grabMzxmlMS2 {RaMS}

Extract the MS2 data from an mzXML nodeset

Description

Extract the MS2 data from an mzXML nodeset

Usage

grabMzxmlMS2(xml_data, file_metadata, rtrange, incl_polarity)

Arguments

xml_data

An 'xml2' nodeset, usually created by applying 'read_xml' to an mzXML file.

file_metadata

Information about the file used to decode the binary arrays containing m/z and intensity information.

rtrange

A vector of length 2 containing an upper and lower bound on retention times of interest. Providing a range here can speed up load times (although not enormously, as the entire file must still be read) and reduce the final object's size.

incl_polarity

Boolean determining whether the polarity of the scan should be returned as a column in the table (positive mode = 1, negative mode = -1)

Value

A 'data.table' with columns for retention time (rt), precursor m/z (premz), fragment m/z (fragmz), collision energy (voltage), and intensity (int).