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 LTQ *.raw
data files converted in the Xconvert program (Xcalibur, Thermo Finnigan).
1 2 3 | fiems_ltq_main(my_path,runinfo, y1,y2,y3,y4,limit=0.7,
itp=65537,itn=131073,hrng=50,lrng=15,
save.file=TRUE,file.name="LTQ-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. |
itp |
|
itn |
|
hrng |
|
lrng |
|
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 four Scan Events (Xcalibur, Thermo
Finnigan). Each *.cdf
-file will result four mass spectra. Principle in
brief: load *.cdf
-file (pathcdf
and filecdf
information in
runinfo.csv
); sort scans (m/z and intensity values) into four lists.
For each list: 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.
See the description in the Examples
below.
A list containing the following components:
posh |
Matrix [runs x nominal masses] of high mass range in positive ionisation mode. |
posl |
Matrix [runs x nominal masses] of low mass range in positive ionisation mode. |
negh |
Matrix [runs x nominal masses] of high mass range in negative ionisation mode. |
negl |
Matrix [runs x nominal masses] of low mass range in negative 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 LTQ-mean.RData
in folder my_path
.
Additionally, single items are saved by default as TEXT files: posh.txt
,
posl.txt
, negh.txt
, negl.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 65 66 67 68 69 70 71 72 73 | ## To run fiems_lqt_main, copy and paste the following code segment. Uncomment
## and change the file path and name appropriately.
## Example profiles can be downloading on the FIEmspro webpage
## 050509-Abr1.zip must be extrated in folder that defines 'my_path'
## For e.g.
## Not run: my_path <- "D:/Temp/050509-Abr1"
## The same folder should also contain a 'runinfo' file
## e.g.
## Not run: runinfo <- "runinfo.csv"
## Process each profile defined in 'runinfo'
## Not run: tmp <- fiems_lct_main(my_path,runinfo,35,95,190,250,limit=0.82,
save.file=TRUE,file.name="LTQ-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:/../070122-ABR1-A-repeat/cdf | 01.cdf | 1
## 2 | D:/../070122-ABR1-A-repeat/cdf | 02.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.
## LTQ Instrument Method for Flow-Injection-ESI-MS (FIE-MS):
## - 1 Segment, 5 min Acquisition
## - 4 Scan Events:
## -- 1: ITMS + c norm o(50.0-2000.0)
## -- 2: ITMS + c low injrf=20.0 o(15.0-200.0)
## -- 3: ITMS - c norm o(50.0-2000.0)
## -- 4: ITMS - c low injrf=20.0 o(15.0-200.0)
## Infusion Profile (Sketch):
## _
## / \
## / \
## / \_
## / \______
## _____/ \________________________
## 0 1 2 3 4 5 [min]
## |--- ---| |-------|
## [x1] [x2] [x3] [x4] [scan reading]
## sample background
## Using the above LTQ Instrument Method for FIE-MS
## the actual scan readings x1 to x4 of e.g. scan event 1 have to be
## subtracted by 1 (the Scan Event) and
## divided by 4 (total of 4 Scan Events):
## e.g. [y1] = ([x1]-1)/4 => scrange = c(y1,y2,y3,y4)
## with (ideally): y2 - y1 = y4 - y3
## Raw data conversion to ANDI NetCDF-file:
## XConvert-program (Xcalibur, Thermo-Finnigan)
|
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