Oded, What settings are you using for the ASAPRatio quantitation? We find that the m/z tolerance value (-r) is critical to getting good quantitation in complex samples. The default is +/- 0.5 m/z units, which is quite wide. If you're using Orbitrap / QTOF data then it definitely needs to be set to something like the actual mass accuracy of the instrument.
I have a comparison somewhere of the Mann Maxquant HeLa dataset from ProteomeCommons run through the TPP with ASAPRatio quantitation, and if I recall correctly the results aren't far off MaxQuant. I'll check for it though. DT On 7 Apr, 08:44, Oded <oded.kleif...@gmail.com> wrote: > Hi All, > Are there any planned improvements or development of new tools for MS1 > quantification. I use Xpress and it work pretty well for me but still > require a bit of manual inspection. As for ASAPratio I find it to be > usually off and to require a lot (too much) of manual inspection and > correction (which is also not too user-friendly but this is a > different story). > More specificially, it would be great to have the ability for Xpress > to calculate the protein ratios following the median of the identified > peptides ratio and not the mean (as in MaxQuant). I tried to use Excel > for such calculation after exporting ProteinProphet output (while > checking the "show peptides" option) but currently only the mean ratio > is being exported and not the specific ratio of each peptide within a > protein. > > Thanks, > Oded -- You received this message because you are subscribed to the Google Groups "spctools-discuss" group. To post to this group, send email to spctools-disc...@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.
