Carcinogenic Helicobacter pylori Strains Selectively Dysregulate the In Vivo Gastric Proteome,Which May Be Associated with Stomach Cancer Progression,

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Highlights

• •H. pylori dysregulates the in vivo gastric proteome of gerbils in a strain-specific manner.
• •H. pylori increases RABEP2 and G3BP2 levels in cell culture.
• •H. pylori upregulates RABEP2 and G3BP2 in gerbil and human gastric epithelium.
• •Levels of RABEP2 and G3BP2 increase with severity of malignant lesions in vivo.

     

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

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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.

     

Glycan Markers of Human Stem Cells Assigned with Beam Search Arrays,

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Highlights

• •R-10G is a mono-sulfated glycan antigen of human iPS and ES cells on podocalyxin.
• •R-10G and nonsulfated i are reciprocal antigens on type 2 glycan backbones.
• •TRA-1–60 and -81 and FC10.2 are antigens expressed on unsulfated type 1 backbones.
• •These assignments open the way to probing their roles in podocalyxin-signaling.

     

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.

     

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

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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.

     

Identification of a Specific Translational Machinery via TCTP–EF1A2 Interaction Regulating NF1-associated Tumor Growth by Affinity Purification and Data-independent Mass Spectrometry Acquisition (AP-DIA),

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Highlights

• •AP-DIA/SWATH analysis to identify TCTP-interacting proteins in NF1 tumor cells.
• •A highly specific TCTP–EF1A2 interaction but rather than TCTP–EF1A1 interaction.
• •TCTP–EF1A2 interaction mediating formation of EF1A2-elogation factor complex.
• •TCTP–EF1A2 dependent translation machinery regulating NF1 tumor cell growth.

     

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

     

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

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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.

     

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.

     

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.

     

microRNA-222 Attenuates Mitochondrial Dysfunction During Transmissible Gastroenteritis Virus Infection

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Highlights

• •microRNA-222 attenuates TGEV-induced mitochondrial dysfunction.
• •microRNA-222 downregulates THBS1 and CD47.
• •THBS1 is the target of microRNA-222 during TGEV infection.
• •THBS1 and CD47 increase mitochondrial Ca²⁺ level and reduced mitochondrial membrane potential (MMP).

     

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.

     

Why Glycosylation Matters in Building a Better Flu Vaccine

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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.

     

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.

     

The Systemin Signaling Cascade As Derived from Time Course Analyses of the Systemin-responsive Phosphoproteome,

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Highlights

• •Definition of early systemin-responsive phosphorylation time course.
• •Reconstruction of kinase-substrate relationships from phosphorylation time profiles.
• •Phosphatase PLL5 rapidly dephosphorylated H⁺-ATPase LHA1 inducing alkalinization of the medium.
• •MAP-Kinase MPK2 re-phosphorylated LHA1 after 15 minutes.

     

Investigating Lactococcus lactis MG1363 Response to Phage p2 Infection at the Proteome Level

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Highlights

• •The proteomes of L. lactis MG1363 and phage p2 at different stages of infection were characterized.
• •16% (226/1412) of the bacterial proteins detected were unique to infected cultures.
• •A targeted approach using synthetic peptides improved the coverage of phage p2 proteome.
• •By means of proteogenomics, we uncovered a conserved phage protein coded by a previously unannotated gene.
• •Deletion of the bacterial gene llmg_0219 (unknown function) impedes phage p2 infection.

     

psims - A Declarative Writer for mzML and mzIdentML for Python

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Highlights

• •Incrementally build mzML 1.1, and mzIdentML 1.2 files in Python over a file stream.
• •Traverse controlled vocabularies using common mapping patterns.
• •Generate byte offset index as the document streams.
• •Manage referential integrity on-the-fly.

     

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.