How to Import Proteomics Data into EDD to Improve Biofuel Production Using the PCAP (Principal Component Analysis of Proteomics) Method.
This video will show a user how to import proteomics data. This specific example will look at how to improve limonene biofuel production in a bioengineered strain using PCAP - Principal Component Analysis of Proteomics)
You can redo this tutorial yourself by using these input files:
And here is the Jupyter notebook that uses the proteomics data from EDD to direct metabolic engineering:
The sample file for Experiment Description uses part IDs from the JBEI Public Registry. If the EDD instance is configured to use a different ICE repository, the strains will not be found. You may proceed with the tutorial by clicking the "Omit Strains" button on the warning message.
The sample file for GC-MS data is updated to use the PubChem format to identify measured metabolites. This format uses a case-insensitive prefix of cid: followed by the numeric identifier of the chemical on PubChem (the "Compound CID" entry). The format can optionally be followed by a colon and a name to assist in reading files later. In the screencast below at about the 1:34 mark, instead of selecting the second row as "Measurement Type", instead select the entire row as "PubChem CIDs" to instruct EDD to interpret the label cid:22311:Limonene as a PubChem reference instead of forcing a search on types that already exist in EDD.