A5039887185- Glycosylation and Glycoproteins Research
- Advanced Proteomics Techniques and Applications
- Carbohydrate Chemistry and Synthesis
- Mass Spectrometry Techniques and Applications
- Genomics and Phylogenetic Studies
- Peptidase Inhibition and Analysis
- Cancer Research and Treatments
- Metabolomics and Mass Spectrometry Studies
- Monoclonal and Polyclonal Antibodies Research
- Cancer, Hypoxia, and Metabolism
- Enzyme Structure and Function
- Proteoglycans and glycosaminoglycans research
- Genomics and Chromatin Dynamics
- Protein purification and stability
- Pancreatic and Hepatic Oncology Research
- RNA and protein synthesis mechanisms
- Identification and Quantification in Food
- Antimicrobial Peptides and Activities
- Ubiquitin and proteasome pathways
Tongji University
2015-2022
N-Glycosylation, being one of the most common and complex protein post-translational modifications (PTMs), is known to have microheterogeneity with presence different N-glycan structures at a single specific glycosite. These may exactly same monosaccharide composition but totally differential expressions pathological relevance. Mass spectrometry-based N-glycoproteomics has so far been successful in large-scale characterization these N-glycans level, structure-level identification...
Most of the current popular tandem mass spectrometers have capability resolving primary structures (monosaccharide composition, sequence and linkage) N-glycans; however, compositions or putative mostly been reported so far. Identification visualization tools N-glycans are needed.The isotopic mass-to-charge ratio envelope fingerprinting algorithm, which has successfully used for intact protein database search identification, was adapted N-glycan search, a stand-alone engine, GlySeeker,...
High-throughput proteome-level characterization of stemness markers MCF-7 cancer stem cells was carried out using our recently developed site- and structure-specific isotopic-labelled quantitative<italic>N</italic>-glycoproteomics pipeline.
Protein structural and functional studies rely on complete qualitative quantitative information protein species (proteoforms); thus, it is important to quantify differentially expressed proteins at their molecular level. Here we report our development of universal pseudoisobaric dimethyl labeling (pIDL) amino groups both the N-terminal lysine residues for relative quantitation intact proteins. Initial proof-of-principle study was conducted standard myoglobin hepatocellular proteomes (HepG2...
Cancer stem cells (CSCs) are reported to be responsible for tumor initiation, progression, metastasis, and therapy resistance where P-glycoprotein (P-gp) as well other glycoproteins involved. Identification of these glycoprotein markers is critical understanding the mechanism developing therapeutics.In this study, we report our comparative quantitative site- structure-specific N-glycoproteomics study MCF-7/ADR cancer vs. cells. With zic-HILIC enrichment, isotopic diethyl labeling, RPLC-MS/MS...
The functional study and application of an intact glycoprotein require the structural characterization both protein backbone glycan moiety; former has been successfully demonstrated with selective fragmentation in CID ExD; whether latter can be achieved moiety remains to explored.RNase B solution was electrosprayed its glycoforms GlcNAc2 Mann (n = 5-9) highest abundance (charge state z 16) were isolated individually fragmented using CID, ETD, HCD, ETciD, EThcD on Orbitrap Fusion Lumos...
Abstract It has long been an analytical challenge to accurately and efficiently resolve extremely dense overlapping isotopic envelopes (OIEs) in protein tandem mass spectra confidently identify proteins. Here, we report a computationally efficient method, called OIE_CARE, OIEs by calculating the relative deviation between ideal observed experimental abundance. In OIE_CARE abundance of particular peak (OIP) is first calculated for all sharing this OIP. The (RD) overall OIP summed value then...
Rationale N‐glycosylation is one of the most common protein post‐translational modifications; it extremely complex with multiple glycoforms from different monosaccharide compositions, sequences, glycosidic linkages, and anomeric positions. Each glycoform functions a particular site‐ structure‐specific N‐glycan that can be fully characterized using state‐of‐the‐art tandem mass spectrometry (MS/MS) intact N‐glycopeptide database search engine GPSeeker we recently developed. Urine has gained...
Abstract Site‐ and structure‐specific quantitative N‐glycoproteomics characterization of differentially expressed N‐glycosylation at the intact N‐glycopeptide level with distinct chromatographic separation fragment ions has become possible recent development RPLC‐pentaHILIC 2DLC use search engine GPSeeker. Here we provide a detailed protocol for this GPSeeker‐centered isotopic‐labeling pipeline. The protocols include sample preparation 1:1 mixture light (‐CH 3 ) 2 heavy (‐ 13 CD H)...
Rationale The mass measurement accuracy (MMA) of Orbitrap spectrometers is 1–5 ppm according to the manufacturer's specification; yet, up 50 has been used as tolerance interpret data in literature. A systematic evaluation MMA thus necessary find optimal be used. Methods Reversed-phase liquid chromatography/tandem spectrometry (RPLC/MS/MS) analyses intact E. coli proteome were carried out on a Q Exactive spectrometer coupled Dionex UltiMate 3000 RSLCnano system. analysis included three...
Abstract Approximately a third of eukaryotic proteins are estimated to be phosphorylated, and the protein phosphorylation is significant in regulating almost all aspects cell life. Due low stoichiometry phosphorylation, efficient enrichment often an essential step phosphoproteomics study. Over decades, lots materials have been successfully developed widely used for intact phosphoproeins. One these immobilized titanium(IV) affinity chromatography (Ti 4+ ‐IMAC) microspheres, which has studied...
Cell-surface N-glycans play important roles in both inter- and intracellular processes, including cell adhesion development, recognition, as well cancer development metastasis; detailed structural characterization of these is thus paramount. Here we report our comparative N-glycomics study cell-surface the hepatocellular carcinoma (HCC) HepG2 cells vs normal liver LO2 cells. With sequential trypsin digestion proteins, C18 depletion peptides without glycosylation, PNGase F N-glycopeptides,...
Top-down characterization of combinatorial and dense post-translational modifications (PTMs) on core histones has long been a big analytical challenge because enormous putative proteoforms for identification simultaneously sites each individual PTM localization. ProteinGoggle 2.0, as implemented with the isotopic mass-to-charge ratio envelope fingerprinting algorithm, multiple unique strengths top-down histone PTMs together high-resolution tandem mass spectrometry. Here we report our...
N-linked glycosylation is one of the most common protein PTMs, and topological structure (monosaccharide composition sequence as well glycosidic linkages) N-glycans vital information to understand their biological functions roles. Tandem mass spectrometry has been widely used for characterization N-glycans, where comprehensive understanding fragmentation pathways characteristics product ions are essential achieve best interpretation MS/MS data highest confidence identification. Here, we...
Histone post-translational modifications (PTMs) play various roles in chromatin-related cellular processes, and comprehensive analysis of these combinatorial PTMs at the intact protein level by top-down proteomics is method choice to reveal their crosstalk biological functions. Here, we report our characterization core histones from mouse fibroblasts cells NIH/3T3, which a classic model used many kinds research. With nanoRPLC-MS/MS ProteinGoggle database search, 547 species were identified...