Dear AD Knowledge Portal team, I am trying to access the TMT proteomics data associated with the Jax.IU.Pitt_LOAD2 / Kotredes et al. 2024 study (DOI: 10.1002/alz.13828). I was able to locate the LOAD2 biospecimen metadata, which includes samples annotated as “TMT quantitation.” I also found candidate Synapse entries including: syn68635585, TMT Quantification syn62753315, proteomics Data View syn64731360, assay_proteomics_Jax.IU.Pitt_LOAD2.csv However, I have not been able to locate or download the actual protein abundance matrix or processed TMT quantification table. The dataset ID I initially accessed, syn53128146, appears to contain RNA-seq FASTQ files rather than proteomics data. Could you please point me to the correct Synapse ID for the processed LOAD2 TMT proteomics data, including the protein abundance matrix and any associated sample annotation files? Thank you very much for your help. Best regards, Shinwon Kang

Created by Shinwon Kang Syn1_kang
Hello, The three files in [syn68635585](https://www.synapse.org/Synapse:syn68635585) appear to be the only TMT abundance matrices we have for LOAD2. If you need raw/un-normalized data or a different level of processing, I think you will need to contact the author of the paper as they did not provide that data to us. For sample annotation files, merging the [assay](syn64731360), [biospecimen](syn63889172), and [individual](syn63888924) metadata files together should give you information about the mice and some technical variables like batch for each sample in the TMT matrices. Merge assay + biospecimen on the `specimenID` field, and then merge the result into the individual metadata on the `individualID` field. The `specimenID` is what the samples should be called in each TMT file. I hope that helps. Let me know if you have any more questions. Jaclyn

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