Maintained by ppernot

pretreatFTICR.R script

Raw FT-ICR DMS files are very large and are painful to analyse directly. Two reduction methods can be used and combined:

  1. filtering the data to match as well as possible a predefined regular grid

  2. keeping only the data that match a list of targets

Combining both methods might enable to reduce the MS size by nearly 90%, in the usual applications.

The script is controlled by the following parameters:

# User configuration params =========================

## Data and results directories
origMsDir = 'Test_FTICR_2/FTICR'
compMsDir = 'Test_FTICR_2/FTICR_compressed'
ms_type   = 'fticr'

## Compress mode
compMode  = c('grid','targets','grid+targets')[3]

## Grid specifications
mzMin     = 70
mzMax     = 250
dmz       = 0.001

## Targets specifications
tgTable   = 'Test_FTICR_2/targets_list.csv'
dmzTarget = 0.5 # Delta m/z to keep around target

## Short run to check ?
test      = FALSE


Note: it is best to store the spectra as compressed .gz files. The disp space is well reduced and all scripts can handle them transparently.