Dear Jimmy, thanks for your quick answer. I will for sure look into the raw data and hope to see a trend which is the reason for this effect.
What I forgot to mention in the post before, is that I post filtered the results with a very stringent PPS cutoff of 0.99. So the reason cannot be false positives. Lukas On Sep 15, 1:19 am, Jimmy Eng <[email protected]> wrote: > Lukas, > > These tools could definitely be optimized and improved, especially for > high res data that didn't really exist when they were first developed. > That said, with respect to question 1, you're using two imperfect > tools on presumably large datasets so it's not surprising to see some > uncorrelated results. If I were you, I would look at the extracted > chromatograms of these peptides to see how the two tools determined > the respective light and heavy areas used to calculate the ratios. > One (or both) likely failed for one reason or another which is one of > the unfortunate reasons why the not-very-user-friendly GUIs exist to > allow the researchers to look at and fix/edit/discard any particular > calculated ratio. I know you don't want to look at chromatograms for > a quarter of your identifications but that's what you probably have to > do at this point. Or throw them out. Or stick with a single tool and > pretend the other didn't exist that gives conflicting results. > > I don't know the answers to your other two questions, not that I > really had an answer to question 1, so hopefully someone else can > address those. > > - Jimmy > > > > On Tue, Sep 14, 2010 at 12:42 PM, lukas <[email protected]> wrote: > > 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 > > > -- > > You received this message because you are subscribed to the Google Groups > > "spctools-discuss" group. > > To post to this group, send email to [email protected]. > > To unsubscribe from this group, send email to > > [email protected]. > > For more options, visit this group > > athttp://groups.google.com/group/spctools-discuss?hl=en. -- You received this message because you are subscribed to the Google Groups "spctools-discuss" group. To post to this group, send email to [email protected]. To unsubscribe from this group, send email to [email protected]. For more options, visit this group at http://groups.google.com/group/spctools-discuss?hl=en.
