A5103157650- Advanced Proteomics Techniques and Applications
- Mass Spectrometry Techniques and Applications
- Metabolomics and Mass Spectrometry Studies
- Adipose Tissue and Metabolism
- Machine Learning in Bioinformatics
- Pancreatic function and diabetes
- Adipokines, Inflammation, and Metabolic Diseases
- Cardiovascular Disease and Adiposity
- Metabolism, Diabetes, and Cancer
- SARS-CoV-2 and COVID-19 Research
- Analytical Chemistry and Chromatography
- Genomics and Phylogenetic Studies
- Mitochondrial Function and Pathology
- Molecular Biology Techniques and Applications
- interferon and immune responses
- Identification and Quantification in Food
- Animal Genetics and Reproduction
- Toxin Mechanisms and Immunotoxins
- Plant Pathogens and Fungal Diseases
- Food Supply Chain Traceability
- Cytokine Signaling Pathways and Interactions
- SARS-CoV-2 detection and testing
- Invertebrate Immune Response Mechanisms
- Telomeres, Telomerase, and Senescence
- Microfluidic and Capillary Electrophoresis Applications
Chinese Academy of Sciences
2010-2024
Center for Excellence in Molecular Cell Science
2009-2024
Zhongshan People's Hospital
2023
Shanghai Institutes for Biological Sciences
2008-2022
Foshan University
2018
University of Michigan
2012-2018
ShanghaiTech University
2015-2017
Shanghai Advanced Research Institute
2015
Children's National
2014
China Agricultural University
2009
Abstract HUPO initiated the Plasma Proteome Project (PPP) in 2002. Its pilot phase has (1) evaluated advantages and limitations of many depletion, fractionation, MS technology platforms; (2) compared PPP reference specimens human serum EDTA, heparin, citrate‐anti‐coagulated plasma; (3) created a publicly‐available knowledge base (www.bioinformatics.med.umich.edu/hupo/ppp; www.ebi.ac.uk/pride). Thirty‐five participating laboratories 13 countries submitted datasets. Working groups addressed...
Perivascular adipose tissue (PVAT) surrounds most vessels and shares common features with brown (BAT). Although adaptive thermogenesis in BAT increases energy expenditure is beneficial for metabolic diseases, little known about the role of PVAT vascular diseases such as atherosclerosis. We hypothesize that thermogenic function regulates intravascular temperature reduces atherosclerosis.PVAT similar structural proteomics BAT. demonstrated has properties to response cold stimuli vivo....
Abstract Background Microarrays revolutionized biological research by enabling gene expression comparisons on a transcriptome-wide scale. Microarrays, however, do not estimate absolute level accurately. At present, high throughput sequencing is emerging as an alternative methodology for transcriptome studies. Although free of many limitations imposed microarray design, its potential to transcript levels unknown. Results In this study, we evaluate relative accuracy microarrays and (RNA-Seq)...
Abstract This paper describes the pFind 2.0 software package for peptide and protein identification via tandem mass spectrometry. Firstly, most important feature of is that it offers a modularized customized platform third parties to test compare their algorithms. The developers can create own modules following open application programming interface (API) standards then add into workflows in place default modules. In addition, accommodate different requirements, provides four automated...
Abstract To better understand the mechanism underlying hepatocellular carcinoma (HCC) metastasis and to search for potential markers HCC prognosis, differential proteome analysis on two cell strains with high low metastatic potentials, MHCC97‐H MHCC97‐L, was conducted using two‐dimensional (2‐D) gel electrophoresis followed by matrix‐assisted laser desorption/time of flight mass spectrometry liquid chromatography ion trap spectrometry. Image silver‐stained 2‐D gels revealed that 56 protein...
With the rapid expansion of protein post-translational modification (PTM) research based on large-scale proteomic work, there is an increasing demand for a suitable repository to analyze PTM data. Here we present curated, web-accessible data base, SysPTM. SysPTM provides systematic and sophisticated platform equipped not only with knowledge base manually curated multi-type but also four fully developed, in-depth mining tools. Currently, contains detailing 117,349 experimentally determined...
Background Leptin is an adipocyte-derived hormone that plays a critical role in energy homeostasis and lipid metabolism. Overnutrition-associated obesity known to be accompanied by hyperleptinemia. However, the physiological actions of leptin metabolic responses high-fat diet (HFD) intake remain completely elucidated. Here we characterized features mice fed diets investigated impact upon lipogenic program which was found suppressed HFD feeding through proteomics approach. Results When...
Objective— Perivascular adipose tissue (PVAT) contributes to vascular homeostasis by producing paracrine factors. Previously, we reported that selective deletion of PPARγ (peroxisome proliferator-activated receptor γ) in smooth muscle cells resulted concurrent loss PVAT and enhanced atherosclerosis mice. To address the causal relationship between atherosclerosis, used BA-PPARγ-KO (brown adipocyte-specific knockout) Approach Results— Deletion brown adipocytes did not affect white or PPARα...
