TMEM175-LAMP1 crosslinking proteomics
Ontology highlight
ABSTRACT:
INSTRUMENT(S): Orbitrap Fusion Lumos
ORGANISM(S): Homo Sapiens (ncbitaxon:9606)
SUBMITTER: 
Jiyuan Zhang Youxing Jiang
PROVIDER: MSV000091672 | MassIVE | Mon Apr 10 08:43:00 BST 2023
REPOSITORIES: MassIVE
Similar Datasets
Project description:Pull-down of poly(A)-mRNA cross linked proteins using two cross-linking methods (conventional cross-linking and PAR-cross-linking) to identify all mRNA-binding proteins (GO:0003729). The provided data is quantitative proteomic data for comparison of cross-linking and control samples.
2012-08-14 | E-MTAB-869 | biostudies-arrayexpress
Project description:Thymidine glycol (Tg) is the most prevalent form of oxidatively induced pyrimidine lesion in DNA. Tg can arise from direct oxidation of thymidine in DNA. In addition, 5-methyl-2¢-deoxycytidine (5-mdC) can be oxidized to 5-mdC glycol and its subsequent deamination also yields Tg. However, its distribution in the human genome remains unknown. Here, we presented a DNA-protein cross-linking sequencing (DPC-Seq) method for genome-wide mapping of Tg in human cells. Our approach is capitalized on the specificity of a DNA glycosylase, i.e., NTHL1, for the covalent labeling, as well as DPC pulldown, SDS-PAGE fractionation, and membrane transfer for highly efficient and selective enrichment of Tg-bearing DNA. By employing DPC-Seq, we detected thousands of Tg sites in HEK293T cells and the isogenic NTHL1 and NEIL1 double knock out cell lines. We found that Tg is depleted in genomic regions associated with active transcription, but enriched at the nucleosome-binding sites, especially at heterochromatin sites. Collectively, our approach allows for comprehensive analysis of Tg in the human genome and provides a robust tool for future functional studies of Tg in DNA. It can be envisaged that the method can be adapted for mapping other modified nucleosides in genomic DNA in the future.
2021-09-18 | GSE184204 | GEO
Project description:Epitope mapping studies aim to identify the binding sites of antibody-antigen interactions to enhance the development of vaccines, diagnostics and immunotherapeutic compounds. However, mapping is a laborious process employing time- and resource-consuming ‘wet bench’ techniques or epitope prediction software that are still in their infancy. For polymorphic antigens, another challenge is characterizing cross-reactivity between epitopes, teasing out distinctions between broadly cross-reactive responses, limited cross-reactions among variants and the truly type-specific responses. A refined understanding of cross-reactive antibody binding could guide the selection of the most informative subsets of variants for diagnostics and multivalent subunit vaccines. We explored the antibody binding reactivity of sera from human patients and Peromyscus leucopus rodents infected with Borrelia burgdorferi to the polymorphic outer surface protein C (OspC), an attractive candidate antigen for vaccine and improved diagnostics for Lyme disease. We constructed a protein microarray displaying 23 natural variants of OspC and quantified the degree of cross-reactive antibody binding between all pairs of variants, using Pearson correlation calculated on the reactivity values using three independent transforms of the raw data: (1) logarithmic, (2) rank, and (3) binary indicators. We observed that the global amino acid sequence identity between OspC pairs was a poor predictor of cross-reactive antibody binding. Then we asked if specific regions of the protein would better explain the observed cross-reactive binding and performed in silico screening of the linear sequence and 3-dimensional structure of OspC. This analysis pointed to the C-terminal helix of the structure as a major determinant of type-specific cross-reactive antibody binding. We developed bioinformatics methods to systematically analyze the relationship between local sequence/structure variation and cross-reactive antibody binding patterns among variants of a polymorphic antigen, and this method can be applied to other polymorphic antigens for which immune response data is available for multiple variants.
2013-04-12 | GSE45996 | GEO
Project description:Transcriptome-wide profiling of RNA-binding by IGF2BP1 and IGF2BP3 in the K562 cell line. Binding sites are characterized by T-to-C cross-linking mutations, depth and location on transcript
2020-02-10 | GSE138063 | GEO
Project description:Transcriptome-wide profiling of RNA-binding by four RBPs in v-Abl transformed 220-8 pro-B mouse cell line. Binding sites are characterized by T-to-C cross-linking mutations, depth, location on transcript, and overlap/exclusivity across different RBPs.
