Characterization of Endogenous Human FcγRIII by Mass Spectrometry Reveals Site,Allele and Sequence Specific Glycosylation*

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Highlights

• •Glycosylation of endogenous FcγRIII from neutrophils and matched plasma from more than 40 donors characterized at two sites involved in IgG binding.
• •Glycosylation of soluble FcγRIII glycosylation at N45 can be used to assign FcγRIIIb alleles.
• •FcγRIIIb allele specific differences in glycosylation at N162 may influence differential activity observed for primary cells.

     

Quantitative Proteomics of the 2016 WHO Neisseria gonorrhoeae Reference Strains Surveys Vaccine Candidates and Antimicrobial Resistance Determinants

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Highlights

• •Quantitative proteomes of the 2016 WHO Neisseria gonorrhoeae reference strains.
• •Novel gonorrhea vaccine candidates and potential global proteomic AMR markers.
• •First large-scale proteomic profiling of gonorrhea vaccine candidates and AMR.
• •A reference proteomics databank for gonococcal vaccine and AMR research endeavors.

     

Glycoproteogenomics: A Frequent Gene Polymorphism Affects the Glycosylation Pattern of the Human Serum Fetuin/α-2-HS-Glycoprotein

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Highlights

• •Frequent genetic polymorphism affects the glycosylation pattern of fetuin.
• •Personalized in-depth proteoform profiling of fetuin purified from 20 donors.
• •Classification of serum donors into three different genotypes.
• •Septic patients show increased level of fucosylation at N-glycolation site N176.

     

Effects of Size and Geographical Origin on Atlantic salmon,Salmo salar,Mucin O-Glycan Repertoire

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Highlights

• •Atlantic salmon O-glycome expanded to 169 structures in three epithelia.
• •Low interindividual variation amongst all populations and geographical regions.
• •Small variations in glycosylation between geographical locations and fish size.
• •Prominent fucosylation in gastrointestinal mucins from Tasmanian fish.

     

Multi-isotype Glycoproteomic Characterization of Serum Antibody Heavy Chains Reveals Isotype- and Subclass-Specific N-Glycosylation Profiles

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Highlights

• •nLC-MS/MS method to analyze immunoglobulin (Ig) N-glycopeptides from human serum.
• •Multi-isotype, site-specific characterization of immunoglobulin N-glycosylation.
• •IgA2 sequence and glycosylation-site variant analyses.
• •Platform to define disease-specific N-glycan signatures for different Ig isotypes.

     

High-density Peptide Arrays Help to Identify Linear Immunogenic B-cell Epitopes in Individuals Naturally Exposed to Malaria Infection

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Highlights

• •Profiling antibody responses of patients with naturally acquired malaria immunity.
• •High-density peptide arrays featuring linear epitopes.
• •Epitope mapping of known and potential novel vaccine candidates.
• •Novel immunogenic epitopes discovered, and known antibody target motifs confirmed.

     

Proteomics,Glycomics, and Glycoproteomics of Matrisome Molecules

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Highlights

• •Highly glycosylated matrisome proteins and their binding partners comprise extracellular networks that mediate tissue-specific cellular microenvironments.
• •Elucidation of roles of matrisome molecules in disease mechanisms requires detailed mapping of matrisome glycosylation and other post-translational modifications.
• •We review tissue workup methods for matrisome proteomics, glycomics and glycoproteomics.
• •The combination of proteomics, glycomics and glycoproteomics profiles matrisome protein modifications distinct from those studied by immunohistochemistry.

     

A New Tool to Reveal Bacterial Signaling Mechanisms in Antibiotic Treatment and Resistance

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Highlights

• •Quantitative (phospho)proteome analysis of antibiotic treatment in E. coli.
• •Largest bacterial phosphorylation catalogue.
• •Specific phosphorylation motifs changes during resistance development.
• •Phosphorylation mediated signaling could be a potential target for drug design.

     

DECA,A Comprehensive,Automatic Post-processing Program for HDX-MS Data*

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Highlights

• •Open source software for comprehensive HDX-MS data analysis.
• •Automatic back-exchange correction options.
• •Rigorous statistical analysis of the significance of uptake differences.
• •High quality visualization tools.

