Why everyone should de novo?

When I was doing some house cleaning on old documents, I found a few slides created 5 years ago about why de novo sequencing should be included in all research workflows. Most of these things still stay true today and it aligns very well with PEAKS development. I'd like to share them here.

Problem:

“The organism I’m studying isn’t in any of the databases.”

Solution:

De novo sequencing is the only way to go.

Problem:

“I need more confidence in the peptides found by MS/MS ion search”

Solution:

Use an orthogonal approach like sequence tag searching or hybrid searching to validate the results

Problem:

“I can only explain <10% of my data. I need to boost my search engine’s performance.”

Solution:

Use two or more unique search engines. Then try de novo sequencing.

Problem:

“I think I’m still missing some peptides, maybe because of with PTM”

Solution:

Use de novo to find a partial sequence; matching this to a database will highlight peptides of interest.

Problem:

“I am still missing some peptides even after trying all PTM. But the data is great!”

Solution:

De novo + peptide homology search like SPIDER or BLAST.

Problem:

“My lab creates too much data for de novo sequencing”

Solution:

Use PEAKS. It’s fast enough.