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SIMAT (version 1.4.0)

GC-SIM-MS data processing and alaysis tool

Description

This package provides a pipeline for analysis of GC-MS data acquired in selected ion monitoring (SIM) mode. The tool also provides a guidance in choosing appropriate fragments for the targets of interest by using an optimization algorithm. This is done by considering overlapping peaks from a provided library by the user.

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Version

Version

1.4.0

License

GPL-2

Maintainer

Mo R Nezami Ranjbar

Last Published

February 15th, 2017

Functions in SIMAT (1.4.0)

Library

Extracted compound information from an MSL library.
getRIStandard

Get the RI standard information
plotTIC

Plotting TIC of one run
Run

Extracted peaks from one SIM run.
getEIC

Get the EIC of a peak
getRI

Generate a calibration function
optFrag

Fragment selection through optimization
getPeakScore

Calculate the similarity score for all peaks
Targets

Targets information in a list.
readMSL

Read mass spectral library (MSL) files
writeMSL

Write targets information into a file with mass spectral library (MSL) format.
RItable

Extracted RI standard information from a csv file.
putTargetTable

Put target table information
getScore

Calculate similarity score for a peak
getTargetTable

Get target table information
target.table

Extracted target information from a csv file.
getTarget

Get target information
SIMAT-package

This package is for processing GC-SIM-MS data
plotEIC

Plotting EIC of one peak
getPeak

Get all peaks corresponding to targets in several runs
readCDF

Read raw mass spectrometry data in netCDF files