Hello Our lab has been trying to use Libra to quantify MS2 (Ion-trap) identification and MS3-based quantification of TMT datasets and we were trying to benchmark with an artificial yeast and mammalian spiked dataset with known fold-change (FC) values. However we observe drastically different values than expected, something we don't observe with other search engines for the same dataset.
Has this issue been encountered before/ is there something obviously wrong when running with TPP that might cause this? Happy to provide further details on the dataset and parameters used to run with (most of them default apart from additions like static modification for TMT and specification of MS3 for quantification among others). Thank you, Shagun -- 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/ce2c75fb-2da1-4e05-8d08-bbe5a30b0495n%40googlegroups.com.
