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 at > http://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.
