Temporal Quantitative Proteomics of mGluR-induced Protein Translation and Phosphorylation in Neurons

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Highlights

• •Integrated phosphoproteomics and analyses of newly synthesized proteins in neurons.
• •Resource of temporal mGluR-induced signaling pathways upon DHPG stimulation.
• •Validation of PKC, MAPK1, CAMKIIa, and CDK2 in mGluR-activation and signaling.
• •Validation of Intersectin-1 in DHPG-induced AMPAR internalization.

     

Developments and Applications of Functional Protein Microarrays

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Highlights

• •Summarize the development of functional protein microarray.
• •Application of functional proteome microarray in basic research.
• •Application of functional proteome microarray in translational research.
• •Fabrication of functional membrane protein array using virion display method.

     

Profiling Cell Signaling Networks at Single-cell Resolution

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Highlights

• •Signaling networks can be highly heterogeneous across cells in a tissue.
• •Various technologies allow analyzing signaling networks at single-cell resolution.
• •The advantages and limitations of each single-cell approach are summarized.
• •Confounding factors in single-cell signaling network analysis are discussed.

     

Integration of IgA and IgG Autoantigens Improves Performance of Biomarker Panels for Early Diagnosis of Lung Cancer

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Highlights

• •HuProt array-based identification of autoantigens in serum of early lung cancer.
• •Independent validation of early lung cancer biomarker candidates with ELISA.
• •Bioinformatics-aided identification of a biomarker panel.
• •Independent verification of the panel with ELISA and immunohistochemistry.

     

Glutathionylation Decreases Methyltransferase Activity of PRMT5 and Inhibits Cell Proliferation

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Highlights

• •PRMT5 glutathionylation is increased in aged mice or under oxidative stress.
• •Deglutathionylation of PRMT5 is catalyzed by glutaredoxin-1.
• •PRMT5 glutathionylation decreases its methyltransferase activity.
• •PRMT5 glutathionylation results in G2/M arrest and inhibits cell proliferation.

     

Profiling the Surfaceome Identifies Therapeutic Targets for Cells with Hyperactive mTORC1 Signaling

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Highlights

• •Quantitative proteomes of the cellular surface changes induced by mTORC1 signaling.
• •Hit validation in human cancer cell lines and biopsies.
• •Functional studies showing new drug targets to which cancer cells with hyperactive mTORC1 may be addicted.
• •A new paradigm for drug development, namely targeting cell surface proteins regulated by mTORC1.

     

Global Proteome and Phosphoproteome Characterization of Sepsis-induced Kidney Injury

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Highlights

• •Cecal Ligation Puncture (CLP) mouse model to study sepsis-induced kidney disease.
• •Quantitative global proteome and phosphoproteome profiling of mouse kidneys.
• •Highly significant candidate markers for onset and progression of AKI to CKD.
• •Mechanistic insights into sepsis-associated kidney injuries.

     

FYN and ABL Regulate the Interaction Networks of the DCBLD Receptor Family

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Highlights

• •FYN and ABL differentially regulate DCBLD Ser/Thr/Tyr phosphorylation.
• •DCBLD1 and DCBLD2 interactomes are modulated by FYN and ABL.
• •ABL drives a direct DCBLD2/14-3-3 interaction.

     

Asparagine Hydroxylation is a Reversible Post-translational Modification

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Highlights

• •Quantitative mass spectrometric method to monitor PTM stability.
• •Pulse labeling reveals dehydroxylation of several asparagine hydroxylation sites.
• •Reversal of TNKS2, TRPV3 and HIF1a asparagine hydroxylation sites.
• •Protein dehydroxylation is an additional level of control for cellular signaling networks.

     

The DNA Sensor cGAS is Decorated by Acetylation and Phosphorylation Modifications in the Context of Immune Signaling

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Highlights

• •cGAS acetylations and phosphorylations under basal and immune-stimulated states.
• •K384 and K414 acetylations and S305 phosphorylation inhibit cGAS-mediated apoptosis.
• •Acetylation at K198 stimulates cGAS-dependent interferon signaling.
• •K198 acetylation is decreased upon herpesvirus infection.

     

Concentration Determination of >200 Proteins in Dried Blood Spots for Biomarker Discovery and Validation

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Highlights

• •Repeatable quantification of 200 proteins in dried blood spots.
• •Determined lower limit of quantification, repeatability, parallelism and stability.
• •Protein stability in DBS stored at ambient temperatures for up to 2 months.
• •Concentration ranges for 200 proteins in 20 healthy individuals.

     

A Cross-linking Mass Spectrometry Approach Defines Protein Interactions in Yeast Mitochondria

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Highlights

• •XL-MS reveals new PPIs in yeast mitochondria under glycerol and glucose condition.
• •Significant but limited results from quantitative XL-MS experiments.
• •Ndi1 participates in a CIII₂CIV₂ respiratory supercomplex.
• •Min8 promotes assembly of Cox12 into an intermediate complex IV.

     

Peptide-based Interaction Proteomics

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Highlights

• •Peptide-based screens provide a scalable approach to study protein-protein interactions.
• •These screens help to characterize the function of structurally disordered regions.
• •The impact of posttranslational modifications can be directly investigated.

     

Identification of Tumor Antigens in the HLA Peptidome of Patient-derived Xenograft Tumors in Mouse

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Highlights

• •Sufficient tumor tissues are often unavailable large HLA peptidome discovery.
• •Using patient derived xenograft (PDX) tumors can overcome this limitation.
• •The large PDX HLA peptidomes expand significantly those of the original biopsies.
• •The HLA peptidomes of the PDX tumors included many tumor antigens.

     

Proteome-wide Analysis Reveals Substrates of E3 Ligase RNF146 Targeted for Degradation

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Highlights

• •Proteome analyses reveal RNF146 and TNKS1/2 substrates targeted for degradation.
• •RNF146 KO and TNKS1/2 DKO cells display significantly different proteomes.
• •RNF146 has both TNKS-dependent and -independent substrates.

     

PolySTest: Robust Statistical Testing of Proteomics Data with Missing Values Improves Detection of Biologically Relevant Features

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Highlights

• •Novel statistical test combining missingness and quantitative profiles.
• •Unification of different statistical tests into a PolySTest FDR provides higher robustness and confidence.
• •PolySTest provides higher coverage of relevant biological pathways.
• •User-friendly interactive web service for statistical analysis and visualization.

     

Phosphoproteomic Approaches to Discover Novel Substrates of Mycobacterial Ser/Thr Protein Kinases

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Highlights

• •Mapping kinase-substrate relationships is vital in discovering new tuberculosis drug targets.
• •LC-MS/MS-based phosphoproteomics expand mycobacterial STPK substrate catalogues.
• •We review and integrate MS-generated datasets on novel candidate substrates.
• •Validation studies are necessary to confirm true physiological substrates of STPKs.

     

Analytical Guidelines for co-fractionation Mass Spectrometry Obtained through Global Profiling of Gold Standard Saccharomyces cerevisiae Protein Complexes

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Highlights

• •Guidelines for studying protein complexes via co-fractionation mass spectrometry.
• •A novel procedure for profiling gold standard protein complexes in CF-MS data.
• •Recommendations for efficient CF-MS fractionation collection.
• •Scoring metric recommendations for precise and sensitive CF-MS data analysis.