issue with loading external search results for inChorus search

[zeyu sun]

Hi, I'm wondering if anybody here knows how to load search results
from other engines into PEAKS inChorus. My issue right now is the loss
of a lots of hits from other engine's results loaded into inChorus. I
tested the inChorus with 1 fraction from my iTRAQ data, and I used the
most current version of Mascot(2.3), OMSSA(2.1.9), X!tandem(GMP 2.2.1)
outside of PEAKS and loaded the results into the PEAKS inChorus. It
went perfectly well with OMSSA omx, but I only got one peptide hit
from both the X!Tandem (xml) files and Mascot (dat). I checked both
results with X!tanderm parser and Mascot itself, there should be over
100 decent protein hits in each file. Is the current PEAKS (5.2) only
works with certain version of other search engines? Or is there any
specific option I shall be aware of when I export search results from
X!tandem and Mascot?
Thank you very much!!

zeyu sun
Colorado State University

[Dan]

Hi Zeyu Sun,

That shouldn't happen. One thing you need to make sure of is that you
select the same database you searched with in Peaks when importing the
result file. You also won't be able to see results below a certain
score threshold. That may be the case as well. Let me know if you
continue to have this problem. I can always take a look at the data
set and see if I can help! My email address is: d...@bioinfor.com