Does anyone know a tool (better and R package) that can do monoisotopic mass extraction and charge state assignment of the entire raw MS1 spectrum?
From a given MS1 spectrum I would like to retrieve the following info: -monoisotopic m/z of all detected peptides -intensity of the monoisotopic masses -isotope envelope of each monoisotopic mass (i.e. m/z and intensity) -charge state
Most of the available tools (like msconvert) only work on the precursors selected for fragmentation, not for all the m/z reported in the MS1 spectrum. Also, MALDIquant::monoisotopicPeaks only return the monoisotopic m/z and its intensity, but not charge state nor isotope envelope information.