Proteomics

Protein Abundance Search Design

1. User has combined protein abundance - like file (combined_protein.tsv, https://fragpipe.nesvilab.org/docs/tutorial_fragpipe_outputs.html#combined_proteintsv)

• PK: This may not be the exact output, Leo, who made FragPipe, sent us a related, but different version of this output
• CT: This is the format we should expect (except we will request the row names are gene not gene|uniprot_id):

2. We create a Python cli tool/api library function, which submits a batch request to filter the protein abundance file using a Bystro annotation.

• This requires the user to first authenticate using our existing Python API for authentication
• The batch submission requires:
  • user id
  • path to protein abundance file or multipart file upload stream of the protein abundance file if local (in v1 ok to support 1 only)
  • the job id
  • basename for the output
  • the query string query

3. The job is processed through our API server, which results in a beanstalkd submission to our cluster, where the filtering of the protein abundance file happens, resulting in a new protein abundance file written to disk, and a path for that file returned to the user.

• We re-use the code (duplication is OK for v1) from bystro/search/save/handler.py for handling the scrolling through annotation index
• We pull down the annotation index as in bystro/search/save/handler.py, and add the protein abundance values
• We persist these values on EFS, return a path to the results

4. We create a Python CLI/API tool/library function to allow the user to pull down the filtered protein abundance results using the user id and the job basename.