Citrullinome of Porphyromonas gingivalis Outer Membrane Vesicles: Confident Identification of Citrullinated Peptides

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Highlights

• •Novel two-dimensional separation system for identification of citrullinated peptides.
• •Dedicated software developed for confident validation of citrullination.
• •P. gingivalis citrullinome: 78 proteins with a total of 161 citrullinated peptides.
• •Confident discrimination of P. gingivalis OMVs from wild-type and PPAD mutants.

     

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.

     

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.

     

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.

     

Metabolic regulation of sexual commitment in Plasmodium falciparum

Factors promoting (orange) and suppressing (blue) the frequency of sexual commitment rate in Plasmodium falciparum.

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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.

     

Functional Characterization and Comparison of Plasmodium falciparum Proteins as Targets of Transmission-blocking Antibodies

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Highlights

• •Characterization of 12 proteins from across the P. falciparum sexual-stages as possible TBV targets.
• •Heterologously expressed recombinant proteins recapitulate native parasite epitopes.
• •Some recombinant proteins exhibit immunoreactivity when tested against sera from individuals from malaria-endemic Burkina Faso and Mali.
• •Purified IgG against the antigen enolase moderately inhibits parasite development in the mosquito midgut.

     

Potential use of microbial engineering in single-cell protein production

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Microbes of interest can be engineered to improve the production of SCPs for human-food and animal-feed applications. These improvements include feedstock conversion, biomass accumulation, protein production, and the production of nutritional and functional compounds.

     

Ionizing Radiation-induced Proteomic Oxidation in Escherichia coli

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Highlights

• •Quantifying ionizing radiation-induced oxidation in E. coli and D. radiodurans.
• •Amelioration of protein damage dependent upon cellular components.
• •GAPDH active site is highly modified and also IR-modified in H. sapiens.

     

Discovery of Species-unique Peptide Biomarkers of Bacterial Pathogens by Tandem Mass Spectrometry-based Proteotyping

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Highlights

• •Discovery of peptide biomarker candidates of respiratory tract pathogens S. pneumoniae, H. influenzae, M. catarrhalis and S. aureus as target pathogens.
• •Peptide biomarker candidates were experimentally verified in clinical samples.
• •Targeted MS using promising peptide biomarker candidates shown as proof-of-concept.

     

Modulation of Natural HLA-B*27:05 Ligandome by Ankylosing Spondylitis-associated Endoplasmic Reticulum Aminopeptidase 2 (ERAP2)

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Highlights

• •HLA-B*27:05 and ERAP2 are risk factors for ankylosing spondylitis.
• •The effects of ERAP2 on the B*27:05 ligandome are defined.
• •P1, P2, P3, P7, and PΩ peptide positions are influenced by ERAP2.
• •These effects provide a basis for the association of ERAP2 with the autoimmune disease.

     

Assessing Protein Sequence Database Suitability Using De Novo Sequencing

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Highlights

• •An automated de novo sequencing program is evaluated with respect to different types of data.
• •The number of unique high scoring de novo sequences that can be assigned to a data set provides a metric of overall data quality.
• •A database suitability metric is presented for situations when the database choice is not obvious, or when the database quality is uncertain.

     

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.

     

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.

     

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.

     

Measuring Site-specific Glycosylation Similarity between Influenza a Virus Variants with Statistical Certainty

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Highlights

• •Changes in N-linked glycosylation in influenza A virus affect antigenicity of the virus.
• •Glycosylation similarity can be quantified, even in heterogeneously glycosylated proteins.
• •Glycosylation is measurably and site-specifically distinct in influenza from related strains.

     

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.

     

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.

     

An Interaction Network of RNA-Binding Proteins Involved in Drosophila Oogenesis

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Highlights

• •Label-free and dimethyl labeling MS analysis of 6 RBPs from Drosophila ovaries.
• •Functionally related RBPs show overlapping proteomes.
• •Selective co-purification of splicing factors and translational regulators.
• •Validation of 26 novel interactions by co-immunoprecipitation.

     

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.