Microvesicle Proteomic Profiling of Uterine Liquid Biopsy for Ovarian Cancer Early Detection

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Highlights

• •Microvesicle proteomics of 187 utero-tubal lavage samples for early diagnosis of HGOC.
• •Machine learning-based classification of a 9-protein signature with high predictive power.
• •Signature has 70‥ sensitivity and 76.2‥ specificity, predicting stage I lesions.

     

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.

     

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.

     

Development of a Gill Assay Library for Ecological Proteomics of Threespine Sticklebacks (Gasterosteus aculeatus)

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Highlights

• •Construction of threespine stickleback gill assay library using DDA proteomics
• •Population-specific gill proteome signatures of four ecotypes identified by DIA
• •HSP47 and extracellular matrix proteins highly elevated in warm-adapted sticklebacks
• •Inflammasome and proteolytic proteins highly elevated in freshwater sticklebacks

     

Integration and Analysis of CPTAC Proteomics Data in the Context of Cancer Genomics in the cBioPortal

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Highlights

• •Support for mass spectrometry-based proteomics in cBioPortal.
• •User-friendly web interface, a web API, and an R client to query proteogenomic data.
• •Integration of Clinical Proteomics Tumor Analysis Consortium data with cBioPortal.

     

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.

     

Reductive Stress Selectively Disrupts Collagen Homeostasis and Modifies Growth Factor-independent Signaling Through the MAPK/Akt Pathway in Human Dermal Fibroblasts

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Highlights

• •Changes to the proteome of skin fibroblasts subjected to reductive stress have been quantitated.
• •Only a small set of proteins is selectively diminished upon exposure to reductants.
• •Collagens (COL1A2 and COL6A2) emerge as sentinels of reductive stress.
• •Reductive stress triggers receptor-independent Akt phosphorylation at Ser473.

     

Global Interactomics Uncovers Extensive Organellar Targeting by Zika Virus

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Highlights

• •BioID and IP-MS were conducted to generate a global ZIKV-host protein interactome
• •Interactome consists of >3000 high confidence ZIKV-host protein interactions
• •Data mining indicates that ZIKV proteins interact with multiple host cell organelles
• •An important role for peroxisomes in ZIKV infection is uncovered

     

Proteomic Analysis of Vocal Fold Fibroblasts Exposed to Cigarette Smoke Extract: Exploring the Pathophysiology of Reinke's Edema,

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Highlights

• •First global study on laryngeal cells cultured with cigarette smoke enriched medium.
• •Vocal fold fibroblasts increased production of ECM component hyaluronan.
• •Expression of several fibrillar collagens was reduced.

     

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.

     

A Targeted Mass Spectrometry Strategy for Developing Proteomic Biomarkers: A Case Study of Epithelial Ovarian Cancer

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Highlights

• •Rigorous experimental design and data analysis for large-scale SRM studies.
• •Plasma-based biomarker signature combined with CA125 for ovarian cancer detection.
• •Broadly applicable strategy for the development of diagnostic biomarker assays.

     

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

     

Integrated Succinylome and Metabolome Profiling Reveals Crucial Role of S-Ribosylhomocysteine Lyase in Quorum Sensing and Metabolism of Aeromonas hydrophila,

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Highlights

• •A global lysine succinylome was investigated in A. hydrophila.
• •The lysine succinylation modifications play crucial role on various metabolic pathways.
• •Reversible succinylation on Lys23 and Lys30 regulates the activity of S-ribosylhomocysteine lyase LuxS.
• •Lysine succinylation modifications of LuxS affect quorum sensing and metabolism.

     

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.

     

Temporal Proteomic Analysis of Pancreatic β-Cells in Response to Lipotoxicity and Glucolipotoxicity

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Highlights

• •Temporal proteome profiling of lipotoxicity and glucolipotoxicity in β-cells
• •Palmitate induced cholesterol metabolism earlier than fatty acid metabolism
• •Setd8 promotes palmitate + glucose-stimulated INS-1 cell proliferation
• •PA induced apoptosis partially via upregulation of Rhob in INS-1 cells

     

PTMiner: Localization and Quality Control of Protein Modifications Detected in an Open Search and Its Application to Comprehensive Post-translational Modification Characterization in Human Proteome,

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Highlights

• •PTMiner software for intelligent post-processing of open-search results.
• •Unrestrictive modification site localization based on a Bayesian model.
• •Extended transfer FDR estimation for accurate grouped FDR estimation.
• •Comprehensive PTM characterization in a draft map of human proteome.

     

Changes in Synaptic Proteins Precede Neurodegeneration Markers in Preclinical Alzheimer's Disease Cerebrospinal Fluid

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Highlights

• •Proteomic analysis of cerebrospinal fluid and identification of synaptic component.
• •Use of super resolution microscopy to verify synapse-specificity in human tissue.
• •Selective reaction monitoring MS (SRM) of synaptic panel in 3 cohorts of Alzheimer's disease cerebrospinal fluid.
• •Synaptic protein changes precede tau in preclinical Alzheimer's disease.

     

Endoglycosidase S Enables a Highly Simplified Clinical Chemistry Procedure for Direct Assessment of Serum IgG Undergalactosylation in Chronic Inflammatory Disease

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Highlights

• •Selective release of IgG Fc glycans in crude serum by endoglycosidase S.
• •CE-LIF-based measurements of IgG undergalactosylation levels (UGS).
• •UGS as a biomarker: Stratification of non-alcoholic steatohepatitis patients and controls.

     

Mapping Spatiotemporal Microproteomics Landscape in Experimental Model of Traumatic Brain Injury Unveils a link to Parkinson's Disease,

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Highlights

• •Spatiotemporal microproteomics analysis of TBI.
• •Injury site microproteomics reveal distinct phases in 10-day frame post TBI.
• •Uninjured proteomic profile is restored in TBI at 10 days post injury.
• •Substantia nigra protein post 3 days suggest link to Parkinson's disease.

     

Analysis of Endogenous Peptides Released from Osteoarthritic Cartilage Unravels Novel Pathogenic Markers,

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Highlights

• •Shotgun identification of neopeptides released from osteoarthritic cartilage.
• •Specific endogenous peptides from the cartilage ECM are measured by MRM.
• •Identification of neopeptides differentially generated from diseased tissue.
• •The peptide DSNKIETIPN shows the best metrics as biomarker of OA cartilage.