Mass Spectrometry Based Immunopeptidomics Leads to Robust Predictions of Phosphorylated HLA Class I Ligands

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Highlights

• •Curation of 2066 phosphorylated HLA class I peptides from immunopeptidomics data.
• •Determination of 22 HLA class I binding motifs for phosphorylated peptides.
• •Observation of a higher frequency of phosphorylated ligands binding HLA-C molecules.
• •Development of a predictor of phosphorylated peptide interactions with HLA class I.

     

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.

     

An Improved Boosting to Amplify Signal with Isobaric Labeling (iBASIL) Strategy for Precise Quantitative Single-cell Proteomics

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Highlights

• •Higher AGC significantly improves quantitation quality in single-cell analysis.
• •The boosting-to-sample ratio should be carefully evaluated and optimized.
• •iBASIL allows for precise quantitation of 1,500 proteins from 104 AML single cells.
• •iBASIL recapitulates major biological differences in different AML single cells.

     

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.

     

Characterizing Patients with Recurrent Urinary Tract Infections in Vesicoureteral Reflux: A Pilot Study of the Urinary Proteome

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Highlights

• •Urinary proteomes of patients with recurrent UTI, renal scarring, and VUR.
• •80 proteins differentially expressed, compared to healthy controls.
• •62 proteins may be indicative of susceptibility for UTI.
• •Altered acute phase response, extracellular matrix and carbohydrate metabolism.

     

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.

     

DEqMS: A Method for Accurate Variance Estimation in Differential Protein Expression Analysis

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Highlights

• •DEqMS is a method for statistical analysis of quantitative MS-data.
• •Variance estimates based on the actual MS-data structure.
• •Improved statistical power and accuracy in protein differential analysis.
• •DEqMS is available as a user-friendly R package in Bioconductor.

     

Acquiring and Analyzing Data Independent Acquisition Proteomics Experiments without Spectrum Libraries

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Highlights

• •Rapid DIA-only library building with gas-phase fractionation.
• •Recommended DIA acquisition strategies with staggered windows and forbidden zones.
• •Optimized DIA instrument settings for several Thermo Orbitrap instruments.
• •Data analysis tutorial using open source DIA software.

     

An in-depth Comparison of the Pediatric and Adult Urinary N-glycomes

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Highlights

• •N-glycan patterns are distinct in pediatric and adult urine.
• •Sex differences of N-glycans are much larger in adults.
• •Pediatric urine has almost no sex differences in N-glycan levels.
• •In adults, the majority of N-glycans were more abundant in males.

     

Proteomic Analysis Reveals that Topoisomerase 2A is Associated with Defective Sperm Head Morphology

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Highlights

• •Human spermatozoa possess cells of poor morphology that lack nuclear integrity.
• •These cells can be isolated by density separation.
• •Mass spectrometry reveals their nuclei contain excess protein.
• •TOP2A is a promising marker of this poor nuclear development.

     

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.

     

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.

     

Next-generation Interactomics: Considerations for the Use of Co-elution to Measure Protein Interaction Networks

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Highlights

• •Co-elution stands out as a global interactome mapping method.
• •Benefits include all-to-all protein analysis and measurement of interactome perturbations.
• •Different separation, quantification and bioinformatic strategies are available.
• •Design considerations depend largely on system under study.

     

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.

     

Phenotypic Adaption of Pseudomonas aeruginosa by Hacking Siderophores Produced by Other Microorganisms

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Highlights

• •P. aeruginosa grown with exosiderophores and analyzed by proteomic and RT-qPCR.
• •Catechol-type exosiderophores strongly induce the expression of their transporters.
• •Repression of the endogenous iron uptake pathways.
• •Complex phenotypic plasticity in the expression of the various iron-uptake pathways.

     

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.

     

Chemical Genetics of AGC-kinases Reveals Shared Targets of Ypk1, Protein Kinase A and Sch9

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Highlights

• •Acute inhibition of growth-regulatory AGC-kinases Sch9, PKA and Ypk1.
• •Phospho-proteomic profiling of 6373 phsopho-sites.
• •Ypk1 regulates phospho-sites in RRxS/T-context and functionally overlaps with PKA.
• •Ypk1 and PKA activate trehalase activity of Nth1.

     

Proteomic Analysis Reveals a Role for RSK in p120-catenin Phosphorylation and Melanoma Cell-Cell Adhesion

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Highlights

• •BioID reveals the proximity partners of RSK family members.
• •All RSK isoforms associate with and phosphorylate p120ctn on Ser320.
• •RSK negatively regulates adherens junctions and reduces cell-cell adhesion.
• •p120ctn phosphorylation plays a role in the reorganization of proximity partners.

     

Genetic Profile and Functional Proteomics of Anal Squamous Cell Carcinoma: Proposal for a Molecular Classification

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Highlights

• •Two molecular groups in anal squamous carcinoma according proteomic profile.
• •Differences in possible targeted processes such as metabolism or immune response.
• •Different percentage of tumor lymphocyte infiltration.
• •Difference in the frequency of ATM variants, related to PPAR inhibitors.

     

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.