A5065584241- Advanced Proteomics Techniques and Applications
- Mass Spectrometry Techniques and Applications
- Digital Filter Design and Implementation
- Image and Signal Denoising Methods
- Metabolomics and Mass Spectrometry Studies
- Environmental Toxicology and Ecotoxicology
- SARS-CoV-2 and COVID-19 Research
- Antibiotic Resistance in Bacteria
- Microbial Natural Products and Biosynthesis
- Advanced Fiber Laser Technologies
- Monoclonal and Polyclonal Antibodies Research
- Biochemical and Molecular Research
- Optical Network Technologies
- Analytical Chemistry and Chromatography
- Blood groups and transfusion
- Agriculture, Soil, Plant Science
- Neonatal Health and Biochemistry
- Advanced Adaptive Filtering Techniques
- Toxic Organic Pollutants Impact
- Antimicrobial Peptides and Activities
- Advanced biosensing and bioanalysis techniques
- Environmental and Agricultural Sciences
- Biosensors and Analytical Detection
- Glycosylation and Glycoproteins Research
- Enzyme Structure and Function
Peking University
2019-2025
UCLA Medical Center
2025
Guangzhou Medical University
2019-2024
Tianjin Medical University
2024
Tianjin First Center Hospital
2024
Academy of Military Medical Sciences
2007-2023
Shaoxing University
2021-2023
State Key Laboratory of Protein and Plant Gene Research
2021-2023
Beijing Municipal Ecological and Environmental Monitoring Center
2022-2023
Albert Einstein College of Medicine
2010-2020
MassMatrix is a program that matches tandem mass spectra with theoretical peptide sequences derived from protein database. The uses accuracy sensitive probabilistic score model to rank matches. MS/MS search software was evaluated by use of high dataset and its results compared those MASCOT, SEQUEST, X!Tandem, OMSSA. For the data, provided better sensitivity than OMSSA for given specificity percentage false positives 2%. More importantly all manually validated true corresponded unique...
Liquid chromatography coupled with tandem mass spectrometry (LC-MS/MS) has become one of the most used tools in based proteomics. Various algorithms have since been developed to automate process for modern high-throughput LC-MS/MS experiments. A probability statistical scoring model assessing peptide and protein matches MS database search was derived. The scores represent that a match is random occurrence on number or total abundance matched product ions experimental spectrum. also...
A new database search algorithm has been developed to identify disulfide-linked peptides in tandem MS data sets. The is included the newly program, MassMatrix. exploits probabilistic scoring model MassMatrix achieve identification of disulfide bonds proteins and peptides. Proteins with can be identified high confidence without chemical reduction or other derivatization. approach was tested on peptide protein standards known bonds. All standard set were by further bovine pancreatic...
Recent proteomics studies have revealed that protein acetylation is an abundant and evolutionarily conserved post-translational modification from prokaryotes to eukaryotes. Although astonishing number of acetylated proteins been identified in those studies, the acetyltransferases target these remain largely unknown. Here we characterized MSMEG_5458, one GCN5-related N-acetyltransferases (GNAT's) Mycobacterium smegmatis, show it a acetyltransferase (MsPat) specifically acetylates ε-amino...
A new database search algorithm has been developed for identification of intact cross-links in proteins and peptides from tandem mass spectrometric data. Using this algorithm, can be identified characterized with high confidence. The was tested using BS(3) (bis[sulfosuccinimidyl] suberate) cross-linked Cytochrome C. Five were verified spatial plausibility by comparison its three-dimensional structure at optimized experimental conditions. distributions statistical scores true false positives...
O-Glycopeptides are often acidic owing to the frequent occurrence of saccharides in glycan, rendering traditional proteomic workflows that rely on positive mode tandem mass spectrometry (MS/MS) less effective. In this report, we demonstrate utility negative ultraviolet photodissociation (UVPD) MS for characterization O-linked glycopeptide anions. This method was evaluated a series singly and multiply deprotonated glycopeptides from model glycoprotein kappa casein, resulting production both...
