Greetings,
Thank you for providing the MSBB dataset.
The folder related to my question is syn5759470.
I am hoping to work with the MSBB TMT Proteomics data. For this purpose I am looking for the final intensities ratio table for collected samples and analyzed by TMT method. These samples are from Human postmortem cortical tissues (Brodmann area 36 of parahippocampal gyrus). Raw files are available for all samples but I was wondering to have access to intensities ratio matrix (proteins * specimenID). I believe based on explanations in "Deep Multilayer Brain Proteomics Identifies Molecular Networks in Alzheimer?s Disease Progression" paper and also provided metadata file for TMT samples (syn21893060) this file should be available, so I was wondering if you let me know how can have access to this file.
Thanks,
Rasool
Created by Rasool Saghaleyni rasools Yes, sorry. Now everything works perfectly. Thanks again for following up on this issue.
Best,
Rasool Or, it looks like you have 2 accounts. Try by switching to the @rasools one There is a 'click wrap' statement where you agree to attribute data providers in publications. Did you click 'agree' on that? Only needs to be done once Dear @Mette , thank you very much for providing the data. But, now I lost my access to the whole MSBB project files. We recently submitted the DUC and got the confirmation. Would you please let me know if I need to submit the DUC again?
Thanks,
Rasool @rasools Please see [here for the data](https://adknowledgeportal.synapse.org/Explore/Data?QueryWrapper0=%7B%22sql%22%3A%22SELECT%20*%20FROM%20syn11346063%22%2C%22limit%22%3A25%2C%22offset%22%3A0%2C%22selectedFacets%22%3A%5B%7B%22concreteType%22%3A%22org.sagebionetworks.repo.model.table.FacetColumnValuesRequest%22%2C%22columnName%22%3A%22study%22%2C%22facetValues%22%3A%5B%22MSBB%22%5D%7D%2C%7B%22concreteType%22%3A%22org.sagebionetworks.repo.model.table.FacetColumnValuesRequest%22%2C%22columnName%22%3A%22assay%22%2C%22facetValues%22%3A%5B%22TMT%20quantitation%22%5D%7D%2C%7B%22concreteType%22%3A%22org.sagebionetworks.repo.model.table.FacetColumnValuesRequest%22%2C%22columnName%22%3A%22dataSubtype%22%2C%22facetValues%22%3A%5B%22normalized%22%5D%7D%5D%7D) We have followed up with the data contributor. Will get back to them again Dear @Mette, I was wondering have you received any update on this issue from data contributors? Thank you for following up. We will follow up with the data contributor Thanks for the reply.
I am aware of database-search results files for each sample. Actually, I am looking for the final condensed table of all samples, containing proteins as rows, samples as columns and filled by (normalized and corrected for batch, sex, pmi, etc) intensity ratios for each protein in its corresponding sample. Like what has provided for RNA-seq data here: syn7391833 but for TMT proteomics data.
Since for downstream analysis of TMT proteomics data this table is necessary, I was wondering if this table could be shared?
Thanks,
Rasool Are you referring to the search results? If you go to the ADKnowledge Portal, see this data query of all the processed search results files [for the MSBB study](https://adknowledgeportal.synapse.org/Explore/Data?QueryWrapper0=%7B%22sql%22%3A%22SELECT%20*%20FROM%20syn11346063%22%2C%22limit%22%3A25%2C%22offset%22%3A0%2C%22selectedFacets%22%3A%5B%7B%22concreteType%22%3A%22org.sagebionetworks.repo.model.table.FacetColumnValuesRequest%22%2C%22columnName%22%3A%22study%22%2C%22facetValues%22%3A%5B%22MSBB%22%5D%7D%2C%7B%22concreteType%22%3A%22org.sagebionetworks.repo.model.table.FacetColumnValuesRequest%22%2C%22columnName%22%3A%22dataType%22%2C%22facetValues%22%3A%5B%22proteomics%22%5D%7D%2C%7B%22concreteType%22%3A%22org.sagebionetworks.repo.model.table.FacetColumnValuesRequest%22%2C%22columnName%22%3A%22assay%22%2C%22facetValues%22%3A%5B%22TMT%20quantitation%22%5D%7D%2C%7B%22concreteType%22%3A%22org.sagebionetworks.repo.model.table.FacetColumnValuesRequest%22%2C%22columnName%22%3A%22dataSubtype%22%2C%22facetValues%22%3A%5B%22processed%22%2C%22metadata%22%5D%7D%5D%7D). Click on the 'Study' link for any of the files and see the MSBB study page with the study and methods description, and all study data and metadata under the study tab
Drop files to upload
Is the final intensities ratio table for MSBB TMT proteomics dataset available? Synapse ID: syn5759470 page is loading…