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.

     

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.

     

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.

     

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.

     

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.

     

Proteomic Analysis of Salmonella-modified Membranes Reveals Adaptations to Macrophage Hosts

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Highlights

• •Affinity-based proteomics of infected macrophage cells.
• •Salmonella-modified membranes exhibit host-specific composition.
• •Proteome differences explain some host-dependent pathophysiological differences.

     

Arginine in C9ORF72 Dipolypeptides Mediates Promiscuous Proteome Binding and Multiple Modes of Toxicity

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Highlights

• •Quantitative proteome interactions with 5 different C9ORF72 dipolypeptides (DPRs).
• •The arg-rich DPRs promiscuously bound to the proteome compared with the other DPRs.
• •Long repeat lengths of arg-rich DPRs, but not short lengths, stalled ribosomes.
• •The arg-rich DPRs also reduced arginine methylation and actin cytoskeleton assembly.

     

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.

     

Proteomics of Campylobacter jejuni Growth in Deoxycholate Reveals Cj0025c as a Cystine Transport Protein Required for Wild-type Human Infection Phenotypes

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Highlights

• •Growth in the bile salt deoxycholate (DOC) induces virulence proteins in C. jejuni.
• •A putative symporter Cj0025c is associated with DOC growth and cystine transport.
• •Deletion of cj0025c results in loss of cystine transport and a sulfur starved proteotype.
• •Cj0025c is required for wild-type virulence phenotypes including human cell invasion.

     

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.

     

Upregulation of CD73 Confers Acquired Radioresistance and is Required for Maintaining Irradiation-selected Pancreatic Cancer Cells in a Mesenchymal State

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Highlights

• •CD73 is one of the most upregulated proteins in the radioresistant cells.
• •CD73 upregulation confers radioresistance and irradiation-induced apoptosis.
• •CD73 confers radioresistance potentially through inactivating protein BAD.
• •Elevated CD73 is required for maintaining the resistant cells in a mesenchymal state.

     

Stoichiometry of Nucleotide Binding to Proteasome AAA+ ATPase Hexamer Established by Native Mass Spectrometry

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Highlights

• •All six binding sites in PAN^WT are occupied by ADP- or ATP-type nucleotides.
• •PAN^KA Walker A mutant substoichiometrically binds ATP- but not ADP-type nucleotides.
• •PAN hexamer dissociation of the solution origin characteristics was observed in MS.
• •We posit that the PAN hexamer dissociation proceeds within the ESI droplets.

     

Improving Identification of In-organello Protein-Protein Interactions Using an Affinity-enrichable,Isotopically Coded,and Mass Spectrometry-cleavable Chemical Crosslinker

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Highlights

• •Used affinity-enrichable, isotopically coded, and MS-cleavable crosslinker.
• •Targeted acquisition strategy based on isotopic-coding described and evaluated.
• •Novel data analysis pipeline developed provides improved crosslink identification.
• •Large dataset reveals hundreds of mitochondrial protein-protein interactions.

     

NIST Interlaboratory Study on Glycosylation Analysis of Monoclonal Antibodies: Comparison of Results from Diverse Analytical Methods

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Highlights

• •A broad-based interlaboratory study of the glycosylation of a reference antibody: NISTmAb.
• •103 reports were received from 76 diverse laboratories worldwide.
• •Analysis involved two samples, the NISTmAb and an enzymatically modified sample, enabling within-lab separation of random and systematic errors using the “Youden two-sample” method.
• •Consensus values were derived and similar performance across all experimental methods was noted.

     

ProAlanase is an Effective Alternative to Trypsin for Proteomics Applications and Disulfide Bond Mapping

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Highlights

• •ProAlanase is a powerful protease for efficient low pH disulfide bond mapping.
• •High suitability for analysis of histone family members and their PTMs.
• •Accurate phosphorylation profiling in proline-rich proteins.
• •Sequence coverage increase and full de novo sequencing in combination with trypsin.

     

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.

     

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.

     

The Aspergillus fumigatus Secretome Alters the Proteome of Pseudomonas aeruginosa to Stimulate Bacterial Growth: Implications for Co-infection

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Highlights

• •Pseudomonas aeruginosa growth increases in Aspergillus fumigatus culture filtrates.
• •A. fumigatus culture filtrates are characterized by a range of peptidases and proteases.
• •LFQ proteomics characterizes the response of P. aeruginosa to A. fumigatus culture filtrates.
• •A. fumigatus creates an environment for P. aeruginosa to proliferate.

     

N-glycosylation Site Analysis Reveals Sex-related Differences in Protein N-glycosylation in the Rice Brown Planthopper (Nilaparvata lugens)

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Highlights

• •N-glycosylation site analysis of the hemipteran pest insect Nilaparvata lugens.
• •Differential N-glycosylation of proteins is observed between male and female adults.
• •Sex-specific glycoproteins are involved in insect reproduction.