Hello, I am trying to analyse my TMT-labelled MS data using Libra. I have already got the *pep.xml* file from comet search and analysed all peptides by Libra. Libra has given me two files, one is a new *pep.xml* which contains several values for each peptide, and the other is a* prot.xml* file, which was output by ProteinProphet.
I hope to generate *a protein quantification matrix*, which contains absolute quantitative value for each protein and each TMT-label, convenient for my subsequent analysis and visualization in R or Python. But I have some problems here: 1) I hoped to use absolute values, for some peptide quantification in my reference group is zero, wich may affect my experiment group data. I used Normalize against sum of reagent profiles in Libra condition file, is that mean I could got the absolute values? Besides in the output *tsv* file from prot.xml, I got the ratio instead of a quantitative value, how could I got that number? 2) Another question is that maybe two or more protein share the same quantification result. I understand MS could not distinguish these protein with high sequence similarity, but could I output a report for every protein directly by TPP tools? 3) In my Libra output *pep.xml*, there're nearly a half peptide abandoned in protein quantification (kept column was set to No or blank). Is this normal or bad TMT-label? Furthermore, there're many proteins even without the ratio value. How could I achieve my goal? If Libra could not output directly, which tools could I use or how could I calculate by myself? Thanks a lot! Respectfully, Jinwang Lu -- 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 view this discussion on the web visit https://groups.google.com/d/msgid/spctools-discuss/25ce0e40-6aad-4e6d-aade-837fd2b91c0bn%40googlegroups.com.
