slavovlab/plexdia

Multiplexed data-independent acquisition (plexDIA) for increasing proteomics throughput. The code is distributed by an MIT license.

plexdia's Issues

plexDIA for TMT labelled sample

Hi,
Just wondering if plexDIA can be used for TMT labeled samples!

Thanks,
Sudip

plexDIA in DIA-NN

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.

Cannot distinguish information from each channel for plexDIA

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.
I’m not sure where I went wrong. Can you help me troubleshoot?

Cell cycle info of each single cell

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?

mTRAQ_DDA_PGs file

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

Quantification strategy

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