2019-06-27 | GSE98465 | GEO
Project description:Mass spectrometry analysis in combination with the site-specific chemical cross-linking has emerged as a powerful method in study of three-dimensional structure of protein complex and in mapping of protein-protein interactions (PPIs). Even though in vitro cross-linking experiments have been widely applied to investigate the specific interactions of a bait protein and its targets, the measurement of in vivo protein tertiary structure and PPIs has been problematic and strenuous due to the dynamic nature of the biological systems and a lower number of cross-linked peptides that can be isolated via MudPIT (Multidimensional Protein Identification Technology) for mass spectrometry analysis. Using Arabidopsis thaliana as a model multicellular eukaryotic organism, we have attempted to develop an improved in vivo chemical cross-linking and mass spectrometry (or IPXL-MS) workflow, which aims at optimizing the in vivo cross-linking conditions, establishing of a MudPIT procedure for enrichment of cross-linked peptides, and developing an integrated software program to identify the in planta chemical cross-linked peptides, by which three pairs of in vivo cross-linked peptides of high-confidence has been identified twice from two independent biological replicates. This work has demarked a beginning of alternative proteomic approach in study of in vivo protein tertiary structure and PPIs in higher plants. This in vivo cross-linking approach may be applied into other model multicellular organisms, such as mouse, for molecular systems biological research.
2016-06-28 | PXD003658 | Pride
Project description:In this study, we used bottom-up proteomics and cross-linking MS (XL-MS) to study the composition and structure of soluble membrane attack complex (sMAC). For bottom-up proteomics sMAC was digested using trypsin and analyzed on Orbitrap Fusion Lumos. For the cross-linking analysis sMAC was cross-linked using DMTMM or DSS. The cross-linked proteins were digested using trypsin and the data was acquired using an Ultimate 3000 system coupled on-line to an Orbitrap Fusion. Proteomics raw data was searched using MaxQuant and cross-linking raw data was searched using pLink.
2021-03-25 | MSV000087092 | MassIVE
Project description:Epitope mapping studies aim to identify the binding sites of antibody-antigen interactions to enhance the development of vaccines, diagnostics and immunotherapeutic compounds. However, mapping is a laborious process employing time- and resource-consuming M-bM-^@M-^Xwet benchM-bM-^@M-^Y techniques or epitope prediction software that are still in their infancy. For polymorphic antigens, another challenge is characterizing cross-reactivity between epitopes, teasing out distinctions between broadly cross-reactive responses, limited cross-reactions among variants and the truly type-specific responses. A refined understanding of cross-reactive antibody binding could guide the selection of the most informative subsets of variants for diagnostics and multivalent subunit vaccines. We explored the antibody binding reactivity of sera from human patients and Peromyscus leucopus rodents infected with Borrelia burgdorferi to the polymorphic outer surface protein C (OspC), an attractive candidate antigen for vaccine and improved diagnostics for Lyme disease. We constructed a protein microarray displaying 23 natural variants of OspC and quantified the degree of cross-reactive antibody binding between all pairs of variants, using Pearson correlation calculated on the reactivity values using three independent transforms of the raw data: (1) logarithmic, (2) rank, and (3) binary indicators. We observed that the global amino acid sequence identity between OspC pairs was a poor predictor of cross-reactive antibody binding. Then we asked if specific regions of the protein would better explain the observed cross-reactive binding and performed in silico screening of the linear sequence and 3-dimensional structure of OspC. This analysis pointed to the C-terminal helix of the structure as a major determinant of type-specific cross-reactive antibody binding. We developed bioinformatics methods to systematically analyze the relationship between local sequence/structure variation and cross-reactive antibody binding patterns among variants of a polymorphic antigen, and this method can be applied to other polymorphic antigens for which immune response data is available for multiple variants. Antibody profiling was performed on sera from Borrelia burgdorferi infected and non-infected humans and Peromyscus leucopus rodents against 23 variants of the surface protein OspC . For infected human serum samples, the OspC type of the infecting B. burgdorferi strain is unknown; for experimentally-infected P. leucopus serum samples, it is known. Of human serum samples, 55 were from infected individuals and 25 from naive controls. Of P. leucopus serum samples, 23 were from infected individuals and 7 were from naive controls.
2013-04-12 | E-GEOD-45996 | biostudies-arrayexpress
Project description:The cross-linking mass spectrometry raw data of NMNAT and amyloid client proteins including α-syn, K19, Aβ40, and IAPP.
2022-02-11 | PXD031653 |
Project description:Cross-linking mass spectrometry data of cross-linked antibody to human leukocyte antigen (HLA-A*11:01). For antibodies 2E3, 1E3 and 3H10.
2023-11-23 | PXD038059 | JPOST Repository