Abstract Chiglitazar is a novel peroxisome proliferator-activated receptor (PPAR) pan-agonist, which passed phase III clinical trials and was newly approved in China for use as an adjunct to diet exercise glycemic control adult patients with Type 2 Diabetes (T2D). To explore the circulating protein signatures associated administration of chiglitazar T2D patients, we conducted comparative longitudinal study using plasma proteome profiling. Of 157 included study, administered specific group,...
The correlation among fragment ions in a tandem mass spectrum is crucial reducing stochastic mismatches for peptide identification by database searching. Until now, an efficient scoring algorithm that considers the correlative information tunable and comprehensive manner has been lacking.This paper provides promising approach to utilizing improving accuracy. kernel trick, rooted statistical learning theory, exploited address this issue with low computational effort. common method, spectral...
Mammalian hibernation involves complex mechanisms of metabolic reprogramming and tissue protection. Previous gene expression studies have mainly focused on changes at the mRNA level. Large scale proteomics lagged behind largely because lack an adequate protein database specific for hibernating species. We constructed a ground squirrel identification used label-free shotgun approach to analyze throughout torpor-arousal cycle during in arctic squirrels (Urocitellus parryii). identified more...
Increasing attention has been paid to the urinary proteome because it holds promise of discovering various disease biomarkers. However, most urine proteomics studies routinely relied on protein pre-fractionation and so far did not present characterization phosphorylation status. Two robust approaches, integrated multidimensional liquid chromatography (IMDL) Yin-yang (MDLC) tandem mass spectrometry, were recently developed in our laboratory, with high-coverage identification peptide mixtures....
Lipid droplets in adipocytes serve as the principal long-term energy storage depot of animals. There is increasing recognition that lipid are not merely a static neutral site, but fact dynamic and multi-functional organelles. Structurally, droplet consists core surrounded by phospholipid monolayer proteins embedded or bound to layer. Proteins on surface crucial structure dynamics. To understand droplet-associated proteome primary adipocyte with large central droplet, white adipose tissue...
Subcellular proteomics, as an important step to functional has been a focus in proteomic research. However, the co-purification of "contaminating" proteins major problem all subcellular research including kinds mitochondrial proteome It is often difficult conclude whether these "contaminants" represent true endogenous partners or artificial associations induced by cell disruption incomplete purification. To solve such problem, we applied high-throughput comparative experimental strategy,...
Abstract We have investigated the serum proteome of Han‐nationality Chinese by using shotgun strategy. A complete proteomics analysis was performed on two reference specimens from a total 20 healthy donors, in which each sample made ten‐pooled male or female serum, respectively. The methodology used encompassed (1) removal six high‐abundant proteins; (2) tryptic digestion low‐ and proteins serum; (3) separation peptide mixture RP‐HPLC followed ESI‐MS/MS identification. 944 nonredundant were...
Most current technologies for the enrichment of phosphopeptides rely on a tandem combination different chromatography modes. Here, fully automatic two-dimensional liquid mass spectrometry method was developed global phosphopeptide identification. The peptide mixtures were loaded strong anion exchange (SAX) column under basic pH conditions and eluted with continuous gradient to 2.0. This SAX system could be coupled online reversed-phase (RP-LC-MS/MS). For digests from standard protein mixture...
Single-nucleotide polymorphisms (SNPs) are recognized as one kind of major genetic variants in population scale. However, at the proteome level scale remain elusive. In present study, we named amino acid variances derived from SNPs within coding regions single (SAPs) level, and developed a pipeline non-targeted targeted proteomics to identify quantify SAP peptides human plasma. The absolute concentrations three selected SAP-peptide pairs among 290 Asian individuals were measured by reaction...
The conventional 2-D LC-MS/MS setup for global proteome analysis was based on online and offline salt gradients (step continuous) using strong-cation-exchange chromatography in conjunction with RP MS. use of the system step elution had possibility resulting peptide overlapping across fractions. mode option to operate continuous gradient decrease peak overlap, but exhibited decreased robustness, lower reproducibility, sample loss during process. Due extensive washing requirement between...
For large-scale analysis of phosphorylation at proteome-wide scale, a variety affinity-based strategies have been developed to enrich phosphopeptide. Because each method differed in their specificity isolation, the global and unbiased enrichment phosphopeptides remains major technical challenge phosphoproteomics. In present work, we demostrate that phosphopeptide based on an online continuous pH gradient strong anion exchange column (SAX method) is highly complementary titanium dioxide...
Database searching is the technique of choice for shotgun proteomics, and to date much research effort has been spent on improving its effectiveness. However, database faces a serious challenge efficiency, considering large numbers mass spectra ever fast increase in peptide databases resulting from genome translations, enzymatic digestions, post-translational modifications. In this study, we conducted systematic speeding up search engines protein identification illustrate key points with...