fiems_lct_main: LCT Mass Binning

Description Usage Arguments Details Value Note Author(s) See Also Examples

Description

Main Routine for ‘Mass Binning’ to nominal mass and ‘Mass Spectrum’ generation in high-throughput Flow Injection Electrospray Ionisation Mass Spectrometry (FIE-MS). This routine reads ANDI NetCDF files (*.cdf) of LCT/Q-ToF *.raw data files converted in the DataBridge program (Dbridge, MassLynx, Micromass).

Usage

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fiems_lct_main(my_path,runinfo,y1,y2,y3,y4,limit=0.82,
               save.file=TRUE,file.name="LCT-mean.RData")

Arguments

my_path

A character string indicating the working directory where runinfo.csv file and folder containing *.cdf-files are located.

runinfo

A *.csv file containing at least the following run information (header row): pathcdf and filecdf . For details, see the description in Examples below.

y1

A numeric value used for mass spectrum generation: start scan ‘sample’. For details, see the description in Examples below.

y2

A numeric value used for mass spectrum generation: end scan ‘sample’. For details, see the description in Examples below.

y3

A numeric value used for mass spectrum generation: start scan ‘background’. For details, see the description in Examples below.

y4

A numeric value used for mass spectrum generation: end scan ‘background’. For details, see the description in Examples below.

limit

A numeric value defining the rounding limit for binning m/z-values to nominal mass.

save.file

A logical value indicating whether or not to save the results (default is TRUE).

file.name

A character for saved file name if save.file is TRUE.

Details

This routine is designed to handle only one MassLynx (Micromass) specific function (e.g. data acquired at one cone voltage). Each *.cdf-file will result in one mass spectrum. Principle in brief: load *.cdf-file (pathcdf and filecdf information in runinfo.csv); bin m/z-values to nominal mass between ‘limit-1’ and ‘limit’; sum up intensities of binned m/z values; generate sample matrix ‘smat’ between scans y1 and y2 and background matrix ‘bmat’ between scans y3 and y4; subtract: mat=smat-bmat; calculate mean of resulting matrix ‘mat’; potential negative values are set to ‘zero’. The implemented timer-function should be accurate for up to 24 hours which could comprise more than 7000 *.cdf-files per experiment.

Value

A list containing the following components:

mat

Single matrix [runs x nominal masses] of the full mass range [0:2000] in the ionisation mode.

runinfo

Same as argument stored for reference purposes. Additional information for each run like sample name or class can be used for further analysis (e.g. nlda).

scrng

A vector of y1, y2, y3 and y4 stored for reference purposes.

limit

Same as argument stored for reference purposes.

Note

The returned values are saved by default as LCT-mean.RData in folder my_path. Additionally, single items are saved by default as TEXT files: mat.txt, myparam.txt (containing scrng and limit for reference purposes).

Author(s)

Manfred Beckmann [email protected]

See Also

fiems_ltq_main

Examples

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## Example profiles can be downloaded on the FIEmspro webpage
## 021016Pot-24_LCT_ESI_-.zip must be extracted in folder that defines 'my_path'

## For e.g.
## Not run: my_path <- "D:/Temp/021016Pot-24_LCT_ESI_-"
## The same folder should also contain a 'runinfo' file
## For e.g.
## Not run: runinfo <- "runinfo.csv"
## Process each profile defined in 'runinfo'
## Not run: tmp <- fiems_lct_main(my_path,runinfo,15, 25,50,	60,limit=0.82,
               save.file=TRUE,file.name="LCT-mean.RData")
## End(Not run)

## ===================================================================
## Arguments and matrices are saved in 'my_path', ideally the working 
## directory of the experiment. For explanations regarding input 
## arguments see below ...

# required is a file named by default 'runinfo.csv'
# (comma separated variables, generated in e.g. MS-Excel);
# the structure should be the following to ease data pre-processing:

#    A     |                  B                   |       C         |  D
# injorder | pathcdf                              | filecdf         |batch
#-------------------------------------------------------------------------
#  1       | D:/../Pot-LCT-2001-bc/Test_LCT_ESI_- | 021016MAN10.CDF | 1
#  2       | D:/../Pot-LCT-2001-bc/Test_LCT_ESI_- | 021016MAN11.CDF | 1
# and so on...

#  Columns:
# 'injorder' is injection order of samples (good for investigating drifts)
# 'pathcdf'  is path of folder containing "*.cdf"-files. Each run-sequence
#            or batch of runs might have its own folder.
# 'filecdf'  is the actual filename of an "*.cdf"-file.
# 'batch'    is the number of the batch the run belongs to (good for
#            investigating batch effects)

# In practice the file will contain further information regarding sample name,
# class/group information and probably other meta-data describing a sample.


## LCT Instrument Method for Flow-Injection-ESI-MS (FIE-MS):
## - 1 Function only, either positive or negative ionization mode
## - m/z range: 65.0-1000.0  (default max = 2000)   resolution: 4000
## - 2 min Acquisition

## Infusion Profile (Sketch):
##          _
##         / \
##        /   \
##       /     \_
##      /        \__
## ____/            \______________________________
## 0         0.5          1          1.5          2 [min]
##       |------|               |------|
##      [y1]   [y2]            [y3]   [y4]   [scan reading]
##        sample               background
## Using the above given LCT Instrument Method for FIE-MS
##   the actual scan readings y1 to y4 are used directly:
##       scrange = c(y1,y2,y3,y4)
##       with (ideally):  y2 - y1 = y4 - y3

## Raw data conversion to ANDI NetCDF-file: 
##       DataBridge program (Dbridge, MassLynx, Micromass)

wilsontom/FIEmspro documentation built on Feb. 19, 2018, 9:03 a.m.