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.

     

Integration of Two In-depth Quantitative Proteomics Approaches Determines the Kallikrein-related Peptidase 7 (KLK7) Degradome in Ovarian Cancer Cell Secretome

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Highlights

• •Kallikrein-related peptidase 7 is over expressed in ovarian cancer.
• •Quantitative PROTOMAP and TAILS approaches identified putative substrates of KLK7.
• •Pro-MMP10 is activated by KLK7.
• •KLK7 cleaves thrombospondin 1 and IGFBP6 in vitro.

     

Critical Role of a Sheath Phosphorylation Site On the Assembly and Function of an Atypical Type VI Secretion System

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Highlights

• •Phosphorylation on Y139 of the sheath protein IglB of Francisella.
• •IglB substitutions Y139A, Y139D or Y139E prevent T6SS formation.
• •Y139F substitution delays but does not abolish phagosomal escape in macrophages.
• •Insight into the role of sheath phosphorylation in T6SS biogenesis.

     

Quantitative Proteomics of the 2016 WHO Neisseria gonorrhoeae Reference Strains Surveys Vaccine Candidates and Antimicrobial Resistance Determinants

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Highlights

• •Quantitative proteomes of the 2016 WHO Neisseria gonorrhoeae reference strains.
• •Novel gonorrhea vaccine candidates and potential global proteomic AMR markers.
• •First large-scale proteomic profiling of gonorrhea vaccine candidates and AMR.
• •A reference proteomics databank for gonococcal vaccine and AMR research endeavors.

     

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.

     

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

     

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.

     

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.

     

NOTCH Activation Promotes Valve Formation by Regulating the Endocardial Secretome

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Highlights

• •MEEC are a reliable endocardial in vitro model.
• •Quantitative proteomics to characterize the NOTCH-driven endocardial secretome.
• •NOTCH pathway status underlies different paracrine biological functions.
• •New insights into secreted factors involved in cardiac valve development.

     

Metabolic Cross-talk Between Human Bronchial Epithelial Cells and Internalized Staphylococcus aureus as a Driver for Infection*

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Highlights

• •Interplay of epithelial cells and internalized S. aureus was dissected over 96 h.
• •Surviving host cells contain nonreplicating bacteria that persists in the cytoplasm.
• •Competition over resources triggers temporal metabolic changes.
• •Metabolic adaptation of host and bacteria determines the outcome of infection.

     

Proteomics of Asrij Perturbation in Drosophila Lymph Glands for Identification of New Regulators of Hematopoiesis

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Highlights

• •First report on the quantitative proteomic profiling of Drosophila lymph glands.
• •Comparative proteomic analysis under conditions of perturbed blood cell homeostasis.
• •Resource for identifying new regulators of insect and vertebrate hematopoiesis.

     

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.

     

Integrated Analysis of Transcriptomic,miRNA and Proteomic Changes of a Novel Hybrid Yellow Catfish Uncovers Key Roles for miRNAs in Heterosis

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Highlights

• •mRNA-seq, miRNA-seq, proteomes of P. fulvidraco, P. vachelli, hybrid Huangyou-1.
• •Predicted miRNA-mRNA-protein pairs were found and validated by qRT-PCR and PRM.
• •Immune, metabolism, digestion, absorption, proliferation, development generate heterosis.
• •High parental gene/protein with low parental miRNAs inherit from the mother or father.

     

Multidimensional Proteomics Identifies Declines in Protein Homeostasis and Mitochondria as Early Signals for Normal Aging and Age-associated Disease in Drosophila,

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Highlights

• •Proteomic landscapes of Drosophila somatic and reproductive tissues during aging.
• •Pulsed metabolic labeling determines a decline in protein synthesis with age.
• •Drosophila model of human Parkinson's disease signifies an early-onset decline in protein synthesis.
• •Collapse of proteostasis and mitochondria are early signals for normal aging.

     

Quantification of Dynamic Protein Interactions and Phosphorylation in LPS Signaling Pathway by SWATH-MS

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Highlights

• •Intensive investigation of dynamic interactions in MyD88, TRAF6, and NEMO complexes.
• •Mechanistic insights into IRAKs proteins' assembly.
• •A signal amplification mechanism for MyD99-denpendent TLR signaling disclosed by stoichiometry of complexes.
• •Quantitative measurement of multiple phosphorylation sites on the key components in TLR signaling pathway.

     

Precision De Novo Peptide Sequencing Using Mirror Proteases of Ac-LysargiNase and Trypsin for Large-scale Proteomics

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Highlights

• •The developed Ac-LysargiNase showed higher stability and activity than before.
• •The merged spectra of the mirror peptides achieved nearly complete ion coverage.
• •pNovoM obviously increased the efficiency and accuracy of peptide sequencing.
• •The mirror enzymatic strategy achieved precision de novo sequencing on proteome scales.

     

An Advanced Strategy for Comprehensive Profiling of ADP-ribosylation Sites Using Mass Spectrometry-based Proteomics*

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Highlights

• •Comparing proteolytic digestions and precursor fragmentation methods for MS of ADPr
• •Identification of 11,265 unique ADPr-modified peptides
• •Mapping of hundreds of peptides co-modified by phosphorylation and ADPr
• •ADPr modification of specific residue types displays spatial preferences

     

Enhanced Salt Tolerance of Rhizobia-inoculated Soybean Correlates with Decreased Phosphorylation of the Transcription Factor GmMYB183 and Altered Flavonoid Biosynthesis

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Highlights

• •Rhizobia affects flavonoid metabolism via GmMYB183 phosphorylation.
• •Flavonoids rebalance the cellular ROS under salt stress.
• •Mechanistic insights into soybean responses to salinity revealed by 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.