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 Capture of a Disabled Proteasome Identifies Erg25 as a Substrate for Endoplasmic Reticulum Associated Degradation

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Highlights

• •Epitope-tagging of a proteasome subunit allows for facile immuno-isolation.
• •An engineered yeast strain permits capture of proteasome-associated substrates.
• •MS/MS identified all 33 resident proteasome subunits in the 20S and 19S particles.
• •Analysis of associated proteins and characterization of newly identified ERAD substrate.

     

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.

     

The Insulin Receptor Adaptor IRS2 is an APC/C Substrate That Promotes Cell Cycle Protein Expression and a Robust Spindle Assembly Checkpoint

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Highlights

• •Chemical proteomics in G₁ cells treated with small molecule APC/C inhibitors reveals novel putative APC/C substrates.
• •The insulin receptor adaptor IRS2 is an APC/C substrate that is targeted for degradation by APC/C^Cdh1.
• •Quantitative proteomics in IRS2 knockout cells reveals a deficiency in cell cycle related protein expression.
• •IRS2 promotes a robust spindle assembly checkpoint (SAC) during M-phase.

     

The Mouse Heart Mitochondria N Terminome Provides Insights into ClpXP-Mediated Proteolysis

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Highlights

• •Mitochondrial heart N terminome shows aminopeptidase processing after MTS cleavage.
• •CLPP-deficiency alters protein processing patterns in mouse heart mitochondria.
• •Candidate substrates identified by N termini accumulation and interaction with inactive ClpXP.
• •UQCRC1, HSPA9 and OAT validated biochemically as high confidence ClpXP substrates.

     

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.

     

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.

     

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.

     

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.

     

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.

     

A Comprehensive Gender-related Secretome of Plasmodium berghei Sexual Stages

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Highlights

• •Quantitative analysis of Plasmodium sexual stage egress secretome.
• •Activated gametocytes release gender-related proteins.
• •Gametocyte egress process involves different types of vesicles.

     

Immune Signature Against Plasmodium falciparum Antigens Predicts Clinical Immunity in Distinct Malaria Endemic Communities

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Highlights

• •A predictive modelling framework has been established to analyze IgG antibody responses against a large panel of P. falciparum-specific antigens to identify a specific antigen signature of NAI.
• •An individual's immune status can be accurately predicted by measuring IgG responses against a small set of 15 defined parasite antigens.
• •Proteins identified in the 15-antigen signature represent potential candidates for next-generation malaria vaccines or biomarkers for monitoring the impact of malaria interventions.
• •The developed predictive framework can be adapted for developing novel surveillance and intervention tools for other infectious diseases.

     

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.

     

Serum Protein Profiling Reveals a Landscape of Inflammation and Immune Signaling in Early-stage COVID-19 Infection

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Highlights

• •In-depth profiling of the serum proteome in early-stage COVID-19 patients.
• •A landscape of inflammation and immune signaling related to the SARS-CoV-2 infection.
• •CCL2 and CXCL10 medicated cytokine signaling pathways may correlate with neutrophil and lymphocyte respectively.

     

Proteaphagy in Mammalian Cells Can Function Independent of ATG5/ATG7

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Highlights

• •Quantitative proteomics of isolated lysosomes, autophagosomes and proteasomes.
• •Pharmacological inhibition of proteasomes leads to their accumulation within lysosomes.
• •Inhibition of classical autophagy pathways cannot completely block this process.
• •Known autophagy adaptor proteins are not involved.

     

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.

     

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.

     

Characterization of Prenylated C-terminal Peptides Using a Thiopropyl-based Capture Technique and LC-MS/MS

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Highlights

• •Brain membrane protein extraction.
• •Protein prenylation.
• •Prenyl peptide capture and characterization by LC-MS/MS.
• •HCD and EThcD peptide fragmentation.