ABSTRACT: LD3 knock out cells were generated in HEK293T and HMC3 cells. Proteomics was done to test if they have any significant changes in the abundance of proteins that metabolize sugar lipids like gangliosides.
Project description:This part of the data submission of PXD046505. LD3 knock out cells were generated in HEK293T and HMC3 cells. Proteomics was done to test if they have any significant changes in the abundance of proteins that metabolize sugar lipids like gangliosides.
Project description:Proteomic analysis of peptides in close association to PacL1 under replete metal conditions (Sauton’s media), in Mycobacterium Tuberculosis (Erdman strain).
Project description:µ-proteins (≤ 70 amino acids) have important and often essential roles in all kingdoms of life, including cell motility, regulation of membrane transport and as transcription factors. In the halophilic archaeon and model system Haloferax volcanii a significant number of µ-proteins were predicted to be zinc finger proteins. Here we used mass spectrometry-based proteomics to systematically investigate the impact of single gene deletions of 19, previously uncharacterized, zinc finger µ-proteins on H. volcanii grown in glycerol media. We employed a state-of-the-art dia-PASEF acquisition strategy, detecting over 3400 proteins across the 19 deletion strains and the wild-type. The comprehensive proteome coverage enabled a systematic analysis of proteome remodeling. We found that in 11 out of the 19 mutants the proteome remodeling involved proteins annotated to play a role in cell motility, matching swarming and cell growth phenotypes we observed for these strains. Taken together, our data provide the most comprehensive proteome coverage of H. volcanii to date, and the effect of 19 different zinc-finger µ-proteins deletion strains on the proteome of this organism. The combined data provide a valuable resource for future research in the field.
Project description:A microfluidics technology was implemented to the immunoaffinity purification process of MHC peptides in Ligandomics/Immunopeptidomics. The thus purified HLA peptides were analysed by LCMS with the nanoElute LC and TimsTOF Pro Mass Spectrometer from Bruker. The aim of the microfluidics implementation was to improve the sensitivity and robustness while also reducing antibody and other material requirements in the immunoaffinity purification protocol.
Project description:We employed PeptiCHIP Immunopeptidomics to profile tumor associated antigens (TAA) actively targeted by tumor specific T cells by exploiting the trogocytosis effect, whereby antigen presenting cells (APCs) nibble portions of the cognate T cell containing the TCR. The antigen presenting cells were then processed by Immunoaffinity purification by peptiCHIP to identify the relevant HLA-I peptides by LCMS on the Bruker Tims TOF Pro instrument.
Project description:The amnion, an essential extra-embryonic tissue in mammalian embryos, is thought to provide crucial signaling, structural and nutritional support during pregnancy. Despite its pivotal importance, studying primate amnion formation and function has been hampered by the lack of accurate in-vitro models. Here, we present a human embryonic stem cell-derived 3D model of the post-gastrulation amnion (PGA) that faithfully recapitulates extra-embryonic development up to 4-weeks post-fertilization closely mimicking the functional traits of the human amniotic sac. PGAs self-organize forming the amnion and the yolk sac and are surrounded by extra-embryonic mesoderm, which forms a connecting stalk. Using PGAs, we show that GATA3 is required and sufficient for amniogenesis and reveal an autoregulatory feedback loop governing amnion formation, whereby extra-embryonic signals promote amnion specification. The reproducibility and scalability of the PGA system, with its precise cellular composition and structural integrity, opens new avenues for investigating embryo-amnion interactions beyond gastrulation and offers an ideal platform for large-scalegenetic, pharmacological, and biomechanical studies.
Project description:We used a streamlined pipeline for the generation of personalized cancer vaccines starting from the isolation and selection of the most immunogenic peptide candidates expressed on the tumour cells and ending in the generation of efficient therapeutic oncolytic cancer vaccines. We used MHC-I immunoaffinity purification in a murine colon tumor model from CT26 cells. The selection of the target candidates was then based on two separate approaches: RNAseq analysis and HEX software.
Project description:Whole brain tissue proteomics from rat models of cerebral small vessel disease and Alzheimer's disease, including the rTg-DI model of Cerebral Amyloid Angiopathy (CAA) Type-1, the rTg-D model of CAA Type-2 with both hemizygous and homozygous animals, and the TgSD-AD model of Alzheimer's Disease.