Approximately one-third of the world's population carries Staphylococcus aureus. The recent emergence extreme drug resistant strains that are to "antibiotic last resort", vancomycin, has caused a further increase in pressing need discover new drugs against this organism. S. aureus enoyl reductase, saFabI, is validated target for discovery. To drive development potent and selective saFabI inhibitors, we have studied mechanism enzyme analyzed interaction with triclosan two related diphenyl...
The genome of Mycobacterium tuberculosis (TB) contains a gene that encodes highly active β-lactamase, BlaC, imparts TB with resistance to β-lactam chemotherapy. structure covalent BlaC-β-lactam complexes suggests site residues K73 and E166 are essential for acylation deacylation, respectively. We have prepared the K73A E166A mutant forms BlaC determined structures Michaelis complex cefamandole covalently bound acyl intermediate at resolutions 1.2 2.0 Å, These provide insight into details...
Abstract Background Rejection of false positive peptide matches in database searches shotgun proteomic experimental data is highly desirable. Several methods have been developed to use the retention time as refine and improve identifications from search algorithms. This report describes implementation an automated approach reduce positives validate matches. Results A robust linear regression based algorithm was automate evaluation obtained experiments. The scores peptides on their predicted...
Protein S-nitrosation has been argued to be the most important signaling pathway mediating bioactivity of NO. This post-translational modification protein thiols is result chemical nitrosation cysteine residues. The term NO-donors covers very different classes, from clinical therapeutics probes routine use in biology; their chemistry predicted distinctive biology regulated by S-nitrosation. To measure extent NO-donors, a proteomic mass spectrometry method was developed, which quantitates...
Mycobacterial siderophores are critical components for bacterial virulence in the host. Pathogenic mycobacteria synthesize iron chelating named mycobactin and carboxymycobactin to extract intracellular macrophage iron. The two differ structure only by a lipophilic aliphatic chain attached on ε-amino group of lysine core, which is transferred MbtK. Prior acyl transfer, requires activation specific fatty acyl-AMP ligase FadD33 (also known as MbtM) then loaded onto phosphopantetheinylated...
The genome of Mycobacterium tuberculosis contains a gene, blaC, which encodes highly active β-lactamase (BlaC). We have previously shown that BlaC has an extremely broad spectrum activity against penicillins and cephalosporins but weak newer carbapenems. carbapenems such as meropenem, doripenem, ertapenem react with the enzyme to form enzyme-drug covalent complexes are hydrolyzed slowly. In current study, we determined apparent Km kcat values 0.8 μM 0.03 min(-1), respectively, for tebipenem,...
Topology has emerged as a unique dimension in protein engineering, drawing attentions to the pursuit of nontrivial topologies due their functional benefits like enhanced stability and rich dynamics. However, complexity diversity artificial topological proteins remain rather limited date. Herein, we report computational design cellular synthesis pair isoforms based on symmetric assembly orthogonal entangling motifs. Two motifs with C2 symmetry, i.e., p53dim HP0242, are fused different ways...
Two new statistical models based on Monte Carlo Simulation (MCS) have been developed to score peptide matches in shotgun proteomic data and incorporated a database search program, MassMatrix (www.massmatrix.net). The first model evaluates the total abundance of matched peaks experimental spectra. second amino acid residue tags within MS/MS two provide complementary scores for that result higher confidence identification when significant are returned from both models. MCS-based use variance...
Chemicals targeting the liver stage (LS) of malaria parasite are useful for causal prophylaxis malaria. In this study, four lichen metabolites, evernic acid (1), vulpic (2), psoromic (3), and (+)-usnic (4), were evaluated against LS parasites Plasmodium berghei. Inhibition P. falciparum blood (BS) was also assessed to determine specificity. Compound 4 displayed highest activity specificity (LS IC50 value 2.3 μM, BS 47.3 μM). The compounds 1–3 inhibited one or more enzymes (PfFabI, PfFabG,...
The use of ultraviolet photodissociation (UVPD) for the activation and dissociation peptide anions is evaluated broader coverage proteome. To facilitate interpretation assignment resulting UVPD mass spectra anions, MassMatrix database search algorithm was modified to allow automated analysis negative polarity MS/MS spectra. new algorithms were developed based on engine by adding specific fragmentation pathways UVPD. in rigorously statistically optimized using two large data sets with high...