tide-index --mods-spec & extract matched b/y ions

[Le Tung]

Hi Crux team,

I'm trying to build a custom database with tide-index where the only static modification is Thr dehydration. I use the following command with the example test files:
crux tide-index --mods-spec T-18.0106 small-yeast.fasta yeast-index

and I noticed that the generated params file(attached) always include the IAM adduct for Cys as the default parameter and I can only override it by specifying C+0. Is this behavior normal or am I using it incorrectly?

My second question regards PSM results of tide-search/percolator. I am interested in all of the matched b/y ions of each hit. What would be a way to generate a list of matched b/y ions that can be parsed for all of the target hits?

Thank you so much for your time.

Tung.

[William Stafford Noble]

Hi Tung,

Yes, this behavior for a static mod on C is normal:

--mods-spec <string> – The general form of a modification specification has three components, as exemplified by 1STY+79.966331.
The three components are: [max_per_peptide]residues[+/-]mass_change
In the example, max_per_peptide is 1, residues are STY, and mass_change is +79.966331. To specify a static modification, the number preceding the amino acid must be omitted; i.e., C+57.02146 specifies a static modification of 57.02146 Da to cysteine. Note that Tide allows at most one modification per amino acid. Also, the default modification (C+57.02146) will be added to every mods-spec string unless an explicit C+0 is included. Default = C+57.02146.

Unfortunately, the answer to your second question is that Crux does not currently have a way to generate lists of matched b/y ions. Sorry about that!

Bill