MSnbase: readSRMData – R documentation

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readSRMData

Read SRM/MRM chromatographic data

Description

The readSRMData function reads MRM/SRM data from provided mzML files and returns the results as a MChromatograms() object.

Usage

readSRMData(files, pdata = NULL)

Arguments

`files`	`character` with the files containing the SRM/MRM data.
`pdata`	`data.frame` or `AnnotatedDataFrame` with file/sample descriptions.

Details

readSRMData supports reading chromatogram entries from mzML files. If multiple files are provided the same precursor and product m/z for SRM/MRM chromatograms are expected across files. The number of columns of the resulting MChromatograms() object corresponds to the number of files. Each row in the MChromatograms object is supposed to contain chromatograms with same polarity, precursor and product m/z. If chromatograms with redundant polarity, precursor and product m/z values and precursor collision energies are found, they are placed into multiple consecutive rows in the MChromatograms object.

Value

A MChromatograms() object. See details above for more information.

Note

readSRMData reads only SRM/MRM chromatogram data, i.e. chromatogram data from mzML files with precursorIsolationWindowTargetMZ and productIsolationWindowTargetMZ attributes. Total ion chromatogram data is hence not extracted.

The number of features and hence rows of the resulting MChromatograms object depends on the total list of unique precursor and product m/z isolation windows (and precursor collision energies) found across all input files. In cases in which not each file has chromatgraphic data for the same polarity, precursor m/z, product m/z and collision energy, an empty Chromatogram() object is reported for the specific precursor and product m/z combination of the respective file (and a warning is thrown).

Author(s)

Johannes Rainer

Examples

## Read an example MRM/SRM data
library(msdata)
fl <- proteomics(full.names = TRUE, pattern = "MRM")

## Read the data
mrm <- readSRMData(fl)

## The data is represented as a MChromatograms object, each column
## containing the data from one input file
mrm

## Access the polarity for each chromatogram (row)
polarity(mrm)

## Access the precursor m/z. The result is returned as a matrix with
## columns representing the minimum and maximum m/z (will be identical in
## most cases).
precursorMz(mrm)

## Access the product m/z.
productMz(mrm)

## Plot one chromatogram
plot(mrm[1, ])

MSnbase

Base Functions and Classes for Mass Spectrometry and Proteomics

v2.16.1

Artistic-2.0

Authors

Laurent Gatto, Johannes Rainer and Sebastian Gibb with contributions from Guangchuang Yu, Samuel Wieczorek, Vasile-Cosmin Lazar, Vladislav Petyuk, Thomas Naake, Richie Cotton, Arne Smits, Martina Fisher, Ludger Goeminne, Adriaan Sticker and Lieven Clement.

Initial release