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

     

Exploring Regulation of Protein O-Glycosylation in Isogenic Human HEK293 Cells by Differential O-Glycoproteomics

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Highlights

• •A panel of HEK293 isogenic cell lines with knockout of GALNT genes.
• •Identification of nonredundant O-glycosylation sites regulated by specific GalNAc-T isoforms.
• •GalNAc-T7 and T10 contribute to follow-up activity in regions of high density O-glycosylation.
• •GalNAc-T11 specifically controls O-glycosylation of specific linker regions in the low-density lipoprotein receptor related proteins.

     

Identification of TEX101-associated Proteins Through Proteomic Measurement of Human Spermatozoa Homozygous for the Missense Variant rs35033974,

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Highlights

• •Missense variant rs35033974 resulted in significantly reduced levels of human TEX101 protein in seminal plasma and spermatozoa.
• •Differential proteomics revealed TEX101-associated testis-specific proteins, including LY6K, which were down-regulated in rs35033974^hh spermatozoa.
• •Deep proteome of human spermatozoa, including some “missing” proteins, was identified.

     

Simultaneous Quantification of Protein Expression and Modifications by Top-down Targeted Proteomics: A Case of the Sarcomeric Subproteome

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Highlights

• •A new strategy for simultaneous quantification of protein expression and modification.
• •This top-down LC/MS-based method shows high reproducibility and high throughput.
• •Quantification at the intact protein level with results comparable to Western blot.
• •This top-down proteomics method is applicable to different species and tissues.

     

Spatial Distribution of Endogenous Tissue Protease Activity in Gastric Carcinoma Mapped by MALDI Mass Spectrometry Imaging

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Highlights

• •New MALDI MS imaging sample preparation workflow reveals tissue protease activity.
• •Differential time- and inhibitor concentration-dependence confirm active proteases.
• •Mouse gastric tumor displays high protease activity compared to surrounding tissue.
• •Proteomic data and biochemical protease activity assay support MALDI MSI results.

     

Comprehensive Analysis of Individual Variation in the Urinary Proteome Revealed Significant Gender Differences

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Highlights

• •Comprehensive analysis of inter-individual variation of normal urinary proteome.
• •Significant gender differences were observed.
• •Proteins increased in female urine are enriched in immunological pathways.
• •Estimated reference intervals of proteins as the baseline for biomarker discovery.

     

HLA-DO Modulates the Diversity of the MHC-II Self-peptidome

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Highlights

• •MHC-II-bound peptide repertoires from DO-sufficient and DO-deficient cells.
• •Fewer unique peptides and core epitopes were presented in the absence of DO.
• •Immunopeptidome differences appeared to result from reduced DM editing.
• •DO-dependent self-epitopes elicited CD4 T cell responses in mice.

     

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.

     

Celastrol Protects From Cholestatic Liver Injury Through Modulation of SIRT1-FXR Signaling

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Highlights

• •1. Celastrol alleviated cholestatic liver injury.
• •2. Celastrol inhibited the decrease of SIRT1 induced by deoxycholic acid.
• •3. SIRT1-FXR signaling pathway mediated the effect of celastrol.

     

Quantitative Multiplex Substrate Profiling of Peptidases by Mass Spectrometry

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Highlights

• •Quantitative substrate profiling method for characterizing peptidase specificity.
• •Applicable to both purified peptidases and peptidases in complex biological samples.
• •TMT labeling improves throughput, accuracy and reproducibility of the assay.
• •Design of fluorescent probes to monitor peptidase activity based on substrate data.

     

Conodipine-P1-3, the First Phospholipases A2 Characterized from Injected Cone Snail Venom*

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Highlights

• •Three novel Conodipines P1-3 in the injected venom of Conus purpurascens.
• •Conodipines P1-3 have consensus catalytic characteristics of sPLA₂.
• •We determined multiple modification sites in Conodipines P1-3.
• •Evaluated the activity of Conohyal-P1 by a MS-based method.

     

High-throughput Identification of FLT3 Wild-type and Mutant Kinase Substrate Preferences and Application to Design of Sensitive In Vitro Kinase Assay Substrates

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Highlights

• •Developed a data processing pipeline to format phosphopeptide identifications.
• •Identified the preferred substrate motif for FLT3 and mutant kinases.
• •Designed and validated a panel of pan-FTL3 artificial substrates.
• •Monitored FLT3 and mutant kinase activity through FAStide phosphorylation.

     

Proteome-wide Analysis of Protein Thermal Stability in the Model Higher Plant Arabidopsis thaliana

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Highlights

• •Over 1700 Arabidopsis proteins with thermal models in multiple replicates.
• •Melting temperature correlates with 1°, 2°, and 3° protein characteristics.
• •Ligand-induced thermal shifts are evident in complex protein extracts.

     

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.

     

Decreased Antibiotic Susceptibility Driven by Global Remodeling of the Klebsiella pneumoniae Proteome

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Highlights

• •Global proteomic remodeling alters antibiotic susceptibility in K. pneumoniae.
• •Drug specific transport, sugar utilization, central metabolism, capsule synthesis.
• •Common pathways of reactive oxygen scavenging, turnover of misfolded proteins.
• •Integrated adjustments and unique drug-specific features for drug combinations.

     

Bayesian Confidence Intervals for Multiplexed Proteomics Integrate Ion-statistics with Peptide Quantification Concordance,

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Highlights

• •Bayesian Beta-Binomial model integrates ion statistics with peptide ratio agreement.
• •Model appropriately interprets information from low signal peptides.
• •Confidence can be assigned even without replicates.
• •Model adds sensitivity to detection of small changes.

     

Data-independent Acquisition Improves Quantitative Cross-linking Mass Spectrometry

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Highlights

• •Quantitative cross-linking mass spectrometry (QCLMS) was automated by Spectronaut.
• •Data-independent acquisition (DIA) was adapted to QCLMS.
• •Accuracy and precision of quantitation improves with DIA over DDA.
• •QCLMS is now ready for use in complex samples.