Last year I make a poster presentation for MS/MS annotation by paired mass distance(PMD) analysis. It’s already been included as pmdanno function in pmd package. Here I will explain the principle of PMD annotation.
Firstly, you need a spectra database. Here I use HMDB MS/MS spectra database as an example. Then you will get a list with each compound as element. The list should have a element of spectra with mz and ins, an element of name, an …