I am new to TPP and proteomics so apologies for asking basic questions. I am able to run Comet and Xtandem and get the protein lists but need help with the following:
1. I have multiple *.raw files that represent biological replicates. Furthermore, I have multiple time points of such replicate samples. With TPP, I need to check fold change (and presence/absence) of proteins in a statistical fashion. But when I am running the COMET or X!Tandem pipelines in TPP, it is combining all the datafiles into one. Is there a way to define data file groups and get comparative proteomics as the output - for example different groups compared for presence/absence or fold change in proteins? 2. How can I combine results of such datasets (as in point 1 above) from two different pipelines? 3. How could I analyse data for a mixture of proteins with uniformly labelled 14N and 15N? I need to detect only back set (for example detect only 15N, in the mixuture and ignore the 14N)? 4. Which pipeline would be best for the point 3 above and if is a .param file for detecting 15N peptides? Thank you. -- 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.
