivity peptide identifications obtained from semitryptic Based on analysis complex data set, approximately 7% more were using than Percolator. Moreover, method generated lower FDR estimations percentage incorrect target (PIT) fixed...
In fetal hematopoietic organs, the switch from hematopoiesis is hypothesized to be a critical time point for organogenesis, but it not yet evidenced. The transient coexistence of will useful understand development liver (FL) around this and its relationship hematopoiesis. Here, temporal comparative transcriptomic proteomic profiles were observed during points corresponding initiation (E11.5), peak (E14.5), recession (E15.5), disappearance (3 ddp) mouse FL We found that E11.5-E14.5...
Our first proteomic exploration of human chromosome 1 began in 2012 (CCPD 1.0), and the genome-wide characterization proteome through public resources revealed that 32–39% proteins on remain unidentified. To characterize all missing proteins, we applied an OMICS-integrated analysis three liver cell lines (Hep3B, MHCC97H, HCCLM3) using mRNA ribosome nascent-chain complex-bound deep sequencing profiling, contributing mass spectrometric evidence 60 additional gene products. Integration...
The Asia Oceania Human Proteome Organisation (AOHUPO) has embarked on a Membrane Proteomics Initiative with goals of systematic comparison strategies for analysis membrane proteomes and discovery proteins. This multilaboratory project is based the subcellular fraction from mouse liver that contains endoplasmic reticulum other organelles. In this study, we present strategy used preparation initial characterization sample, including validation carbonate-washing step enriches integral...