HIGD2A is Required for Assembly of the COX3 Module of Human Mitochondrial Complex IV

1. Download : Download high-res image (369KB)
2. Download : Download full-size image

Highlights

• •Quantitative proteomics reveals HIGD2A is required for assembly of the COX3 module.
• •Pulse-SILAC demonstrates that HIGD2A is involved in COX3 biogenesis.
• •Supercomplexes in HIGD2A knockout cells are depleted of COX3.
• •HIGD2A is the first assembly factor identified for the COX3 module of Complex IV.

     

Proteomic Analysis Reveals that Topoisomerase 2A is Associated with Defective Sperm Head Morphology

1. Download : Download high-res image (183KB)
2. Download : Download full-size image

Highlights

• •Human spermatozoa possess cells of poor morphology that lack nuclear integrity.
• •These cells can be isolated by density separation.
• •Mass spectrometry reveals their nuclei contain excess protein.
• •TOP2A is a promising marker of this poor nuclear development.

     

AMPK Interactome Reveals New Function in Non-homologous End Joining DNA Repair

1. Download : Download high-res image (195KB)
2. Download : Download full-size image

Highlights

• •Each component of the AMPK trimeric complex was profiled by interaction proteomics.
• •The subunit composition of the AMPK complex directs interactions to distinct proteins.
• •AMPK interacts with Artemis and plays a role in Non-Homologous End Joining.

     

Organellar Maps Through Proteomic Profiling – A Conceptual Guide

1. Download : Download high-res image (233KB)
2. Download : Download full-size image

Highlights

• •Organelle profiling maps capture localizations of 1000s of proteins in one experiment.
• •Comparing maps +/− perturbation reveals disease mechanisms & cellular responses.
• •A conceptual guide to planning and interpreting organellar profiling experiments.
• •A cross-study consensus set of human organellar marker proteins.

     

Improving Identification of In-organello Protein-Protein Interactions Using an Affinity-enrichable,Isotopically Coded,and Mass Spectrometry-cleavable Chemical Crosslinker

1. Download : Download high-res image (248KB)
2. Download : Download full-size image

Highlights

• •Used affinity-enrichable, isotopically coded, and MS-cleavable crosslinker.
• •Targeted acquisition strategy based on isotopic-coding described and evaluated.
• •Novel data analysis pipeline developed provides improved crosslink identification.
• •Large dataset reveals hundreds of mitochondrial protein-protein interactions.

     

Proteomic Analysis of Salmonella-modified Membranes Reveals Adaptations to Macrophage Hosts

1. Download : Download high-res image (255KB)
2. Download : Download full-size image

Highlights

• •Affinity-based proteomics of infected macrophage cells.
• •Salmonella-modified membranes exhibit host-specific composition.
• •Proteome differences explain some host-dependent pathophysiological differences.

     

Proteaphagy in Mammalian Cells Can Function Independent of ATG5/ATG7

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

Highlights

• •Quantitative proteomics of isolated lysosomes, autophagosomes and proteasomes.
• •Pharmacological inhibition of proteasomes leads to their accumulation within lysosomes.
• •Inhibition of classical autophagy pathways cannot completely block this process.
• •Known autophagy adaptor proteins are not involved.

     

MaxQuant Software for Ion Mobility Enhanced Shotgun Proteomics

1. Download : Download high-res image (140KB)
2. Download : Download full-size image

Highlights

• •Highly parallelizable 4D feature detection in ion mobility enhanced shotgun proteomics.
• •Multidimensional non-linear mass, retention time and ion mobility recalibration.
• •Collision cross section aware matching between runs.
• •Label-free quantification of ion mobility MS data.

     

Identification of a Multiplex Biomarker Panel for Hypertrophic Cardiomyopathy Using Quantitative Proteomics and Machine Learning

1. Download : Download high-res image (95KB)
2. Download : Download full-size image

Highlights

• •Quantitative proteomics and machine learning to study plasma biomarkers in HCM.
• •Six peptides are increased in plasma of LVH+ HCM compared to controls.
• •Peptide biomarkers correlate with imaging markers of phenotype severity.
• •Peptide biomarkers correlate with the estimated sudden cardiac death risk.

     

A Cross-linking Mass Spectrometry Approach Defines Protein Interactions in Yeast Mitochondria

1. Download : Download high-res image (250KB)
2. Download : Download full-size image

Highlights

• •XL-MS reveals new PPIs in yeast mitochondria under glycerol and glucose condition.
• •Significant but limited results from quantitative XL-MS experiments.
• •Ndi1 participates in a CIII₂CIV₂ respiratory supercomplex.
• •Min8 promotes assembly of Cox12 into an intermediate complex IV.

