Hello! I have proteomic data for our bacteria in different conditions, so I would like to perform DPE. The data is in the form of tables, which have identified peptides with assigned PSMs (spectral counts) and assigned proteins. So my questions are:
1) How to combine peptide PSMs into protein PSMs (is it ok to just sum up all PSMs for the peptides that belong to a particular protein? with a possible weighting if a peptide occurs in more than one protein)? 2) How to normalize these PSMs for different samples and conditions (is it enough to normalize it by the total number of PSMs in sample, like in RNA seq libraries)? 3) How to perform DPE analysis (Are there any tools specifically designed for proteomics, or it is ok too use the same as for microarrays or RNA-seq)? I would really appreciate if somebody mentions tools that can perform all these steps or some steps. Thank you, Margarita -- 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 http://groups.google.com/group/spctools-discuss. For more options, visit https://groups.google.com/d/optout.
