Hello David,
Before wrinting the post, the last trys were done with a +/- 0.6 Da of
mass tolerance which are the same values I used in MASCOT. I have
noticed a small decrease in the duration of the search.
Another question : do I have to think about the size of my database too ?
Anyway, thanks for your help and I will think about using more static
modification.
Fred
Le 10/20/2014 9:03 PM, David Shteynberg a écrit :
Dear Fred,
Every time you add a variable modification the algorithm has to
evaluate an order-of-magnitude more possibilities. Thus, you should
use static mods as much as possible or try to limit your search space
in other ways (e.g. use a more narrow mass tolerance).
-David
On Mon, Oct 20, 2014 at 6:42 AM, DELOLME Frederic
<frederic.delo...@ibcp.fr> wrote:
Hello TPP team,
At this time, I'm using TPP for iTRAQ quantitation after a search with
X!Tandem.
I'm facing some problems with the duration of the search. In my case, I use
1 static modification and I'd like to include seven others potential
modifications.
With only one static and one or two potential, it's quite faste (around
20-30 min on my system 2 processors, 8 virtual cores). As soon as I increase
the number of potential modif the duration increase dramatically. Did you
observe such issue ? If not, do you use a refinement search ?
I'm wondering if it's only a matter of power of my computer or if it's
rather due to X!Tandem algorithm.
Thanks in advance for any advice.
Fred
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Frédéric DELOLME
Frédéric DELOLME
Institut de Biologie et Chimie des Protéines - CCMP - Spectrométrie de
masse
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