     

The Aspergillus fumigatus Secretome Alters the Proteome of Pseudomonas aeruginosa to Stimulate Bacterial Growth: Implications for Co-infection

1. Download : Download high-res image (146KB)
2. Download : Download full-size image

Highlights

• •Pseudomonas aeruginosa growth increases in Aspergillus fumigatus culture filtrates.
• •A. fumigatus culture filtrates are characterized by a range of peptidases and proteases.
• •LFQ proteomics characterizes the response of P. aeruginosa to A. fumigatus culture filtrates.
• •A. fumigatus creates an environment for P. aeruginosa to proliferate.

     

Asparagine Hydroxylation is a Reversible Post-translational Modification

1. Download : Download high-res image (146KB)
2. Download : Download full-size image

Highlights

• •Quantitative mass spectrometric method to monitor PTM stability.
• •Pulse labeling reveals dehydroxylation of several asparagine hydroxylation sites.
• •Reversal of TNKS2, TRPV3 and HIF1a asparagine hydroxylation sites.
• •Protein dehydroxylation is an additional level of control for cellular signaling networks.

     

Identification of Tumor Antigens in the HLA Peptidome of Patient-derived Xenograft Tumors in Mouse

1. Download : Download high-res image (147KB)
2. Download : Download full-size image

Highlights

• •Sufficient tumor tissues are often unavailable large HLA peptidome discovery.
• •Using patient derived xenograft (PDX) tumors can overcome this limitation.
• •The large PDX HLA peptidomes expand significantly those of the original biopsies.
• •The HLA peptidomes of the PDX tumors included many tumor antigens.

     

Proteomic Analysis Reveals a Role for RSK in p120-catenin Phosphorylation and Melanoma Cell-Cell Adhesion

1. Download : Download high-res image (164KB)
2. Download : Download full-size image

Highlights

• •BioID reveals the proximity partners of RSK family members.
• •All RSK isoforms associate with and phosphorylate p120ctn on Ser320.
• •RSK negatively regulates adherens junctions and reduces cell-cell adhesion.
• •p120ctn phosphorylation plays a role in the reorganization of proximity partners.

     

Integrative Metabolic Pathway Analysis Reveals Novel Therapeutic Targets in Osteoarthritis

1. Download : Download high-res image (221KB)
2. Download : Download full-size image

Highlights

• •SILAC-based protein quantification of OA hBMSCs undergoing chondrogenesis.
• •Spatially-resolved metabolomics by MSI of hBMSCs in chondrogenic differentiation.
• •Differential metabolic pathways involved in OA compared to control hBMSCs.
• •UDP-glucuronic acid/UDP-GlcNAc synthesis is decreased in chondrogenic OA hBMSCs.

     

Quantitative Proteomics Links the LRRC59 Interactome to mRNA Translation on the ER Membrane

1. Download : Download high-res image (272KB)
2. Download : Download full-size image

Highlights

• •Identification of subcellular protein interactomes via proximity labeling and quantitative multiplexed proteomics.
• •SEC61β and RPN1 interactomes overlap with translocon-associated protein networks.
• •SEC62 interacts with redox-linked proteins and ER luminal chaperones.
• •LRRC59 directly interacts with mRNA translation factors and SRP machinery on the ER.

     

Chemical Genetics of AGC-kinases Reveals Shared Targets of Ypk1, Protein Kinase A and Sch9

1. Download : Download high-res image (245KB)
2. Download : Download full-size image

Highlights

• •Acute inhibition of growth-regulatory AGC-kinases Sch9, PKA and Ypk1.
• •Phospho-proteomic profiling of 6373 phsopho-sites.
• •Ypk1 regulates phospho-sites in RRxS/T-context and functionally overlaps with PKA.
• •Ypk1 and PKA activate trehalase activity of Nth1.

     

An Interaction Network of RNA-Binding Proteins Involved in Drosophila Oogenesis

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

Highlights

• •Label-free and dimethyl labeling MS analysis of 6 RBPs from Drosophila ovaries.
• •Functionally related RBPs show overlapping proteomes.
• •Selective co-purification of splicing factors and translational regulators.
• •Validation of 26 novel interactions by co-immunoprecipitation.

     

Next-generation Interactomics: Considerations for the Use of Co-elution to Measure Protein Interaction Networks

1. Download : Download high-res image (64KB)
2. Download : Download full-size image

Highlights

• •Co-elution stands out as a global interactome mapping method.
• •Benefits include all-to-all protein analysis and measurement of interactome perturbations.
• •Different separation, quantification and bioinformatic strategies are available.
• •Design considerations depend largely on system under study.