Hi all, As I mentioned in the title, I was confused by this question. For currently used PSM validation methods by such as machine learning algorithms (e.g. Peptide Prophet), they constructed models for different charge states as the number distribution of precursors and distribution of scores in these charges are significantly different. But for extracting confident PSMs via target-decoy database search, I noticed that the researches extracted results from the whole data sets, regardless of the precursors' charge states. Though there had discussions about the significance of correct PSMs in small size of database search results, can I extract PSMs according to the charge states of precursors by setting certain FDR level (e.g. 0.01)? I found that if I extracted PSMs from the whole search results, almost all are doubly and triply charged PSMs, whereas singly or other PSMs are rare. Any suggestions?
Best regards, Nai-ping -- 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.
