You probably need to do 2 separate analyses for your M/L, and H/L ratio. As far as I know, there is no way you can do triple-SILAC in TPP environment. Maxquant is the only free tool you can try, since it runs in a desktop, it is slow, but try the 64-bit version if possible. Mascot also support triple-SILAC, if your data set is not too huge, just merge all files while searching, the Mascot will report triple-SILAC ratios automatically. An upgraded choice is to add the Distiller module for better raw data conversion and downstream MS1 quantitation. hope that helps.
SunSun On Tue, Nov 6, 2012 at 6:58 AM, Brian Hampton <bhamp...@my.abrf.org> wrote: > I haven't had the opportunity for a triplex quant expt. but from my usage > of ASAPRatio for duplex quant., I don't believe it would have that > limitation. Have you tried ASAPRatio? > > Brian > > > On Mon, Nov 5, 2012 at 5:23 PM, kshitiz tyagi <tyagi....@gmail.com> wrote: > >> A very big limitation of TPP at the moment. MaxQuant, unfortunately seems >> to be the only option to process triply labelled data and maxquant is very >> slow for big data sets. We often have to break up our analysis into 3 pair >> wise comparison. it will be great to have an XPRESS version that can do >> triple label quant. >> >> >> On Mon, Nov 5, 2012 at 10:18 PM, Pitter <pit...@interchange.ubc.ca>wrote: >> >>> Hi all, >>> >>> as far as I'm aware there's no straightforward way to quantify >>> triplex-SILAC or triplex-dimethylation data within the TPP. >>> Has anyone found a workaround (other than using MaxQuant)? >>> >>> Thanks! >>> >>> Pitter >>> >>> -- >>> You received this message because you are subscribed to the Google >>> Groups "spctools-discuss" group. >>> To view this discussion on the web visit >>> https://groups.google.com/d/msg/spctools-discuss/-/taVQrqscfNoJ. >>> To post to this group, send email to spctools-discuss@googlegroups.com. >>> To unsubscribe from this group, send email to >>> spctools-discuss+unsubscr...@googlegroups.com. >>> For more options, visit this group at >>> http://groups.google.com/group/spctools-discuss?hl=en. >>> >> >> >> >> -- >> Kshitiz Tyagi >> >> >> -- >> You received this message because you are subscribed to the Google Groups >> "spctools-discuss" group. >> To post to this group, send email to spctools-discuss@googlegroups.com. >> To unsubscribe from this group, send email to >> spctools-discuss+unsubscr...@googlegroups.com. >> 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 spctools-discuss@googlegroups.com. > To unsubscribe from this group, send email to > spctools-discuss+unsubscr...@googlegroups.com. > For more options, visit this group at > http://groups.google.com/group/spctools-discuss?hl=en. > -- *Sun* -- You received this message because you are subscribed to the Google Groups "spctools-discuss" group. To post to this group, send email to spctools-discuss@googlegroups.com. To unsubscribe from this group, send email to spctools-discuss+unsubscr...@googlegroups.com. For more options, visit this group at http://groups.google.com/group/spctools-discuss?hl=en.
