mzID is a package that allows parsing of mzIdentML files. The mzIdentML file format has been created by HUPO as a standardized format for collecting data from peptide identification analyses based on LC-MS type experiments. The parser is kept bare bone in order to make it as general as possible.
mzID is part of Bioconductor and can be installed through there.
mzID(filename)parses the mzIdentML file at the location specified by filename into an mzID object
flatten(mzID_object)flatten the content of the mzID object into a data frame with a row for each psm
XMLpackage (which uses libxml2) for parsing
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