Proteomic Profiling of Human Prostate Cancer-associated Fibroblasts (CAF) Reveals LOXL2-dependent Regulation of the Tumor Microenvironment

1. Download : Download high-res image (105KB)
2. Download : Download full-size image

Highlights

• •Quantitative (phoshpo)proteome of primary cell cultures of patient-matched prostate CAF and NPF.
• •Key CAF-associated proteins validated using orthogonal methodologies.
• •LOXL2 inhibitors D-penicillamine and PXS-S2A impaired CAF migration and ECM alignment.
• •Pre-treatment with LOXL2 inhibitors impaired migratory capacity of RWPE-2 cells in co-culture.

     

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.

     

Estimating the Contribution of Proteasomal Spliced Peptides to the HLA-I Ligandome*

1. Download : Download high-res image (105KB)
2. Download : Download full-size image

Highlights

• •Reported proteasomal spliced HLA peptides do not fit the consensus binding motifs.
• •Their MS/MS spectrum matches suggest that many of them are ambiguous.
• •Our workflow is based on de novo sequencing, alignment, and multiple search tools.
• •The upper bound proportion of cis-spliced peptides is 2–6% and likely much smaller.

     

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.

     

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

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

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.

     

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.

     

Chasing Tails: Cathepsin-L Improves Structural Analysis of Histones by HX-MS,

1. Download : Download high-res image (82KB)
2. Download : Download full-size image

Highlights

• •Cathepsin-L is introduced as a novel protease for HX-MS studies.
• •Cathepsin-L improves resolution of traditionally challenging histone tails.
• •Cathepsin-L can be readily combined with pepsin for improved protein coverage.
• •In-solution dynamics of the H3.1 and H4 monomers reveal extensive EX1 kinetics.

     

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

1. Download : Download high-res image (130KB)
2. Download : Download full-size image

Highlights

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

     

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

1. Download : Download high-res image (92KB)
2. Download : Download full-size image

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.

     

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.

     

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.

     

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.

     

Data-independent Acquisition Improves Quantitative Cross-linking Mass Spectrometry

1. Download : Download high-res image (126KB)
2. Download : Download full-size image

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.

     

N-terminal Acetylation Levels Are Maintained During Acetyl-CoA Deficiency in Saccharomyces cerevisiae

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

Highlights

• •First global study on metabolic regulation of Nt-acetylation.
• •Yeast cells maintain global Nt-acetylation levels during prolonged starvation.
• •Nt-acetylation can in some cases be either up- or downregulated by starvation.
• •Naa10/NatA affects the steady-state protein levels of Rsa3 and Rpl7a.

     

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.

     

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.

     

Proteomic Profiling of Paired Interstitial Fluids Reveals Dysregulated Pathways and Salivary NID1 as a Biomarker of Oral Cavity Squamous Cell Carcinoma,

1. Download : Download high-res image (123KB)
2. Download : Download full-size image

Highlights

• •Proteome profiling of tissue interstitial fluids (TIFs) of oral cancer.
• •Pathway of aminoacyl tRNA biosynthesis enriched in proteome of TIFs.
• •Verification of nidogen-1 as a salivary biomarker of oral cancer.
• •High correlation between elevated tissue level of nidogen-1 and poor survival.

     

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

1. Download : Download high-res image (133KB)
2. Download : Download full-size image

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