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 objectflatten(mzID_object)flatten the content of the mzID object into a data frame with a row for each psm- The parser is written to support the multitude of different ways peptide identification can be performed and thus be recorded in the mzIdentML format
- Defines a class to handle a collection of identification results efficiently
- Relies heavily on the
XMLpackage (which uses libxml2) for parsing - Respects the fact that peptide identification results are not inherently tabular in format. The mzID class contains several different classes each handling different part of the analysis data
- The parser is being optimized for speed within the bounds of needing to be general for all mzIdentML files. This means that a parser only handling a very specific analysis pipeline could likely be faster, but still the parser is fairly fast
- Make the parser software aware, so that it can create more beautiful output based on the software used in the analysis
- Performance improvements