I was running a iTRAQ sample on TPP with sequest in it. I have come to 2 problems with the sequest.params
1) in the part of add mass to N-term and lysine, do we do 305 for 8plex as that is the whole mass of the label? Do the search also take 305 in to the search of Ms2 spectrum? 2) I find out that in the Ms2 part some search result took my 118 peak (one of the labels) as a peptide fragment peak and tried to match it up with the peptide spectrum getting a lot of poor mismatching results. Is there any way I can prevent this? I was considering to let the search start from m/z 200, without the labeled area. Can I change this in sequest.params or in any other file? Can any one help me with these questions? Thanks a lot~~~ Yue --~--~---------~--~----~------------~-------~--~----~ You received this message because you are subscribed to the Google Groups "spctools-discuss" group. To post to this group, send email to [email protected] To unsubscribe from this group, send email to [email protected] For more options, visit this group at http://groups.google.com/group/spctools-discuss?hl=en -~----------~----~----~----~------~----~------~--~---
