I'm using TPP v4.4 vuvuzela rev 1 and I'm working with SILAC cells. Everything is going right until the quantification time, when my result seems to be very bad. After 8 runs with different proportions of heavy/light cells (1:1, 2:1) in a following conditions (Thermo Orbitrap -> Mascot Search with Fixed Mod. on Carbamidomethyl and Variable Mod. on Label(6)K and Oxidation(M) -> Analysis Pipeline with XPRESS mass diference (K) 6.02 and ASAPRatio with change label K and Specific mass residue K 134.114), my results are around 70% N_A, and just 20% really quantified. My question is: why there is so much N_A in my results? I know that N_A is something about cannot quantify, but what it is exactly? Is it something experimental or is it a bad use of TPP?
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