Spatiotemporal Changes of the Phagosomal Proteome in Dendritic Cells in Response to LPS Stimulation*

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Highlights

• •Characterization of the phagosomal proteome comparing resting and LPS-treated BMDCs.
• •Label-free quantification determined 2843 phagosomal proteins.
• •Reduced recruitment of hydrolases and V-ATPase to phagosomes of LPS-treated cells.
• •Increased recruitment of antigen cross-presentation molecules to these phagosomes.

     

Phytoplasma-induced Changes in the Acetylome and Succinylome of Paulownia tomentosa Provide Evidence for Involvement of Acetylated Proteins in Witches' Broom Disease

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Highlights

• •Quantitative global proteome, acetylome and succinylome of phytoplasma-infected Paulownia tomentosa seedlings.
• •Acetylation may be more important than succinylation in response to phytoplasma infection.
• •Acetylation modified the activities of POR and RuBisCO.
• •Possible model to elucidate the molecular mechanism responses to PaWB from proteome and PTMs.

     

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.

     

Glycoproteogenomics: A Frequent Gene Polymorphism Affects the Glycosylation Pattern of the Human Serum Fetuin/α-2-HS-Glycoprotein

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Highlights

• •Frequent genetic polymorphism affects the glycosylation pattern of fetuin.
• •Personalized in-depth proteoform profiling of fetuin purified from 20 donors.
• •Classification of serum donors into three different genotypes.
• •Septic patients show increased level of fucosylation at N-glycolation site N176.

     

Regulated Phosphosignaling Associated with Breast Cancer Subtypes and Druggability,

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Highlights

• •Our search identifies 2,134 kinase-substrate phosphosite pairs in breast cancer.
• •CDKs and MAPKs are dominant regulators of trans substrate-phosphorylation.
• •Druggability, outcomes, and immune signatures related to kinase-substrates.
• •Experimentally validated activated phosphosites of ERBB2, EIF4EBP1, and EGFR.

     

Sucrose-induced Receptor Kinase 1 is Modulated by an Interacting Kinase with Short Extracellular Domain,

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Highlights

• •Functional role of a yet uncharacterized receptor kinase QSK1.
• •Activation model for SIRK1 receptor kinase in a heteromer with QSK1.
• •Role of QSK1 in substrate recruitment and stabilization of the complex.

     

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

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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.

     

Apolipoprotein A1 Forms 5/5 and 5/4 Antiparallel Dimers in Human High-density Lipoprotein

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Highlights

• •Zero-length chemical cross-linking of APOA1 peptides in HDL.
• •Cross-links match antiparallel isomers of APOA dimers in molecular modeling.
• •Identical MS/MS spectra of native and synthetic cross-linked peptides.
• •First biochemical evidence of LL5/5 and LL5/4 isomers in human HDL.

     

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.

     

In-depth Proteome of the Hypopharyngeal Glands of Honeybee Workers Reveals Highly Activated Protein and Energy Metabolism in Priming the Secretion of Royal Jelly

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Highlights

• •In-depth proteome underpins the gland ontogeny and age-specific activity of the HGs.
• •The well-developed acini in the HGs of NBs promote the RJ secretary activities.
• •The enhanced protein and energy metabolism in the HGs boost the stronger RJ secretion of RJBs.

     

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

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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.

     

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.

     

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.

     

Small-protein Enrichment Assay Enables the Rapid,Unbiased Analysis of Over 100 Low Abundance Factors from Human Plasma

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Highlights

• •Development of a method for low-abundance small protein analysis in human plasma.
• •Deep proteome profiling demonstrated unbiased identification of diverse factors.
• •Method enabled identification of a novel human plasma protein C5ORF46.
• •Analysis of intermittent fasting response showed changes in iron regulation.

     

Unraveling Hidden Components of the Chloroplast Envelope Proteome: Opportunities and Limits of Better MS Sensitivity

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Highlights

• •Identification of previously undetected chloroplast envelope proteins.
• •Up to date manual annotation of genuine (or shared) envelope components.
• •New hypotheses for localizations, functions, interactions among cell compartments.
• •A new resource of significant value to the broader plant science community.

     

Posttranslational Modifications Drive Protein Stability to Control the Dynamic Beer Brewing Proteome

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Highlights

• •SWATH-MS profiles protein abundance and modification during mashing in beer brewing.
• •Proteolysis due to barley proteases leads to extreme proteoform diversity.
• •Sequence-specific proteolytic clipping of proteins controls their stability.