Hi, Yes I am aware of the tolerance value and usually for Orbitrap data I use 0.1 or 0.05Da for Orbitrap (0.02 or 0.01 in XPRESS). I never check the Maxquant dataset so I can not comment on it but I used to run XPRESS and ASAPratio side by side and while XPRESS require only few manual changes ASAPratio required much more. I should say that I also compared XPRESS and Maxquant using some of my own datasets and the results were more or less the same. Oded
On Apr 7, 12:08 pm, dctrud <[email protected]> wrote: > 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 <[email protected]> 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 [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.
