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1.
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Highlights
  • •Open source software for comprehensive HDX-MS data analysis.
  • •Automatic back-exchange correction options.
  • •Rigorous statistical analysis of the significance of uptake differences.
  • •High quality visualization tools.
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2.
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Highlights
  • •Glycosylation is not currently considered in flu vaccine design.
  • •Glycosylation influences on immunodominance are not well understood.
  • •Identification of site-specific glycosylation using mass spectrometry has matured.
  • •New methods are needed to quantify site-specific glycosylation for vaccine design.
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3.
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Highlights
  • •In-depth proteome profiling of primary human myeloma cells
  • •Characteristics of myeloma cells are related to hypoxic bone marrow conditions
  • •Myeloma cells show specific immune evasion strategies
  • •Metabolic adaptations involve tumor and stroma cells
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4.
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Highlights
  • •quantitative phosphoproteome analysis of TDM-activated macrophages.
  • •distinct Mincle-dependent and independent phosphorylation and gene regulations.
  • •Mincle-dependent activation of PI3K/AKT signaling by TDM.
  • •Mincle-independent macrophage response is linked to cell cycle regulation.
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5.
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Highlights
  • •Unified identification and quantification error rates for protein quantification.
  • •Error propagation using graphical models and Bayesian statistics.
  • •Account for uncertainty of missing values instead of overconfident point estimates.
  • •Control of differential expression false discovery rate at increased sensitivity.
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6.
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Highlights
  • •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.
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7.
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Highlights
  • •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
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8.
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Highlights
  • •MaxQuant.Live controls Orbitrap mass analyzers in real-time.
  • •Freely available apps enable advanced data acquisition strategies.
  • •On-the-fly mass, retention time and intensity recalibration.
  • •Global targeting unifies shotgun and targeted proteomics.
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9.
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Highlights
  • •OMICS distinguish cancer cells from resistant or cancer stem cells.
  • •Bactericidal antibiotics and mitochondria.
  • •Linezolid and anticancer therapy.
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10.
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Highlights
  • •Quantitative changes in global proteome and ubiquitinome in Huntington's disease.
  • •Differential ubiquitination of wild-type and mutant Htt in mice brain.
  • •Enriched pathways include vesicle transport and mRNA processing.
  • •Correlation between protein and diGly site fold changes.
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11.
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Highlights
  • •Quantitative (phospho)proteome analysis of antibiotic treatment in E. coli.
  • •Largest bacterial phosphorylation catalogue.
  • •Specific phosphorylation motifs changes during resistance development.
  • •Phosphorylation mediated signaling could be a potential target for drug design.
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12.
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Highlights
  • •iTRAQ-based analysis of saliva samples from oral cancer patients.
  • •Proteome profiling of saliva samples from patients with oral premalignant lesions.
  • •Verification of salivary biomarker candidates with MRM-MS and immunoassays.
  • •Identification of salivary proteins as potential biomarkers of oral cancer.
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13.
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Highlights
  • •Chromobodies are stabilized by antigen binding in live cells.
  • •Monitoring changes of endogenous protein levels in living cells with chromobodies.
  • •Broadly applicable system to generate turnover-accelerated chromobodies.
  • •Quantification of time- and dose-dependent compound effects.
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14.
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Highlights
  • •BioID with Golgi fractions identified C10orf76 as proximal to GBF1.
  • •Tagged C10orf76 overlaps with Golgi markers.
  • •C10orf76 binds GBF1 and exchanges rapidly between free and bound forms.
  • •C10orf76 is essential for maintenance of the Golgi and for secretion.
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15.
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Highlights
  • •Zero-length chemical cross-linking of APOA1 peptides in HDL.
  • •Cross-links match antiparallel isomers of APOA dimers in molecular modeling.
  • •Identical MS/MS spectra of native and synthetic cross-linked peptides.
  • •First biochemical evidence of LL5/5 and LL5/4 isomers in human HDL.
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16.
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Highlights
  • •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.
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17.
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Highlights
  • •microRNA-222 attenuates TGEV-induced mitochondrial dysfunction.
  • •microRNA-222 downregulates THBS1 and CD47.
  • •THBS1 is the target of microRNA-222 during TGEV infection.
  • •THBS1 and CD47 increase mitochondrial Ca2+ level and reduced mitochondrial membrane potential (MMP).
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18.
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Highlights
  • •HLA-B*40:02 and ERAP2 are risk factors for ankylosing spondylitis.
  • •The effects of ERAP2 on the B*40:02 peptidome are defined.
  • •ERAP2 has a major influence mainly due to alterations of N-terminal residues.
  • •These effects provide a basis for the association of ERAP2 with disease.
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19.
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Highlights
  • •Proteome profiling of tissue interstitial fluids (TIFs) of oral cancer.
  • •Pathway of aminoacyl tRNA biosynthesis enriched in proteome of TIFs.
  • •Verification of nidogen-1 as a salivary biomarker of oral cancer.
  • •High correlation between elevated tissue level of nidogen-1 and poor survival.
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20.
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Highlights
  • •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.
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