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Home Page: https://scp.slavovlab.net/plexDIA
Multiplexed data-independent acquisition (plexDIA) for increasing proteomics throughput. The code is distributed by an MIT license.
Home Page: https://scp.slavovlab.net/plexDIA
Hi,
Just wondering if plexDIA can be used for TMT labeled samples!
Thanks,
Sudip
Hi,
I'm a little unclear about the actual processing of plexDIA data. Is it fully incorporated in DIA-NN or do you have to run your script after DIA-NN analysis? if so, on what files and what settings in DIA-NN?
Thanks!
David.
Dear Pro. f Slavov:
My name is Ningzaizia and from China.
Now I have a question for plexDIA by using your paper data (MassIVE MSV000088302 Files) to test the plexDIA workflow in my Lab. I load your pipeline (Report.auto.pipeline) and raw data (eJD905.raw,eJD906.raw,eJD907.raw) into the DIANN(1.8.1) and run successfully.
However, my results just contain 14 files, please read the screenshot (diaNN-result), and It does not contain channels-relative files. Importantly, I cannot tell which protein comes from which channel, please read the screenshot (diaNN-result2).
These parameters I set in the DIA-NN is coincident with the Report.auto.pipeline, apart from modifying the path of raw data, fasta file and output.
Iโm not sure where I went wrong. Can you help me troubleshoot?
Hi, cell ids in Proteins_SC.txt are different with those in Meta_SingleCell.tsv. Can you help me with the cell cycle info of each single cell in Proteins_SC.txt file? How to match these cell id with Meta file's cell id?
Hi, as I was trying to replicate the data analysis with your code it appears I cannot find the report file labelled mTRAQ_DDA_PGs in the MassIVE MSV000089093 Files database.
Thanks
-Jonathan
Hi Drs. Derks and Slavov,
In your tutorial, I noticed that 'peak height' was advised to set in quantification strategy field. I'm wondering is there any particular reason for choosing it, how it would impact the data?
Best,
Weixian
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