Hi I have a data set with three replicates in the control group and three replicates in treated groups. I have performed the entire processing using TPP i. e. converting raw file to mzml, identifying peptides and then identified proteins and quantified the proteins using StPeter. I have used all default parameters for the quantifications. However, on reviewing the results I am hardly getting any significant changes in protein levels. The SIN scores range from -17 to -25. Is that how it should be? Should I convert these cores into dSIN? Do I have to use the loading volumes? I am hardly getting a fold change of about 1.3 in 5 proteins and less than 0.7 in two proteins, although around 6,000 proteins are identified.
I have gone through the Moritz et. al paper in JPR but I am still not able to get past this problem. Thanks in advance Debangana -- You received this message because you are subscribed to the Google Groups "spctools-discuss" group. To unsubscribe from this group and stop receiving emails from it, send an email to [email protected]. To view this discussion on the web visit https://groups.google.com/d/msgid/spctools-discuss/58de3273-59ed-40e2-94af-3650c125762b%40googlegroups.com.
