DIA Protocol Step 3a-b

[grace-ac]

QUESTION FOR 3A: do I just put the paths to these files in a .txt file and then upload that to GitHub?
Step 3a.

• The reference peptide list is in the folder "grace" on the desktop.
• The .mzML files are in downloads.

QUESTION FOR 3B: The link to the example doesn't work and I'm having a generally difficult time understanding what this step calls for. What is the mass spectrometry method file?
Step 3b

[kubu4]

QUESTION FOR 3A: do I just put the paths to these files in a .txt file and then upload that to GitHub?

Yes, paths to those files in a .txt file.

No, do not upload to GitHub.

QUESTION FOR 3B: The link to the example doesn't work and I'm having a generally difficult time understanding what this step calls for. What is the mass spectrometry method file?

I think this is the correct URL for the isolation scheme file: https://github.com/RobertsLab/project-oyster-oa/blob/master/analyses/DNR_PECAN_20170228/PECAN-inputs/2017-03-03-isolation-windows.csv

Please confirm prior to updating link in protocol, though.