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

1. Download : Download high-res image (129KB)
2. Download : Download full-size image

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.

     

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

1. Download : Download high-res image (68KB)
2. Download : Download full-size image

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.

     

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

1. Download : Download high-res image (240KB)
2. Download : Download full-size image

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.

     

Proteaphagy in Mammalian Cells Can Function Independent of ATG5/ATG7

1. Download : Download high-res image (123KB)
2. Download : Download full-size image

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

1. Download : Download high-res image (101KB)
2. Download : Download full-size image

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.

     

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

1. Download : Download high-res image (229KB)
2. Download : Download full-size image

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.

     

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

1. Download : Download high-res image (208KB)
2. Download : Download full-size image

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

1. Download : Download high-res image (202KB)
2. Download : Download full-size image

Highlights

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

     

Sample Preparation by Easy Extraction and Digestion (SPEED) - A Universal,Rapid, and Detergent-free Protocol for Proteomics Based on Acid Extraction

1. Download : Download high-res image (62KB)
2. Download : Download full-size image

Highlights

• •Universal and detergent-free proteomic sample preparation.
• •Based on three simple mandatory steps (acidification, neutralization, digestion).
• •Enhances proteome coverage especially for challenging samples.
• •Improves quantitative reproducibility compared with ISD-Urea, FASP and SP3.

     

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

1. Download : Download high-res image (146KB)
2. Download : Download full-size image

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

1. Download : Download high-res image (114KB)
2. Download : Download full-size image

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.

     

Characterization of Signaling Pathways Associated with Pancreatic β-cell Adaptive Flexibility in Compensation of Obesity-linked Diabetes in db/db Mice

1. Download : Download high-res image (239KB)
2. Download : Download full-size image

Highlights

• •db/db β-cells restores appropriate insulin stores and normalize secretory function.
• •Numerous changes in the phosphorylation and sialylation states by euglycemic rest.
• •Restoration of numerous dysfunctional biological processes following euglycemic rest.
• •β-cell adaptive flexibility may lead to improvement in endogenous β-cell function.

     

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

1. Download : Download high-res image (158KB)
2. Download : Download full-size image

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

1. Download : Download high-res image (194KB)
2. Download : Download full-size image

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.

     

Ionizing Radiation-induced Proteomic Oxidation in Escherichia coli

1. Download : Download high-res image (161KB)
2. Download : Download full-size image

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.

     

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

1. Download : Download high-res image (225KB)
2. Download : Download full-size image

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.

     

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

1. Download : Download high-res image (146KB)
2. Download : Download full-size image

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.

     

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

1. Download : Download high-res image (213KB)
2. Download : Download full-size image

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.

     

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

1. Download : Download high-res image (245KB)
2. Download : Download full-size image

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.