Hello, I'm used to using command line TPP for combining search engines and replicates etc, but I'm new to metabolic labelling.
I have a comparison of 14N vs 15N grown cells, and I would like to generate differential expression data using ASAPRatio. Unfortunately, I'm finding it really hard to piece together the basics of how to go about this from the various questions here and the tutorials. I would be very grateful if someone could fill in the gaps I'm missing! So first I would do two sets of database searches, one will 15N amino acid masses, the other with 14N masses. Then run TPP and ASAPRatio via xinteract. Do I have to tell it which search results are heavy and which are light? Or are they simply combined into a single interact.pep.xml file and processes by ASAPRatio all together? Should it be run without peptide prophet? Presumably the presence of two sets of amino acid masses would cause issues... Do you have to set the ASAPRatio -l tag to include all the amino acids in the case of 15N labelling? How does it know which mass differences to look for? The data come from a modern LTQ-orbitrap - is the -r 0.5 parameter likely to be appropriate? Especially since the mass by which a heavy peptide differs from the light peptide is going to differ widely depending on the amino acid composition. If it turns out to be too difficult to use ASAPRatio, then I guess xpress is probably easier. For this, do you simply provide the outputs of the different searches to xinteract, set the -X tag and let it do it's magic? Is there anything else I particularly need to consider? Thanks! Alastair -- 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 spctools-discuss+unsubscr...@googlegroups.com. To view this discussion on the web visit https://groups.google.com/d/msgid/spctools-discuss/404fa1d3-56df-4d58-a1c7-ae288dabfaafo%40googlegroups.com.
