Description Usage Arguments Details Value Note Author(s) See Also Examples
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).
1 2 | fiems_lct_main(my_path,runinfo,y1,y2,y3,y4,limit=0.82,
save.file=TRUE,file.name="LCT-mean.RData")
|
my_path |
A character string indicating the working directory where
|
runinfo |
A |
y1 |
A numeric value used for mass spectrum generation: start scan
‘sample’. For details, see the description in |
y2 |
A numeric value used for mass spectrum generation: end scan
‘sample’. For details, see the description in |
y3 |
A numeric value used for mass spectrum generation: start scan
‘background’. For details, see the description in |
y4 |
A numeric value used for mass spectrum generation: end scan
‘background’. For details, see the description in |
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 |
file.name |
A character for saved file name if |
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.
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 |
limit |
Same as argument stored for reference purposes. |
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).
Manfred Beckmann meb@aber.ac.uk
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 | ## 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)
|
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