Hello,
It would depend on what search engine you are using. If its Tandem, then
look in the directory containing the parameter files. On my install
(Linux) its in /usr/local/tpp/data/parameters/. The input parameter xml
file you are using, either K-score or Native has an entry that should look
like the below. Modify the line for the cleavage site to suit your needs.
The <note> about enzyme specificity describes what I believe you want to
do. Notice that these are Tandem parameter files. If you use the Comet
search engine (or something else supported by TPP) it has its own parameter
file and convention for specifying cleavage specificity. For more
information about using Tandem you should see <
http://www.thegpm.org/TANDEM/api/index.html>
Cheers,
Brian
------- excerpt from isb_default_input_kscore.xml -------
<note>protein parameters</note>
<note type="input" label="protein, taxon">no default</note>
<note>SEQUENCE DATABASE TO SEARCH. This refers to identifiers in
taxonomy.xml.</note>
<note type="input" label="protein, cleavage site">[RK]|{P}</note>
<note>ENZYME SPECIFICITY. This setting corresponds to the enzyme
trypsin. The first characters in brackets represent residues N-terminal to
the bond - the '|' pipe - and the second set of characters represent
residues C-terminal to the bond. The characters must be in square brackets
(denoting that only these residues are allowed for a cleavage) or french
brackets (denoting that these residues cannot be in that position). Use
UPPERCASE characters. To denote cleavage at any residue, use [X]|[X] and
reset the scoring, maximum missed cleavage site parameter (see below) to
something like 50. </note>
-------
Brian Hampton
Protein Analysis Lab
Center for Vascular and Inflammatory Diseases
University of Maryland School of Medicine
800 West Baltimore Street Rm 307
Baltimore MD 21201
V: 410-706-8207
F: 410-706-8234
On Wed, Oct 16, 2013 at 9:55 AM, Theofilos <[email protected]> wrote:
> Hello,
>
> I just installed TPP and I am trying to find out how it works. I am trying
> to analyze samples that have not been treated with any enzyme (native
> samples). By default the program analyzes with trypsin cleavages. So, I am
> trying to find the option for enzyme specificity and use "non specific" or
> something like that.
>
> Could somebody tell me where to look and what to change in the parameters?
>
> Thank you
>
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