getFragmentErrors: Extract fragment mass deviation errors from a data.frame from...

In PTXQC: Quality Report Generation for MaxQuant and mzTab Results

Extract fragment mass deviation errors from a data.frame from msms.txt

Description

Given a data.frame as obtainable from a msms.txt with - a 'mass.analyzer' column which contains only a single value for the whole column - a 'mass.deviations..da.' and (if available) 'mass.deviations..ppm.' - a 'masses' column (only required if 'mass.deviations..ppm.' is unavailable and the mass.analyzer indicates hig-res data)

Usage

getFragmentErrors(x, recurse = 0)

Arguments

x	Data frame in long format with numerical expression data
recurse	Internal usage only. Leave at 0 when calling.

Details

Mass deviations are extracted from the columns, e.g. each cell containing values separated by semicolons is split into single values. The appropriate unit is chosen (Da or ppm, depending on ITMS or FTMS data). Also the fragmentation type can be used: CID indicates ITMS, HCD to FTMS. This is not 100

Sometimes, peptides are identified purely based on MS1, i.e. have no fragments. These will be ignored.

If ppm mass deviations are not available, errors in Da will be converted to ppm using the corresponding mass values.

Value

Data frame with mass errors ('msErr') and their 'unit' (Da or ppm) or NULL (if no fragments were given)

PTXQC documentation built on July 26, 2023, 5:27 p.m.