LC-MS data pre-processing
Input peak data and information to allow all possible combinations of the follow pre-processing operations to be downloaded in a zip file:
Removal of variables with too many zeros (Z):
You will be asked for the percentage of zeros you would be pre-pared to accept for a variable.
Variables with more than this percentage of zeros will be removed (and the variable information file updated accordingly);
Normalisation to total ion count (N)
QC correction (QC):
Each variable will be corrected for batch differences by subtracting the mean of the closest (in data collection order) two QC values for this variable
BG correction (BG)
Each variable will be corrected for batch differences by subtracting the relevant value from a smoothed trend obtained over all observations (QC and non-QC, in data collection order) for this variable.
See Rusilowicz et al.2016 for more details of correction methods.
The data file should be a space-delimited text file with batch information given on the first line as:
m1 m2 m3 … mN where mi is the number of non-QC observations between the consecutive QCs, QCi and QCi+1 and there are N+1 QCs and M = m1 + m2 + m3 + … + mN + N + 1 observations in total.
For example, if there are 4 QCs with 3 observations between the QC1 and QC2, 5 observations between the QC2 and QC3 and 4 observations between the QC3 and QC4, the first line of the data file would be:
3 5 4
The following M lines of the file should consist of the LC-MS data with a new line for each observation (example) in run order.
Download Example data file
Variable information should be given in a space-delimited text file with a variable number followed by the m/z value and retention time on each line.
Example variable information file