Hi, I am using the TPP to analyse Q-Exactive data using X!tandem (k-score or hrk-score) searches using similar settings that I used successfully with Orbitrap data: search against fwd+decoy database, running Xinteract with the following options:accurate mass binning, *Do not* use the NTT model, Use decoy hits to pin down the negative distribution and selecting peptide with PP probability that corresponds to 1% error. >From reviewing the MS/MS of the selected peptides it seems like there are more peptides with questionable MS/MS data in comparison to what I used to get with Orbitrap data (unfortunately I don't have data of the same sample measured on QE and Orbi so this is based more on observation...but still I see the same trend in different QE data files). In addition I find odd correlation between the reported number of assigned ms/ms peaks (IONS column) to those observed in Lorikeet (and Comet) viewer - usually for lower-mid quality spectra there are less peak observed than those reported. Can someone please advise? Thanks, OK
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