I recently met you at LMB where you gave a wonderful talk on PsychENCODE data analysis.
You mentioned that there were MS datasets in the PsychENCODE. I am unable to find it. Is it possible for you to point me to that or point me to someone who may know about this? Is it possible for you to point out the MS data in the PschENCODE datasets?
Could you please explain a little more about what dataset you need?
I am looking for Mass Spec data sets in PsychEncode. Mark mentioned that MS analysis were done for some samples. I wonder whether you could help me in identifying them?
I just checked with our DCC team and currently we don’t have any Mass Spec data available for public sharing.
What is dcc team? I was given to believe from the publications that this data was available along with others for analysis. i would not have asked otherwise. is there a way i can reach out to any group among your dcc team that has this data to see whether i can formally collaborate with them? Can you kindly let me know who may be the best person to ask for the details of the group that may have the MS datasets? I am looking for MS data (even if it is published) from any of the samples that were used in the Psychencode project.
I am willing to collaborate and share authorships with the scientists who generated these datasets?
Would it be possible for you to point out to any one whom you may know who may have this dataset (published or unpublished)?
I have contacted the group that is generating the Mass Spec data. Are you specifically interested in proteomics related to donors with neuropsychiatric disorders? We (Sage Bionetworks) also function as the data coordination center for the NIA funded Accelerating Medicines Partnership – Alzheimer’s Disease (AMP-AD). There are a variety of studies in AMP-AD with Mass Spec proteomics on post mortem brain tissue, that also have other genomic data such as WGS and RNAseq. Included in that is the Religious Orders Study and Memory and Aging project (ROS/MAP) from the Rush Alzheimer’s Disease Center. See here for information on the cohorts. There will be TMT labeled MS on ~400 ROS/MAP donors released this fall.
Thank you for getting in touch with me. Thank you for your pointer. Indeed, we will be interested in the Alzheimer’s samples (all the three WGS, RNAseq and Proteomics).
I will write a separate note to you on this.
At the moment, we are looking for MS samples from donors with neuropsychiatric disorders.
Actually, my lab is doing something very similar as well, validating novel ORFs identified from our third generation sequencing, and riboseq data.
If you use other approaches that we did not use yet, or with some special goals more than just validating ORFs in brain, I will be happy to collaborate.
I have two students/collaborators on this.
Is it possible for me to make a quick call?
…(resolved via phone call on Jul 9, 2019)…