version: 1.0.0
mzmatch version: 1.0.2
author: RA Scheltema (

Filters all the non-reproducibly detected signals from the given PeakML file. The approach loads the PeakML file and determines based on the set-information, which of the sets of peaks contain signals that were not reproducibly detected in the replicates. The reproducability measure is defined as the Reproducibility Standard Deviation (RSD; stddev/mean), which is calculated from all the intensity values in a set. When the PeakML file contains multiple sets (in the header) the RSD is evaluated for each of the sets, and an entry is discarded when all of the sets fail the set threshold.


Windows batch-file:
SET JAVA=java -cp mzmatch.jar -da -dsa -Xmn1g -Xms1425m -Xmx1425m -Xss128k -XX:+UseParallelGC -XX:ParallelGCThreads=10

REM extract all the mass chromatograms
%JAVA% mzmatch.ipeak.ExtractMassChromatograms -v -i raw\*.mzXML -o peaks\ -ppm 3

REM combine the extracted mass chromatograms
%JAVA% mzmatch.ipeak.Combine -v -i peaks\24hr_*.peakml -o 24hr.peakml -ppm 3 -rtwindow 30 -combination biological
%JAVA% mzmatch.ipeak.Combine -v -i peaks\28hr_*.peakml -o 28hr.peakml -ppm 3 -rtwindow 30 -combination biological
%JAVA% mzmatch.ipeak.Combine -v -i peaks\32hr_*.peakml -o 32hr.peakml -ppm 3 -rtwindow 30 -combination biological

REM remove unstable signals
%JAVA% mzmatch.ipeak.filter.RSDFilter -v -rsd 0.35 -i 24hr.peakml -o 24hr_rsd.peakml -rejected rsd\24hr.peakml
%JAVA% mzmatch.ipeak.filter.RSDFilter -v -rsd 0.35 -i 28hr.peakml -o 28hr_rsd.peakml -rejected rsd\28hr.peakml
%JAVA% mzmatch.ipeak.filter.RSDFilter -v -rsd 0.35 -i 32hr.peakml -o 32hr_rsd.peakml -rejected rsd\32hr.peakml

REM combine the extracted mass chromatograms
%JAVA% mzmatch.ipeak.Combine -v -i *hr_rsd.peakml -o timeseries.peakml -ppm 3 -rtwindow 30 -combination set

1. Shah V, Midha K, Findlay J, et al: Bioanalytical Method Validation—A Revisit with a Decade of Progress. Pharmaceutical Research. 2000, 17:1551-1557

Commandline options*
-i [filename] Option for the input file(s). The only allowed format is PeakML and when it is not set the input is read from standard in.
-o <filename> Option for the ouput file(s). The file is written in the PeakML file format and peaks that passed the defined filter are saved here. When this option is not set the output is written to the standard out. Be sure to unset the verbose option when setting up a pipeline reading and writing from the standard in- and outputs. When multiple input files are defined this option needs to point to a directory.
-rejected <filename> Option for the file where to write all the rejected peaksets. When this option has not been set the rejected peaksets are not written.
-rsd <double> The RSD value as a percentage between [0..1]. This percentage indicates the maximum an individual measurement can deviate from the mean intensity of all the peaks in the set.
-h   When this is set, the help is shown.
-v   When this is set, the progress is shown on the standard output.
* per option: [] denotes multiple input values; <> denotes a single input value