Hello all, a noobie here.
I am trying to make sense of my LC-MS^n data. Before running my samples on the instrument, I spiked them with two internal standards (lidocaine and biochanin A). I preprocessed my files using the standard xcms pipeline, but I cannot find my standards in the rowData(results) file. I know what m/z and RT to expect, but the compounds that best correspond to these, differ in RT time by 20.33 and 0.248 seconds (respectively). This is a big difference, isn't it?
I then used m/z only search of compounds in MassBank using these data, and neither lidocaine not biochanin were identified as matches.
What should I do with all this? are the peak-picking parameters my problem? The parameters I used were chosen by IPO package using polled samples. How do I now that my tweaking them improved the situation rather than made it worse?