Today I worked on the DIA protocol and now have an exported report that I think I can start using with MS Stats. Still waiting on some input from Emma, but details are below:
DIA Protocol
I split the protocol into two parts, so far:
They are still works in progress, and I’ll add more details to them later.
What I have to show:
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OWL folder devoted to this new protocol and the outputs:
scaphapoda/grace/2015-Cgseed-DIA -
new .zip SkylineDaily file: 20181210-2015Cgseed-DIA.sky.zip
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SkylineDaily report file: 20181210-SkylinetoMSStats-report.csv
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EncylopeDIA suite output data file: 20181210-Cg-quant-reps.elib.peptides.txt
Next steps:
Use Yaamini’s notebook as a guide for using MSStats to analyze the SkylineDaily report .csv.
However, I still need to hear back from Emma, so I’ll hold off on the MSStats until she has time to take a look at the report .csv.