mzmatch.ipeak.util
Recovery

version: 1.0.0
mzmatch version: 1.0.2
author: RA Scheltema (r.a.scheltema@rug.nl)


mzmatch.ipeak.util.Recovery
Complements missing signals to a combination file produced by mzmatch.ipeak.Combine (or another combine tool for that matter), containing sets of signals (mass chromatograms or backgroundions) produced by the same analyte in different measurements. It is possible that the combiner incorrectly missed signals, or was offered files lacking the missing signals (eg signals from a timepoint removed by the tool mzmatch.filter.RSDFilter, which can be linked to a stable signal from another timepoint).

For this application to function correctly it is required that the files containing the missing signals are generated from the same measurement, as the id's for the measurement needs to correspond.

Example(s)

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

REM recover mass chromatograms
%JAVA% mzmatch.ipeak.util.Recovery -v -i timeseries.peakml -bins rsd\*.peakml -o timeseries_recovered.peakml -ppm 3 -rtwindow 30

References:


Commandline options*
-i <filename> Option for the input files. The only allowed file format is PeakML containing either mass chromatograms or backgroundions at the lowest level (ie the result of another Combine can be used).
-o <filename> Option for the ouput file. The resulting matches are written to this file in the PeakML file format.
When this option has not been set the output is written to the standard output. Be sure to unset the verbose option when setting up a pipeline reading and writing from the standard in- and outputs.
-recovered <filename> Optional output file where the all the sets that have been complemented with missing signals are written.
-bins [filename] Option for the files containing the missing signals. The only allowed file format is PeakML containing either mass chromatograms or backgroundions at the lowest level (ie the result of another Combine can be used).
-ppm <double> The accuracy of the measurement in parts-per-milion. This value is used for the matching of mass chromatogram (collections) and needs to bereasonable for the equipment used to make the measurement (the LTQ-Orbitrap manages approximately 3 ppm).
-rtwindow <double> The retention time window in seconds, defining the range where to look for matches.
-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