version: 1.0.1
mzmatch version: 1.0.2
author: RA Scheltema (

Converts the contents of a PeakML file to a tab-separated text file. In order to make the file useable in a spreadsheet environment, only the top-level data for each measurement is given in the file. This application has been extended with support for outputting annotations.


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.convert.ConvertToText -v -i file.peakml -o file.txt -annotations ",charge"


Commandline options*
-i [filename] The input file in the PeakML file format. When this option is not set, the input is read from the standard input.
-o <filename> The output file in text format. When this option is not set, the ouput 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.
-databases [filename] Optional list of database-files in the moleculedb format. These databases are used to translate the id's in the annotation 'identifications' to full molecule names.
-annotations [label] Optional list of annotations to be exported.
-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