Proposed Analysis: Test Thermo Files run with LFQ-MBR workflow

[jharenza]

What are the scientific goals of the analysis?

To test the implementation of Fragpipe/MSFragger using the Label-free workflow.

What methods do you plan to use to accomplish the scientific goals?

https://github.com/Nesvilab/FragPipe/blob/develop/workflows/LFQ-MBR.workflow

Use MSFragger closed search for faster searching, fewer artifacts, opposed to open

Edit this to include:

• LysC digestion
• missed cleavages = 2
• minimum peptide length = 8
• precursor mass tolerance of 10 ppm
• fragment mass tolerance of 0.02 Da.

It may also be easier to create a new shell script for impact specifically.

I have uploaded the Normal CBM and 7316-922 raw proteomics files to s3://bti-private-us-east-1-prd-impact-trial/source/

What input data are required for this analysis?

Thermo RAW files, custom fasta, uniprot fasta

How long do you expect is needed to complete the analysis? Will it be a multi-step analysis?

half day

Who will complete the analysis (please add a GitHub handle here if relevant)?

@rjcorb

What relevant scientific literature relates to this analysis?

Please do not commit custom/output files, but instead, add the workflow to this code.