Dear list,
I have three question regarding ASAP and XPRESS:
1)
I analyzed a data set generated from a SILAC sample on an Orbitrap.
The data was searched using Sequest with variable modifications on R
and K. I used ASAP and XPRESS for quantitaton with the following
command (TPP v4.3 JETSTREAM rev 1, Build 201004270833 (linux)):
xinteract -dreverse_ -p0.8 -OAlpd -X-m0.1-nK,8.014199-nR,10.008269 -A-
Z-r0.1-F-C-lKR-mK136.10916R166.109379 *.pep.xml
When I make the correlation between log2("asap mean") and
log2("xpress") I can see a large part of the data points nicely
correlating but also many data points (roughly a quarter) having close
to zero regulation by XPRESS but non-zero regulation by ASAP.
I wonder whether I chose any wrong options or what the reason for this
effect could be? Any hint would be greatly appreciated.
2)
ASAP threw the warning message:
WARNING: Found more than one variable mod on 'K'. Please make sure to
specify a heavy mass for this residue.
WARNING: Found more than one variable mod on 'R'. Please make sure to
specify a heavy mass for this residue.
Could it be that the reason for this are peptides that were identified
with one light and one heavy K/R and are most likely false positives?
3)
Where can I read about the difference between "asap mean" and
"asapratio_HL"?
Thanks for any help,
Lukas
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