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

1. Download : Download high-res image (116KB)
2. Download : Download full-size image

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

     

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

1. Download : Download high-res image (128KB)
2. Download : Download full-size image

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.

     

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

1. Download : Download high-res image (96KB)
2. Download : Download full-size image

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.

     

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

1. Download : Download high-res image (102KB)
2. Download : Download full-size image

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.

     

Why Glycosylation Matters in Building a Better Flu Vaccine

1. Download : Download high-res image (59KB)
2. Download : Download full-size image

Highlights

• •Glycosylation is not currently considered in flu vaccine design.
• •Glycosylation influences on immunodominance are not well understood.
• •Identification of site-specific glycosylation using mass spectrometry has matured.
• •New methods are needed to quantify site-specific glycosylation for vaccine design.

     

Delta-S-Cys-Albumin: A Lab Test that Quantifies Cumulative Exposure of Archived Human Blood Plasma and Serum Samples to Thawed Conditions,

1. Download : Download high-res image (132KB)
2. Download : Download full-size image

Highlights

• •Endogenous plasma/serum QC marker that quantifies cumulative sample thawed time.
• •Mechanism of marker change known, and rate law established.
• •Data interpretation based on documented population averages and rate law.
• •Blind-challenge verified; utility proven via exposure of undisclosed freezer outage.

     

Identification of Candidate Plasma Protein Biomarkers for Cervical Cancer Using the Multiplex Proximity Extension Assay

1. Download : Download high-res image (94KB)
2. Download : Download full-size image

Highlights

• •HPV is being introduced as the primary test in cervical cancer screening programs.
• •New biomarkers are needed for co-testing of women HPV positive in screening.
• •Analysis of plasma from women with invasive cervical cancer identified a 11-marker panel.
• •This signature shows high sensitivity and specificity to identify women with cancer.

     

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

1. Download : Download high-res image (74KB)
2. Download : Download full-size image

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.

     

DIAlignR Provides Precise Retention Time Alignment Across Distant Runs in DIA and Targeted Proteomics

1. Download : Download high-res image (90KB)
2. Download : Download full-size image

Highlights

• •Retention time shift can lead to inversion of elution order of peptides.
• •Global alignment methods are suboptimal for alignment of distant runs.
• •DIAlignR employs hybrid (global + local) RT alignment approach.
• •DIAlignR can align swapped peaks accurately across distant runs.

     

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

1. Download : Download high-res image (173KB)
2. Download : Download full-size image

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.

     

Substantial Influence of ERAP2 on the HLA-B*40:02 Peptidome: Implications for HLA-B*27-Negative Ankylosing Spondylitis

1. Download : Download high-res image (115KB)
2. Download : Download full-size image

Highlights

• •HLA-B*40:02 and ERAP2 are risk factors for ankylosing spondylitis.
• •The effects of ERAP2 on the B*40:02 peptidome are defined.
• •ERAP2 has a major influence mainly due to alterations of N-terminal residues.
• •These effects provide a basis for the association of ERAP2 with disease.

     

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

1. Download : Download high-res image (128KB)
2. Download : Download full-size image

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.

     

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

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

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.

     

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

1. Download : Download high-res image (86KB)
2. Download : Download full-size image

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.

     

Chromobodies to Quantify Changes of Endogenous Protein Concentration in Living Cells

1. Download : Download high-res image (90KB)
2. Download : Download full-size image

Highlights

• •Chromobodies are stabilized by antigen binding in live cells.
• •Monitoring changes of endogenous protein levels in living cells with chromobodies.
• •Broadly applicable system to generate turnover-accelerated chromobodies.
• •Quantification of time- and dose-dependent compound effects.

     

Redundancy and Complementarity between ERAP1 and ERAP2 Revealed by their Effects on the Behcet's Disease-associated HLA-B*51 Peptidome,

1. Download : Download high-res image (120KB)
2. Download : Download full-size image

Highlights

• •HLA-B*51 and ERAP1, but not ERAP2, are risk factors for Behçet's disease.
• •The HLA-B*51 peptidome and the effects of ERAP1 and ERAP2 on it are analyzed.
• •ERAP1 and ERAP2 alter multiple features of the HLA-B*51 peptidome in distinct ways.
• •Both enzymes act independently with complementary and partially redundant functions.

     

A Combined N-terminomics and Shotgun Proteomics Approach to Investigate the Responses of Human Cells to Rapamycin and Zinc at the Mitochondrial Level

1. Download : Download high-res image (83KB)
2. Download : Download full-size image

Highlights

• •Rapamycin and zinc induce moderate but significant mitochondrial proteome changes.
• •The mitochondrial proteins processing system is robust under subtoxic conditions.
• •Rapamycin and zinc perturb the mitochondrial proteins processing system.
• •Rapamycin and zinc perturb the mitochondrial proteins homeostasis.

     

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

1. Download : Download high-res image (61KB)
2. Download : Download full-size image

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.

     

Sample Preparation Scale-Up for Deep N-glycomic Analysis of Human Serum by Capillary Electrophoresis and CE-ESI-MS*

1. Download : Download high-res image (84KB)
2. Download : Download full-size image

Highlights

• •Efficient sample preparation workflow for deep N-glycomics analysis from serum.
• •Temperature gradient denaturing protocol to prevent protein precipitation.
• •Decrease of free sugar content in serum enhanced PNGase F digestion efficiency.
• •Modified evaporative labeling method increased fluorophore labeling yield.

     

Deep Protein Methylation Profiling by Combined Chemical and Immunoaffinity Approaches Reveals Novel PRMT1 Targets

1. Download : Download high-res image (87KB)
2. Download : Download full-size image

Highlights

• •Enrichment of methyl peptides using two orthogonal techniques.
• •Knockdown of PRMT1 leads to substantial changes in protein arginine “methylome”.
• •Discrimination of ADMA and SDMA using characteristic neutral losses.
• •Identification of PRMT1 targets and substrate scavenged by other PRMTs in the absence of PRMT1 activity.