Cross-linking Proteomics Indicates Effects of Simvastatin on the TLR2 Interactome and Reveals ACTR1A as a Novel Regulator of the TLR2 Signal Cascade

1. Download : Download high-res image (107KB)
2. Download : Download full-size image

Highlights

• •An innovative co-IP crosslinking proteomics study was designed for the TLR2 interactome.
• •Proteomic profiling revealed combinatorial effects of simvastatin and Pam3CSK4 on the TLR2 interactome.
• •ACTR1A and MARCKSL1 proteins were identified as potential interactors of TLR2 during the immune response.
• •ACTR1A has important modulatory actions on the TLR2 pro-inflammatory signaling cascade.

     

Macrophage Phosphoproteome Analysis Reveals MINCLE-dependent and -independent Mycobacterial Cord Factor Signaling

1. Download : Download high-res image (102KB)
2. Download : Download full-size image

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.

     

Celastrol Protects From Cholestatic Liver Injury Through Modulation of SIRT1-FXR Signaling

1. Download : Download high-res image (152KB)
2. Download : Download full-size image

Highlights

• •1. Celastrol alleviated cholestatic liver injury.
• •2. Celastrol inhibited the decrease of SIRT1 induced by deoxycholic acid.
• •3. SIRT1-FXR signaling pathway mediated the effect of celastrol.

     

A New Tool to Reveal Bacterial Signaling Mechanisms in Antibiotic Treatment and Resistance

1. Download : Download high-res image (86KB)
2. Download : Download full-size image

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.

     

ComplexBrowser: A Tool for Identification and Quantification of Protein Complexes in Large-scale Proteomics Datasets

1. Download : Download high-res image (53KB)
2. Download : Download full-size image

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.

     

DECA,A Comprehensive,Automatic Post-processing Program for HDX-MS Data*

1. Download : Download high-res image (128KB)
2. Download : Download full-size image

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.

     

Quantitative Proteomics Links the Intermediate Filament Nestin to Resistance to Targeted BRAF Inhibition in Melanoma Cells

1. Download : Download high-res image (124KB)
2. Download : Download full-size image

Highlights

• •Quantitative phosphoproteome of BRAF drug-resistance in melanoma cells.
• •Cytoskeletal proteins are downregulated in resistant vs. sensitive cells.
• •Nestin is associated with an invasive phenotype and resistance to MEK and BRAF inhibitors.
• •Nestin depletion affects PI3K/AKT and integrin signaling similar to resistant cells.

     

Intact Transition Epitope Mapping – Targeted High-Energy Rupture of Extracted Epitopes (ITEM-THREE),

1. Download : Download high-res image (162KB)
2. Download : Download full-size image

Highlights

• •Multiplex epitope mapping/antigenic determinant identification in the gas phase.
• •Intact transition and controlled dissociation of immune complexes by MS.
• •Simultaneous identification and amino acid sequence determination of epitopes.
• •Simplified in-solution sample handling because of ion manipulation and filtering by MS.

     

Metabolic,Anti-apoptotic and Immune Evasion Strategies of Primary Human Myeloma Cells Indicate Adaptations to Hypoxia*

1. Download : Download high-res image (116KB)
2. Download : Download full-size image

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

     

Hepatic Mitochondrial Defects in a Nonalcoholic Fatty Liver Disease Mouse Model Are Associated with Increased Degradation of Oxidative Phosphorylation Subunits

1. Download : Download high-res image (100KB)
2. Download : Download full-size image

Highlights

• •Stability of oxidative phosphorylation subunits are reduced in a diet-induced mouse model of NAFLD.
• •These changes are associated with impaired activities of electron transport chain complexes and ATP synthesis.
• •Increased mitophagy contributed to enhanced degradation of mitochondrial proteins.

     

Why Glycosylation Matters in Building a Better Flu Vaccine

1. Download : Download high-res image (59KB)
2. Download : Download full-size image

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.

     

Sample Preparation Scale-Up for Deep N-glycomic Analysis of Human Serum by Capillary Electrophoresis and CE-ESI-MS*

1. Download : Download high-res image (84KB)
2. Download : Download full-size image

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.

     

Deep Protein Methylation Profiling by Combined Chemical and Immunoaffinity Approaches Reveals Novel PRMT1 Targets

1. Download : Download high-res image (87KB)
2. Download : Download full-size image

Highlights

• •Enrichment of methyl peptides using two orthogonal techniques.
• •Knockdown of PRMT1 leads to substantial changes in protein arginine “methylome”.
• •Discrimination of ADMA and SDMA using characteristic neutral losses.
• •Identification of PRMT1 targets and substrate scavenged by other PRMTs in the absence of PRMT1 activity.

     

A Curated Resource for Phosphosite-specific Signature Analysis

1. Download : Download high-res image (123KB)
2. Download : Download full-size image

Highlights

• •Database of PTM site-specific phosphorylation signatures of kinases, perturbations and signaling pathways (PTMsigDB).
• •PTM signature enrichment analysis (PTM-SEA) outperformed gene-centric analysis in detection of EGF induced phospho signaling events.
• •PI3K perturbation signatures were readily detected in PI3Ka inhibited human breast cancer cells.
• •PTMsigDB and PTM-SEA can be freely accessed at https://github.com/broadinstitute/ssGSEA2.0.

     

MaxQuant.Live Enables Global Targeting of More Than 25,000 Peptides

1. Download : Download high-res image (92KB)
2. Download : Download full-size image

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.

     

Common Metabolic Pathways Implicated in Resistance to Chemotherapy Point to a Key Mitochondrial Role in Breast Cancer,

1. Download : Download high-res image (130KB)
2. Download : Download full-size image

Highlights

• •OMICS distinguish cancer cells from resistant or cancer stem cells.
• •Bactericidal antibiotics and mitochondria.
• •Linezolid and anticancer therapy.

     

Probing H2O2-mediated Structural Dynamics of the Human 26S Proteasome Using Quantitative Cross-linking Mass Spectrometry (QXL-MS)

1. Download : Download high-res image (128KB)
2. Download : Download full-size image

Highlights

• •Two-step cross-linking coupled with affinity purification to facilitate structural analysis of protein complexes.
• •Integrated QXL-MS workflow for studying condition-dependent structural changes of protein complexes.
• •Mechanistic insights on in vivo H₂O₂-induced conformational dynamics of proteasome complexes.

     

Data-independent Acquisition Improves Quantitative Cross-linking Mass Spectrometry

1. Download : Download high-res image (126KB)
2. Download : Download full-size image

Highlights

• •Quantitative cross-linking mass spectrometry (QCLMS) was automated by Spectronaut.
• •Data-independent acquisition (DIA) was adapted to QCLMS.
• •Accuracy and precision of quantitation improves with DIA over DDA.
• •QCLMS is now ready for use in complex samples.

     

Global Proteome and Ubiquitinome Changes in the Soluble and Insoluble Fractions of Q175 Huntington Mice Brains

1. Download : Download high-res image (74KB)
2. Download : Download full-size image

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.