     

Metabolic,Anti-apoptotic and Immune Evasion Strategies of Primary Human Myeloma Cells Indicate Adaptations to Hypoxia*

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Highlights

• •In-depth proteome profiling of primary human myeloma cells
• •Characteristics of myeloma cells are related to hypoxic bone marrow conditions
• •Myeloma cells show specific immune evasion strategies
• •Metabolic adaptations involve tumor and stroma cells

     

Macrophage Phosphoproteome Analysis Reveals MINCLE-dependent and -independent Mycobacterial Cord Factor Signaling

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Highlights

• •quantitative phosphoproteome analysis of TDM-activated macrophages.
• •distinct Mincle-dependent and independent phosphorylation and gene regulations.
• •Mincle-dependent activation of PI3K/AKT signaling by TDM.
• •Mincle-independent macrophage response is linked to cell cycle regulation.

     

A Robust and Versatile Automated Glycoanalytical Technology for Serum Antibodies and Acute Phase Proteins: Ovarian Cancer Case Study

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Highlights

• •Quantitative high-throughput glycoanalytical technology as a diagnostic tool for ovarian cancer detection.
• •Multiplexed approach harnessing N-glycan data for six glycoproteins from a single biological sample.
• •Detailed characterization of human serum N-glycans from antibodies IgG, IgM and IgA and acute phase proteins transferrin, haptoglobin and alpha-1-antitrypsin.
• •Structural differences in antibody and acute phase protein glycosylation for mechanistic insights.

     

A Curated Resource for Phosphosite-specific Signature Analysis

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Highlights

• •Database of PTM site-specific phosphorylation signatures of kinases, perturbations and signaling pathways (PTMsigDB).
• •PTM signature enrichment analysis (PTM-SEA) outperformed gene-centric analysis in detection of EGF induced phospho signaling events.
• •PI3K perturbation signatures were readily detected in PI3Ka inhibited human breast cancer cells.
• •PTMsigDB and PTM-SEA can be freely accessed at https://github.com/broadinstitute/ssGSEA2.0.

     

MaxQuant.Live Enables Global Targeting of More Than 25,000 Peptides

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Highlights

• •MaxQuant.Live controls Orbitrap mass analyzers in real-time.
• •Freely available apps enable advanced data acquisition strategies.
• •On-the-fly mass, retention time and intensity recalibration.
• •Global targeting unifies shotgun and targeted proteomics.

     

Common Metabolic Pathways Implicated in Resistance to Chemotherapy Point to a Key Mitochondrial Role in Breast Cancer,

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Highlights

• •OMICS distinguish cancer cells from resistant or cancer stem cells.
• •Bactericidal antibiotics and mitochondria.
• •Linezolid and anticancer therapy.

     

Complexome Profiling Reveals Association of PPR Proteins with Ribosomes in the Mitochondria of Plants

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Highlights

• •Plant mitoribosomes contain several pentatricopeptide repeat proteins.
• •The small mitoribosomal subunit is of an exceptionally large size.
• •Protein units not directly related to translation may be attached to plant mitoribosomes to confer additional functions to these molecular machines.

     

Identification of Salivary Biomarkers for Oral Cancer Detection with Untargeted and Targeted Quantitative Proteomics Approaches

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Highlights

• •iTRAQ-based analysis of saliva samples from oral cancer patients.
• •Proteome profiling of saliva samples from patients with oral premalignant lesions.
• •Verification of salivary biomarker candidates with MRM-MS and immunoassays.
• •Identification of salivary proteins as potential biomarkers of oral cancer.

     

Global Proteome and Ubiquitinome Changes in the Soluble and Insoluble Fractions of Q175 Huntington Mice Brains

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Highlights

• •Quantitative changes in global proteome and ubiquitinome in Huntington's disease.
• •Differential ubiquitination of wild-type and mutant Htt in mice brain.
• •Enriched pathways include vesicle transport and mRNA processing.
• •Correlation between protein and diGly site fold changes.

     

BioID Performed on Golgi Enriched Fractions Identify C10orf76 as a GBF1 Binding Protein Essential for Golgi Maintenance and Secretion

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Highlights

• •BioID with Golgi fractions identified C10orf76 as proximal to GBF1.
• •Tagged C10orf76 overlaps with Golgi markers.
• •C10orf76 binds GBF1 and exchanges rapidly between free and bound forms.
• •C10orf76 is essential for maintenance of the Golgi and for secretion.