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1.
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Highlights
  • •Automated analysis of protein complexes in proteomic experiments.
  • •Quantitative measurement of the coordinated changes in protein complex components.
  • •Interactive visualizations for exploratory analysis of proteomic results.
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2.
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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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3.
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Highlights
  • •Identification of the substrates profile of the endothelial phosphatase VE-PTP.
  • •A large fraction of VE-PTP substrate candidates (29%) is cell junction related.
  • •Tie-2 and EPHB are substrates which associate as ternary complex with VE-PTP.
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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
  • •Enough CD16a from NK cells can be isolated from a single donor following apheresis.
  • •NK cell CD16a shows variability between different donors.
  • •NK cells preferentially bind IgG1 that lacks core fucosylation.
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6.
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Highlights
  • •A panel of HEK293 isogenic cell lines with knockout of GALNT genes.
  • •Identification of nonredundant O-glycosylation sites regulated by specific GalNAc-T isoforms.
  • •GalNAc-T7 and T10 contribute to follow-up activity in regions of high density O-glycosylation.
  • •GalNAc-T11 specifically controls O-glycosylation of specific linker regions in the low-density lipoprotein receptor related proteins.
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7.
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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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8.
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Highlights
  • •Functional role of a yet uncharacterized receptor kinase QSK1.
  • •Activation model for SIRK1 receptor kinase in a heteromer with QSK1.
  • •Role of QSK1 in substrate recruitment and stabilization of the complex.
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9.
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Highlights
  • •First report on the quantitative proteomic profiling of Drosophila lymph glands.
  • •Comparative proteomic analysis under conditions of perturbed blood cell homeostasis.
  • •Resource for identifying new regulators of insect and vertebrate hematopoiesis.
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10.
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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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11.
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Highlights
  • •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
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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
  • •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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14.
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Highlights
  • •Identification of previously undetected chloroplast envelope proteins.
  • •Up to date manual annotation of genuine (or shared) envelope components.
  • •New hypotheses for localizations, functions, interactions among cell compartments.
  • •A new resource of significant value to the broader plant science community.
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15.
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Highlights
  • •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.
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16.
17.
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Highlights
  • •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
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18.
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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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19.
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Highlights
  • •MHC-II-bound peptide repertoires from DO-sufficient and DO-deficient cells.
  • •Fewer unique peptides and core epitopes were presented in the absence of DO.
  • •Immunopeptidome differences appeared to result from reduced DM editing.
  • •DO-dependent self-epitopes elicited CD4 T cell responses in mice.
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20.
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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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