Hi there, I am pretty new to TMT quantitation. Apologies if my questions are too naive.
I am recently tackling iodoTMT6plex labeling on Cys. Libra algorithm, originally designed for itraq labelled at N term and Lys, is claimed to be also suitable for TMT on TPP wiki page. So I assume that labkey would also be capable of handling my situation. However, there is limited introduction to the Libra, and the main one: http://sashimi.svn.sourceforge.net/viewvc/sashimi/trunk/trans_proteomic_pipeline/src/Quantitation/Libra/docs/libra_info.html is pretty out of date. I generated the condition.xml file as attached file pretty much as indicated this page. My questions are: 1. can anybody help me look into the condition.xml file to see if there is any problem? 2. TPP wiki pages says: "If you would like to generate a condition.xml file, please use http://db.systemsbiology.net/webapps/conditionFileApp/";. But the link is dead already. Can anybody update the link possibly? 3. Our TMT is labeled on Cys; so for a lot of identified peptides, if they don't have a cys, then it shouldn't display the quant information for that peptide. Thermo's proteome discoverer deals with this very good. However, when I tried TPP Libra, it gives all quant information even if that peptide does not have Cys. I guess I have to program to get rid of these fake quant information and re-assemble the protein quantitation offline. With that being said, Is there automatic way or update to automate this process? I am using TPP 4.5 right now. Thanks for any input in this thread! You guys are awesome to make beautiful stuff happening. -- 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/groups/opt_out.
