Hi Ankit, both strategies would likely work okay. I would prefer first combining all your data with iProphet and then creating the library with SpectraST. An issue to consider: if you combine several libraries that have been processed or thresholded individually, the final FDR will be higher for the combined dataset than the individual ones. This is because the correct identifications will mostly be in common, but the false identifications will be mostly different in the different experiments and so they will accumulate. So combining everything first with iProphet will give you a better understanding of your FDR.
Regards, Eric *From:* [email protected] <[email protected]> *On Behalf Of *Ankit Balhara *Sent:* Thursday, March 14, 2019 11:47 PM *To:* spctools-discuss <[email protected]> *Subject:* [spctools-discuss] Combining the data on two tissues in one library Hi, I have acquired the DDA and DIA data on various tissues, and trying to build a spectral library by combining the DDA results of all tissues, that can be used further for the DIA data analysis. I am trying two approaches- one assay library generation with SpectraST and other using skyline to build the library. Now, I confused, how should I proceed. Should I combine the peptideprophet results of various tissues by using iProphet? Or, create assay libraries for each tissue separately using the SpectraST and then import them separately in a common Skyline document? I would be very grateful for your help. Thanks in advance. -- 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 post to this group, send email to [email protected]. Visit this group at https://groups.google.com/group/spctools-discuss. For more options, visit https://groups.google.com/d/optout. -- 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 post to this group, send email to [email protected]. Visit this group at https://groups.google.com/group/spctools-discuss. For more options, visit https://groups.google.com/d/optout.
