Depolarization-dependent Induction of Site-specific Changes in Sialylation on N-linked Glycoproteins in Rat Nerve Terminals

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Highlights

• •Comprehensive sialiomics of isolated rat synaptosomes.
• •Site-specific modulation of sialic acids on surface glycoproteins after brief depolarization.
• •Sialylation as dynamic modification important for synaptic depolarization-dependent processes.

     

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.

     

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.

     

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.

     

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.

     

Integration of IgA and IgG Autoantigens Improves Performance of Biomarker Panels for Early Diagnosis of Lung Cancer

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Highlights

• •HuProt array-based identification of autoantigens in serum of early lung cancer.
• •Independent validation of early lung cancer biomarker candidates with ELISA.
• •Bioinformatics-aided identification of a biomarker panel.
• •Independent verification of the panel with ELISA and immunohistochemistry.

     

Proteomics and Metaproteomics Add Functional,Taxonomic and Biomass Dimensions to Modeling the Ecosystem at the Mucosal-luminal Interface

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Highlights

• •The gut mucosal-luminal interface is a spatiotemporal heterogeneous ecosystem.
• •Proteomics and metaproteomics are tools to study the host and microbiome functionality.
• •Insights into functional diversity, biomass, and matter flow can be obtained.
• •Such data can be complementary inputs for building ecology models of the microbiome.

     

Spatially Resolved Activity-based Proteomic Profiles of the Murine Small Intestinal Lipases

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Highlights

• •Activity based serine hydrolase profiles in 11 fractions along the murine small intestine.
• •AADAC and Ces2e activity profiles correlate with chylomicron secretion.
• •Ces2e shows the highest activity based enrichment in the entire small intestine.

     

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.

     

Analytical Guidelines for co-fractionation Mass Spectrometry Obtained through Global Profiling of Gold Standard Saccharomyces cerevisiae Protein Complexes

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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.

     

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.

     

High-speed Analysis of Large Sample Sets – How Can This Key Aspect of the Omics Be Achieved?

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Highlights

• •Future proteomic analyses for longitudinal studies and P4 medicine arguably require ≥1M samples/day.
• •Proteome depth/coverage is commonly the focus whereas analytical speed is typically neglected.
• •A compromise between analytical depth and speed is needed for future large-scale studies.
• •Ultrahigh-speed ‘omic’ analyses require tools that are intrinsically fast such as laser-based MS.

     

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.

     

OpenPepXL: An Open-Source Tool for Sensitive Identification of Cross-Linked Peptides in XL-MS

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Highlights

• •OpenPepXL is a new XL-MS identification tool with a high sensitivity.
• •It is available for all common operating systems and remote computing environments.
• •OpenPepXL is open source and supports open OpenPepXL is available as part of OpenMS data formats like mzML and mzIdentML.
• •at https://www.openms.de/openpepxl.

     

Peptide-based Interaction Proteomics

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Highlights

• •Peptide-based screens provide a scalable approach to study protein-protein interactions.
• •These screens help to characterize the function of structurally disordered regions.
• •The impact of posttranslational modifications can be directly investigated.

     

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.

     

Serum Protein Profiling Reveals a Landscape of Inflammation and Immune Signaling in Early-stage COVID-19 Infection

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Highlights

• •In-depth profiling of the serum proteome in early-stage COVID-19 patients.
• •A landscape of inflammation and immune signaling related to the SARS-CoV-2 infection.
• •CCL2 and CXCL10 medicated cytokine signaling pathways may correlate with neutrophil and lymphocyte respectively.

     

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.

     

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.