Hi! I wish to run some iTRAQ labeled data through the TPP using the embedded search engine xtandem! The peptides have been alkylated using MMTS and labeled with the iTRAQ 4-plex (114-117). The data was acquired on a Waters Synapt using DDA mode. I have converted the .raw data to both mzML and mxXML format and thus have the data in the format ready to use for the database searching. My question regards how to define the search tandem parameter file to be set up using isobaric labeling?
Firstly, the default parameter file is set up for carbamidomethylation but I need to change it to MMTS which I assume just needs to be changed from <note label="residue, modification mass" type="input">57.021464@C</note> into <note label="residue, modification mass" type="input">45.987721@C</note> But how do I define the search for iTRAQ? I assume, a mass addition for the isobaric label is needed for the MS scan as well as a exclusion of 114-117 in the MS/MS scan is needed? Is there any easy way of doing this? Is there a GUI to define the correct search settings for this that works with the xtandem in TPP? I would greatly appreciate any help on this topic! Sincerely, Marcus Sjödin -- You received this message because you are subscribed to the Google Groups "spctools-discuss" group. To view this discussion on the web visit https://groups.google.com/d/msg/spctools-discuss/-/d0rlZFFdG6cJ. 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.
