Dear Support Team,
I am working on the DDA-LFQ proteomics data of the MSBB cohort. And I am looking for the "**evidence.txt**" file, which is part of the MaxQuant output. I would need to do the QC in MSstats v4.0. Here is the link to the directory: https://www.synapse.org/Synapse:syn6100410
Could anyone help me to locate this **evidence.txt** file? If it is not there yet, could someone upload it to Synapse? Many thanks in advance!
Created by Gerardo Garcia gerardo_garcia Yes, thanks to Duc for making me aware of this request and finding that I was the one who did the search 9 years back!
The files are uploading via SynapseUtils in R (tens of GB), will take much of today. But I have already shared the repo with you, Gerardo, and the Sage admin and curation accounts.
https://synapse.org/LFQsinaiBM10 is the alias for the repo at https://www.synapse.org/Synapse:syn61847071
Best regards. Dear Dr. Dammer, @edammer
Glad to hear that you have the data archived! Thank you so much!
I have been trying different data analysis methods/pipelines in R for LFQ proteomics. Most of them require not only the "proteinGroups.txt", but "evidence.txt" or "peptides.txt" as well. You really helped me a lot.
@ductyler Thank you, too, Duc!
I am the person who performed the search in December 2015 at Emory where the proteomics were generated. I have the full MaxQuant output folder (txt) and am uploading it to a repo. I will post the synID once it completes and is public later today. Thanks for letting us know. I am looking forward! Thanks! They won't have the full folder output as the Proteomics was performed at Emory. I'll ask the team here at Emory if they have the folder. Dear Duc, @ductyler
Many thanks for your prompt reply!
Yes, if you could help to find the whole MaxQuant output folder, that would be even better! This is the minimum set of input files needed: evidence.txt, peptides.txt, proteinGroups.txt. Also, the parameters.txt/mqpar.xml and summary.txt files are useful as well, in order to document the configuration and result summary.
Meanwhile, I sent emails to the authors of the original publication entitled ?The Mount Sinai cohort of large-scale genomic, transcriptomic and proteomic data in Alzheimer's disease? (Scientific Data, 2018 doi: 10.1038/sdata.2018.185), and asked for the same files (MaxQuant output folder). However, I haven't got their reply yet.
Thanks in advance for your time and efforts! HI Gerardo,
I don't think the team every uploaded the evidence.txt file. This is from a while ago so it might not be something I can locate very readily. I'll ask the team to see if they have a backup of the maxquant output folder.
Best,
Duc Hi @lheath,
I do appreciate your kind support very much.
Yet I haven't got any updates from Duc @ductyler. Could you please remind him again about this thread? The "evidence.txt" file is essential for my analysis.
Thanks again!
Hi @gerardo_garcia,
I am tagging the data contributor to see if they can supply this file, since I do not believe it was ever uploaded to synapse.
Hi Duc @ductyler, do you have the 'evidence.txt' file for this [MSBB proteomics](syn20801227) data? If you do have it, could you please upload it [here](syn6100410), or direct the user to where it might be found?
Thanks!
Laura
Drop files to upload
syn6100410_MSBB_Proteomics Data_DDA-LFQ_MaxQuant output_evidence.txt page is loading…