The basic process of GFS includes 4 major steps:

1. Digest the genome into trypsin cleaved peptides
2. Create sequence tags from our MS/MS data
3. Reduce the list of genome peptides based on masses
4. Analyze the peptide list and sequence tags with HMM_Score

For next week:

• have some performance data to show where the program is taking most time
• Have some program output along with some real data to compare.

Future work: Generate probable MS/MS that corresponds to a protein where we know its locus.