:cake: It’s not as easy as pie :cake:

PECAN matches the peptides in DNR samples to the peptides in the entire C. gigas proteome. It took me a few days to prepare the following inputs:

• Convert .raw files to .mzML files
• In Silico Tryptic Digest of C. gigas proteome and QC peptides
• Path files for converted .mzML files and background proteome
• Isolation window file

Because Laura’s run of all her samples will take 12 days, we decided that it would be best for me to first run five oyster sample files. Then, I can proceed with analyzising them on Skyline and concurrently run other samples with PECAN.

I then ran pecanpie on Roadrunner. It worked! Here’s a picture of it going:

And here’s the Jupyter notebook detailing my work.