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ProteomicsHuman Immunoglobulin Repertoire-Guided Immunogen Design Targeting HIV V2-Apex Broadly Neutralizing Antibody Precursors
Broadly neutralizing antibodies (bnAbs) to the HIV envelope (Env) V2-apex region are important leads for HIV vaccine design. Most V2-apex bnAbs engage Env with an uncommonly long heavy chain complementarity-determining region 3 (HCDR3), suggesting that rarity of bnAb precursors poses a challenge for...
ORGANISM(S): Homo sapiens (Human) Human immunodeficiency virus 
2023-03-11 | PXD033766 | Pride
Hiv antibodies Aids vaccines Structural vaccinology Immunoinformatics 
ProteomicsIntercepting IRE1 Kinase-FMRP Signaling Prevents Atherosclerosis Progression
Fragile X Mental Retardation protein (FMRP), widely known for its role in hereditary intellectual disability, is an RNA-binding protein (RBP) that controls translation of select mRNAs. We discovered that endoplasmic reticulum (ER) stress induces phosphorylation of FMRP on a site that is known to enh...
ORGANISM(S): Homo sapiens (Human) Escherichia coli 
2022-02-15 | PXD030594 | Pride
Cholesterol homeostasis Translational regulation Kinase-substrate Atherosclerosis Efferocytosis 
ProteomicsQuantitative proteomic analysis reveals JMJD6 and DNAJB11 as endogenous substrates of E3 ligase RFFL
Immunoprecipitation experiments using anti-RFFL antibody. Samples were loaded in technical duplicates in EvoTips, and chromatographic separation was done on an in-house column and the 30 samples per day (SPD) method on Evosep One system (Evosep). Peptides were detected and fragmented using timsTOF P...
ORGANISM(S): Homo Sapiens (ncbitaxon:9606) 
2025-01-16 | MSV000096868 | MassIVE
ProteomicsQuantitative proteomic analysis reveals JMJD6 and DNAJB11 as endogenous substrates of E3 ligase RFFL
A549 cells were washed with ice-cold PBS three times and harvested using mechanical scraping. Cell pellets were processed as described previously (Marathe et al., 2021). Briefly, the pellet was re-solubilized in Urea-Thiourea Buffer (6M Urea, 2M Thio-urea in Tris-Cl) containing protease inhibitor co...
ORGANISM(S): Homo Sapiens (ncbitaxon:9606) 
2025-01-15 | MSV000096861 | MassIVE
ProteomicsProteomics analysis of nuclear envelope, cytoplasmic membrane and nuclear contents fractions isolated from mesenchymal stem cells, adipocytes and myocytes
We used shotgun proteomics to analyze three subcellular fractions isolated from mesenchymal stem cells and from differentiated adipocytes and myocytes: nuclear envelopes (NEs), cytoplasmic membranes and nuclear contents. The proteomics data were analyzed by a NSAF-based scoring system to calculate...
ORGANISM(S): Mus Musculus (ncbitaxon:10090) 
2018-11-27 | MSV000083166 | MassIVE
ProteomicsComparative membrane proteomics reveals diverse cell regulators concentrated at the nuclear envelope
The nuclear envelope (NE) is a subdomain of the ER with a distinctive protein composition that underpins its role in nuclear compartmentalization. To expand an understanding of NE functions, we refined methods to reveal low abundance transmembrane (TM) proteins concentrated at the NE. De facto, th...
ORGANISM(S): Mus Musculus (ncbitaxon:10090) 
2023-01-25 | MSV000091154 | MassIVE
ProteomicsAn ultrasensitive method for analysis of viral spike N-glycoforms
Viruses can evade the host immune system by displaying numerous glycans on their surface "spike-proteins" that cover immune epitopes. We have developed an ultrasensitive "single pot" method to assess glycan occupancy and the extent of glycan processing from high-mannose to complex forms at each N-gl...
ORGANISM(S): Bg505 Sosip.664 Md39 Bg505 Sosip.664 Homo Sapiens (ncbitaxon:9606) 
2021-05-12 | MSV000087414 | MassIVE
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