Exploring Regulation of Protein O-Glycosylation in Isogenic Human HEK293 Cells by Differential O-Glycoproteomics

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

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.

     

Single-cell Proteomics: Progress and Prospects

1. Download : Download high-res image (315KB)
2. Download : Download full-size image

Highlights

• •Label-free and isobaric labeling approaches for in-depth profiling of single cells.
• •Miniaturization and simplification of sample processing reduce surface losses.
• •Nanoflow separations enhance ionization efficiency and reduced chemical noise.
• •Ultrasensitive mass spectrometry and gas-phase separation add selectivity.

     

Top-down Proteomics: Technology Advancements and Applications to Heart Diseases

Introduction: Heart diseases are a leading cause of morbidity and mortality for both men and women worldwide, and impose significant economic burdens on the healthcare systems. Despite substantial effort over the last several decades, the molecular mechanisms underlying diseases of the heart remain poorly understood.

Areas covered: Altered protein post-translational modifications (PTMs) and protein isoform switching are increasingly recognized as important disease mechanisms. Top-down high-resolution mass spectrometry (MS)-based proteomics has emerged as the most powerful method for the comprehensive analysis of PTMs and protein isoforms. Here, we will review recent technology developments in the field of top-down proteomics, as well as highlight recent studies utilizing top-down proteomics to decipher the cardiac proteome for the understanding of the molecular mechanisms underlying diseases of the heart.

Expert commentary: Top-down proteomics is a premier method for the global and comprehensive study of protein isoforms and their PTMs, enabling the identification of novel protein isoforms and PTMs, characterization of sequence variations, and quantification of disease-associated alterations. Despite significant challenges, continuous development of top-down proteomics technology will greatly aid the dissection of the molecular mechanisms underlying diseases of the hearts for the identification of novel biomarkers and therapeutic targets.     

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.

     

Development of a Gill Assay Library for Ecological Proteomics of Threespine Sticklebacks (Gasterosteus aculeatus)

1. Download : Download high-res image (97KB)
2. Download : Download full-size image

Highlights

• •Construction of threespine stickleback gill assay library using DDA proteomics
• •Population-specific gill proteome signatures of four ecotypes identified by DIA
• •HSP47 and extracellular matrix proteins highly elevated in warm-adapted sticklebacks
• •Inflammasome and proteolytic proteins highly elevated in freshwater sticklebacks

     

Discovery of a Human Testis-specific Protein Complex TEX101-DPEP3 and Selection of Its Disrupting Antibodies

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

Highlights

• •Quantitative co-IP-MS approach to discover the human TEX101 interactome.
• •Validation of the human testis-specific protein complex TEX101-DPEP3.
• •Development of a hybrid immunoassay to screen for disruptors of TEX101-DPEP3 complex.

     

TMT Labeling for the Masses: A Robust and Cost-efficient,In-solution Labeling Approach

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

Highlights

• •TMT labeling protocol with excellent intra- and interlaboratory reproducibility.
• •Complete in-solution labeling of peptides using 1/8 of recommended TMT quantities.
• •Demonstration of utility for deep-scale (phospho)proteome analysis.

     

gpGrouper: A Peptide Grouping Algorithm for Gene-Centric Inference and Quantitation of Bottom-Up Proteomics Data

1. Download : Download high-res image (162KB)
2. Download : Download full-size image

Highlights

• •Gene-centric inference algorithm with classification for distinguishable groups.
• •Shared peptides are split proportionally to corresponding unique peptide ratios.
• •iBAQ values are calculated for label-free, isotopic or isobaric labeling methods.
• •Universally handles single or mixed species PDX data with accurate deconvolution.

     

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.

     

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.

     

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.

     

Simultaneous Improvement in the Precision,Accuracy, and Robustness of Label-free Proteome Quantification by Optimizing Data Manipulation Chains,

1. Download : Download high-res image (158KB)
2. Download : Download full-size image

Highlights

• •High-quality LFQ is valuable technique yet remains extremely challenging.
• •Fluctuating precision, limited robustness, and compromised accuracy are known issues.
• •We proposed a strategy collectively improving LFQ precision, robustness, and accuracy.
• •An online tool incorporating this novel strategy was also developed.

     

Hydrolysis of cyclosporin A: Identification of 1,11 seco-cyclosporin A and 4,5 secoisoCyclosporin A by FAB-MS/MS

We have previously reported that treatment of CsA with aqueous HCl gives rise to the formation of a number of water-soluble compounds. Two of these were identified from their FAB-MS/MS spectra as open-chain nona- and decapeptides. We describe here the identification of two other main compounds deriving from the same treatment. Identification was rendered possible from the comparison of their FAB-MS/MS spectra with those of methyl and acetyl derivatives. The two compounds are water-soluble, open-chain undecapeptides corresponding to 1,11 seco-CsA and of 4,5 seco-isoCsA, respectively.