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1.
Domain-specific Quantification of Prion Protein in Cerebrospinal Fluid by Targeted Mass Spectrometry
《Molecular & cellular proteomics : MCP》2019,18(12):2388-2400
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- •Targeted mass spectrometry assay to quantify prion protein (PrP) in spinal fluid.
- •Precise measurement of PrP peptide concentration across protein domains.
- •Peptides are uniformly decreased in symptomatic prion disease patients.
- •Assay applicable to humans and preclinical species for drug development.
2.
《Molecular & cellular proteomics : MCP》2018,17(11):2146-2163
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- •Construction of threespine stickleback gill assay library using DDA proteomics
- •Population-specific gill proteome signatures of four ecotypes identified by DIA
- •HSP47 and extracellular matrix proteins highly elevated in warm-adapted sticklebacks
- •Inflammasome and proteolytic proteins highly elevated in freshwater sticklebacks
3.
《Molecular & cellular proteomics : MCP》2019,18(1):151-161
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- •New MALDI MS imaging sample preparation workflow reveals tissue protease activity.
- •Differential time- and inhibitor concentration-dependence confirm active proteases.
- •Mouse gastric tumor displays high protease activity compared to surrounding tissue.
- •Proteomic data and biochemical protease activity assay support MALDI MSI results.
4.
《Molecular & cellular proteomics : MCP》2019,18(5):968-981
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- •Quantitative substrate profiling method for characterizing peptidase specificity.
- •Applicable to both purified peptidases and peptidases in complex biological samples.
- •TMT labeling improves throughput, accuracy and reproducibility of the assay.
- •Design of fluorescent probes to monitor peptidase activity based on substrate data.
5.
《Molecular & cellular proteomics : MCP》2019,18(3):461-476
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- •Genital samples were analyzed using a high-throughput bead-based affinity assay.
- •Proteins were validated by tandem mass spectrometry with concordant results.
- •Genital epithelial proteins were increased in HIV-serodiscordant women.
6.
《Molecular & cellular proteomics : MCP》2019,18(4):622-641
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- •Serial biopsies and autopsy from a metastatic lung cancer patient over 7 years.
- •Tumor heterogeneity characterized by quantifying the proteome and phosphoproteome.
- •Patient-specific database built using whole genome sequencing data from tumors.
- •MRM assay and functional validation of a novel lung-specific CDK12-G879V mutant.
7.
《Molecular & cellular proteomics : MCP》2019,18(2):169-181
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- •Quantitative proteomics of mitotic chromosome scaffold isolated from chicken DT40 cells.
- •BAZ1B identified in the isolated mitotic chromosome scaffold localizes to mitotic chromosome axes.
- •BAZ1B knockout caused prophase delay because of altered chromosome condensation timing and impaired mitosis progression.
- •BAZ1B knockout did not affect prometaphase chromosome structure.
8.
Spatiotemporal Changes of the Phagosomal Proteome in Dendritic Cells in Response to LPS Stimulation*
《Molecular & cellular proteomics : MCP》2019,18(5):909-922
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- •Characterization of the phagosomal proteome comparing resting and LPS-treated BMDCs.
- •Label-free quantification determined 2843 phagosomal proteins.
- •Reduced recruitment of hydrolases and V-ATPase to phagosomes of LPS-treated cells.
- •Increased recruitment of antigen cross-presentation molecules to these phagosomes.
9.
《Molecular & cellular proteomics : MCP》2019,18(10):2108-2120
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- •Bayesian Beta-Binomial model integrates ion statistics with peptide ratio agreement.
- •Model appropriately interprets information from low signal peptides.
- •Confidence can be assigned even without replicates.
- •Model adds sensitivity to detection of small changes.
10.
《Molecular & cellular proteomics : MCP》2019,18(3):477-489
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- •Developed a data processing pipeline to format phosphopeptide identifications.
- •Identified the preferred substrate motif for FLT3 and mutant kinases.
- •Designed and validated a panel of pan-FTL3 artificial substrates.
- •Monitored FLT3 and mutant kinase activity through FAStide phosphorylation.
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12.
《Molecular & cellular proteomics : MCP》2018,17(11):2119-2131
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- •Temporal proteome profiling of lipotoxicity and glucolipotoxicity in β-cells
- •Palmitate induced cholesterol metabolism earlier than fatty acid metabolism
- •Setd8 promotes palmitate + glucose-stimulated INS-1 cell proliferation
- •PA induced apoptosis partially via upregulation of Rhob in INS-1 cells
13.
《Molecular & cellular proteomics : MCP》2018,17(11):2242-2255
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- •BioID and IP-MS were conducted to generate a global ZIKV-host protein interactome
- •Interactome consists of >3000 high confidence ZIKV-host protein interactions
- •Data mining indicates that ZIKV proteins interact with multiple host cell organelles
- •An important role for peroxisomes in ZIKV infection is uncovered
14.
《Molecular & cellular proteomics : MCP》2019,18(12):2524-2531
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- •Efficient sample preparation workflow for deep N-glycomics analysis from serum.
- •Temperature gradient denaturing protocol to prevent protein precipitation.
- •Decrease of free sugar content in serum enhanced PNGase F digestion efficiency.
- •Modified evaporative labeling method increased fluorophore labeling yield.
15.
《Molecular & cellular proteomics : MCP》2019,18(6):1110-1122
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- •Comprehensive analysis of inter-individual variation of normal urinary proteome.
- •Significant gender differences were observed.
- •Proteins increased in female urine are enriched in immunological pathways.
- •Estimated reference intervals of proteins as the baseline for biomarker discovery.
16.
《Molecular & cellular proteomics : MCP》2019,18(8):1479-1490
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- •Frequent genetic polymorphism affects the glycosylation pattern of fetuin.
- •Personalized in-depth proteoform profiling of fetuin purified from 20 donors.
- •Classification of serum donors into three different genotypes.
- •Septic patients show increased level of fucosylation at N-glycolation site N176.
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18.
《Molecular & cellular proteomics : MCP》2019,18(9):1745-1755
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- •We have developed a decellularization protocol for ECM protein enrichment.
- •We have characterized the proteome of adult zebrafish heart ECM.
- •We describe dynamic changes in heart ECM proteome during regeneration.
- •We describe changes in heart ECM stiffness during regeneration.
19.
《Molecular & cellular proteomics : MCP》2019,18(3):571-575
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- •Incrementally build mzML 1.1, and mzIdentML 1.2 files in Python over a file stream.
- •Traverse controlled vocabularies using common mapping patterns.
- •Generate byte offset index as the document streams.
- •Manage referential integrity on-the-fly.
20.
《Molecular & cellular proteomics : MCP》2019,18(5):1010-1026
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- •Comparing proteolytic digestions and precursor fragmentation methods for MS of ADPr
- •Identification of 11,265 unique ADPr-modified peptides
- •Mapping of hundreds of peptides co-modified by phosphorylation and ADPr
- •ADPr modification of specific residue types displays spatial preferences