Read mass spectral library (MSL) files

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Description

This funtion read data in NIST mass spectral library (MSL) format and returns a list of compounds, with their names, retention times, retention indexes (if provided), together with mass and intensity of all fragments.

Usage

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readMSL(file.name = character(), path = getwd(), Save = FALSE)

Arguments

file.name

a string including the full name of a .MSL file including the library information.

path

a string including the full path to the location of the file.name, optional

Save

if TRUE, the function also saves the list as an RDdata object. It always returns the targets as list.

Details

NIST mass spectral library, i.e. MSL, data files include compound names and their spectral information. The spectral information consist of number of fragments for each compound, together with the mass and relative and usually normalized intensity of each fragment. Also, the retention time and retention index of the compounds are provided which helps improve the identification by avoding false positives. This functions usually is used indirectly by calling getTarget function.

Value

A list including target information:

rt

a numeric vector of retention times

rt

a numeric vector of retention indexes

ms

a list including vectors of fragment masses of each target

sp

a list including vectors of fragment intensities of each target

compound

a list including character vectors of the target chemical names

Author(s)

Mo R. Nezami Ranjbar

References

http://omics.georgetown.edu/SIMAT.html

See Also

writeMSL, readCDF

Examples

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    # load an example data set
    extdata.path <- system.file("extdata", package = "SIMAT")
    
    # get the list of targets in a file with MSL format from Example Data Set
    Targets1 <- readMSL(file.name="Targets_1.MSL", path = extdata.path)