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.

     

Immunopeptidomic Analysis Reveals That Deamidated HLA-bound Peptides Arise Predominantly from Deglycosylated Precursors

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Highlights

• •A predominance of HLA-I bound deamidated peptides are generated through ERAD pathway.
• •Deamidation of peptides with N-glycosylation motifs not in peptidome of HLA-II or proteolysis.
• •Many precursors of ERAD generated deamidated peptides are glycoproteins.

     

Benefits of Collisional Cross Section Assisted Precursor Selection (caps-PASEF) for Cross-linking Mass Spectrometry

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Highlights

• •Cross-linked peptides are physically separated from mono-linked peptides in the gas-phase by TIMS ion mobility.
• •Development of a novel data acquisition routine that a-priori distinguishes cross-linked from mono-linked peptides called caps-PASEF.
• •First application of PhoX-driven cross-linking mass spectrometry on the timsTOF Pro.
• •Application of cross-linking mass spectrometry to medium to high complexity samples.

     

Multi-omic Characterization of the Mode of Action of a Potent New Antimalarial Compound,JPC-3210, Against Plasmodium falciparum

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Highlights

• •Multi-omics analysis on mode of action of novel antimalarial, JPC-3210
• •JPC-3210 has rapid parasite killing kinetics.
• •Metabolomics and peptidomics demonstrated JPC-3210 inhibits hemoglobin digestion.
• •Proteomics demonstrated JPC-3210 enriches for translation regulation proteins.

     

A Quantitative Tri-fluorescent Yeast Two-hybrid System: From Flow Cytometry to In cellula Affinities

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Highlights

• •Simultaneous quantification of Bait, Prey and Reporter at the single cell level.
• •Two hours of reaction are enough instead of 24–48 h for conventional assays.
• •Potential expression problems of the Bait and Prey can be easily detected.
• •True positive PPIs feature a distinct pattern of Reporter level versus Bait/Prey level.
• •PPIs with unknown affinities can be ranked using an affinity ladder.

     

Novel Proteome Extraction Method Illustrates a Conserved Immunological Signature of MSI-H Colorectal Tumors

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Highlights

• •TOP: robust, bio-friendly FFPE proteome extraction method with less fixation bias.
• •Proteome of MSI-H colorectal cancer identifies immunobiology key elements.
• •MSI-H tumor displays an “INFg-STAT1 centric signature”.
• •Long-term IFNg induction In-vitro mimicks MSI-H signature.

     

Tandem Mass Tag Approach Utilizing Pervanadate BOOST Channels Delivers Deeper Quantitative Characterization of the Tyrosine Phosphoproteome

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Highlights

• •Detection of low-abundance phosphotyrosine-containing peptides is challenging.
• •Multiplexed TMT allows inclusion of modification(pTyr)-saturated boost channels.
• •Boost channels facilitate selection of pTyr precursor ions for fragmentation.
• •Quantitation depth is increased while maintaining accuracy and precision.

     

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.

     

MaXLinker: Proteome-wide Cross-link Identifications with High Specificity and Sensitivity

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Highlights

• •New quality assessment metrics to evaluate proteome-wide cross-linking mass spectrometry (XL-MS) data sets.
• •New “MS3-centric” cross-link search engine named MaXLinker with high sensitivity and specificity.
• •More than 9300 cross-links from our human proteome-wide XL-MS study.
• •Orthogonal experimental validation of novel interactions identified in our study.

     

Data,Reagents, Assays and Merits of Proteomics for SARS-CoV-2 Research and Testing

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Highlights

• •In-depth proteomes of 4 SARS-CoV-2 cell line models (Vero E6, Calu-3, Caco-2, A549).
• •Proteomic evidence for thousands of Chlorocebus sabaeus proteins.
• •Proteomic response of Vero E6 cells to SARS-CoV-2 infection.
• •Synthetic peptides, spectral libraries, and targeted assays for SARS-CoV-2 proteins.

     

Guidance Document: Validation of a High-Performance Liquid Chromatography-Tandem Mass Spectrometry Immunopeptidomics Assay for the Identification of HLA Class I Ligands Suitable for Pharmaceutical Therapies

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Highlights

• •Validation of an omic method for antigen identification using LC-MS/MS.
• •Validation of accuracy, precision, specificity, limit of detection and robustness.
• •Validation according to the current FDA and EMA guidelines.

     

Peptidomic Analysis of Urine from Youths with Early Type 1 Diabetes Reveals Novel Bioactivity of Uromodulin Peptides In Vitro

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Highlights

• •Urinary peptide profiling of youths with type 1 diabetes before clinical injury.
• •Internal validation of uromodulin peptides by parallel reaction monitoring.
• •Discovery of novel bioactivity of uromodulin peptides in vitro.
• •In silico prediction of proteases involved in uromodulin processing.

     

Identification of a Multiplex Biomarker Panel for Hypertrophic Cardiomyopathy Using Quantitative Proteomics and Machine Learning

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Highlights

• •Quantitative proteomics and machine learning to study plasma biomarkers in HCM.
• •Six peptides are increased in plasma of LVH+ HCM compared to controls.
• •Peptide biomarkers correlate with imaging markers of phenotype severity.
• •Peptide biomarkers correlate with the estimated sudden cardiac death risk.

     

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.

     

Selection of Features with Consistent Profiles Improves Relative Protein Quantification in Mass Spectrometry Experiments

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Highlights

• •Automated statistical approach for detecting uninformative features and outliers.
• •Improved performance on relative protein quantification.
• •An option in the open-source R-based software MSstats.

     

A Novel Mechanism for NF-κB-activation via IκB-aggregation: Implications for Hepatic Mallory-Denk-Body Induced Inflammation

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Highlights

• •Liver Mallory-Denk-Body inducers elicited an IκBα-loss and NF-κB-activation.
• •IκBα-loss was due to its sequestration into insoluble cytoplasmic aggregates.
• •Four proteomic approaches identified 10 IκBα-interacting/aggregating proteins.
• •Nup153/RanBP2-aggregation prevented IκBα nuclear entry for ending NF-κB-activation.

     

The Proteome of the Dentate Terminal Zone of the Perforant Path Indicates Presynaptic Impairment in Alzheimer Disease

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Highlights

• •Laser microdissection of highly vulnerable hippocampal region.
• •Proteomic analysis of postmortem human brain tissue of AD and control cases.
• •Decreased levels of presynaptic proteins, but not postsynaptic proteins, in AD.
• •Immunohistochemistry verifies decreased levels of selected presynaptic proteins.

     

Immediate Adaptation Analysis Implicates BCL6 as an EGFR-TKI Combination Therapy Target in NSCLC

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Highlights

• •EGFR-TKI molecular response profiling covering 10138 proteins and 13486 mRNAs.
• •EGFR-TKI combination therapy screen using a library of 528 compounds.
• •Several new candidate EGFR-TKI escape mechanisms and combination therapy targets.
• •Combined targeting of the oncogene BCL6 and EGFR results in synergy in NSCLC cells.