Hello. I have a question about the sample ID for the Diverse Cohorts Proteomics Data I tried to add sample information to final_traits_to_be_published_frontal.xlsx and final_traits_to_be_published_temporal.xlsx (syn55249984 and syn55249983) using AMP-AD_DiverseCohorts_biospecimen_metadata.csv (syn51757645), AMP-AD_DiverseCohorts_individual_metadata.csv (syn51757646) and AMP-AD_DiverseCohorts_assay_TMTproteomics_metadata.csv (syn53185805). However, when I matched the IDs of final_traits_to_be_published_frontal.xlsx and final_traits_to_be_published_temporal.xlsx (syn55249984 and syn55249983) with batchChannel of AMP-AD_DiverseCohorts_assay_TMTproteomics_metadata.csv (syn53185805) and the specimenID of AMP-AD_DiverseCohorts_biospecimen_metadata.csv (syn51757645), I noticed that there is a discrepancy between their individualIDs. Could you please provide me with the correct information? My thinking is that the channel information seems to be off. Thank you for your cooperation. Misato

Created by Misato Kaishima K-Misato
@ryaxley @Fatimasf Could you please let us know about the question from @misato.kaishima? Thanks!
Hi @Fatimasf and @ryaxley The final_traits_to_be_published_frontal.xlsx (syn55249984) contains 26 individual IDs that are not present in the metadata file AMP-AD_DiverseCohorts_biospecimen_metadata.csv (syn51757645). Could you please advise on how to link information for these individuals? Additionally, 4 IDs in thefinal_traits_to_be_published_frontal.xlsx (syn55249984) have blank entries in the individuals ID column. Could you also provide this information? Here are the unidentified individuals IDs: 1494 1503 1509 1511 1513 1522 1533 1555 1578 1593 1604 1626 1661 1669 1674 1682 1686 1690 1700 1705 1709 1721 1722 1733 1736 1759 Here are the IDs with blank entries in the individuals ID column: mssm_b10.127C mssm_b03.131N mssm_b01.130N mssm_b05.128C Best, Misato
Hi @Fatimasf, I have confirmed that your paper has been published. Could you please let me know the conclusion regarding the issue with the sample information? Thank you very much for your time and assistance. Best, Misato
Fatemeh, Thanks for your reply. So if I analyze raw proteome data, I should not use batch.channel ID to link sample information to proteome values? I would appreciate it if you could let me know when the final trait files are uploaded. I appreciate your cooperation. Best, Misato
Misato, Thanks for raising this concern. I can see what you are saying now. For each sample, we have an IndividualId -which will help you to map them to synapse traits- and ProjID/ samplesID. I think for Rush samples and a few Emory-Sinai samples we included sampleIDs instead of individual IDs in the syn55249984 file. My recommendation would be using the IndividualIDs in the metadata.csv file, since it maps all the samples to Synapse traits. I will revise the final trait files, soon. Let me know if this solves the issue for you. Best, Fatemeh
Hi Fatemeh, As far as I can tell, all of the samples seem to have been swapped. It may not just be an issue with the channels, but I’m not certain what the underlying issue is. Misato
Misato, Thanks for sharing your feedback. If I am understanding correctly, you are saying that C and N in all channels are exchanged, is that correct? Or are there specific samples assigned to different individual IDs? Fatemeh
Thanks for the reply. Here are all the samples. I think the C and N of the channel are interchanged. Best, Misato
Hi, Could you share with me which samples had discrepancies in individual IDs? Best, Fatemeh
Hi @ryaxley , Thanks for your support! Hi @nseyfried and @Fatimasf , Nice to meet you. I am currently analyzing the proteomics data from the AMP-AD Diverse Cohort and have noticed what appears to be an error in the dataset. I suspect that the sample information in the analysis data posted on bioRxiv may not match the sample information in the raw data. Could you kindly verify this for me? I’ve provided more details in the message above. Thank you in advance for your assistance. Best, Misato
Hi @K-Misato, Thanks for reaching out about the issue with matching the sample IDs in the proteomics data. The best person to assist with this is Nick Seyfried (@nseyfried) at Emory University, the main contact for the proteomics dataset. Fatemar Seifar (@Fatimasf) may also be a good person to contact. They'll have the detailed insights needed to address the discrepancies you’re seeing. Please connect with them directly for the quickest resolution. We look forward to supporting any data, metadata, or documentation updates in the portal if needed. If you need help connecting with Nick or further assistance, just let us know! Best, Rich @ryaxley
@SageCurators @abby.vanderlinden is there someone who can help @K-Misato with her question? Not sure if these are the right `@` names, but it would be very helpful. Thanks! Mike
Hello. Is there any progress on this question? I would appreciate it if you could let me know the status.

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