QuickMod is a spectral library search based MSMS data analysis tool,
designed to identify modified peptides.
Ahrné E., Nikitin F., Lisacek F., Müller, QuickMod: A Tool for Open Modification
Spectrum Library Searches, J. Proteome Res., 2011, 10 (7), pp 2913–2921
A short description of the tool is available
A spectral library is a database of already identified MSMS spectra.
Typically a peptide entry in the library is represented by a consensus
spectrum; an averaged spectrum compiled from multiple, same precursor
charge state, spectra representing the same peptide species.
The QuickMod algorithm assumes that the precursor mass difference
between a query spectrum and a candidate library spectrum can be
explained by a modification. Based on this assumption the two spectra
are aligned and a list of similarity measures calculated.
In a second step the most likely attachment position of the modification
The QuickMod scoring scheme was developed by carefully examining and
combining various peak intensity and peak coverage based scoring features.
QuickMod provides efficient means to evaluate the quality of a
MS/MS dataset by revealing modifications induced by sample handling
and preparation such as oxidation, pyro-Glu and salt adducts.
More importantly, the search algorithm is capable of identifying
known PTMs while suggesting a list of previously unknown or
unexpected PTMs, to be verified in targeted experiments.
usage: java -jar QM-x.x.jar -h
-h Print QuickMod help
-i <arg> Absolute path to parameters file, (Required)
-s <arg> library name for binary file creation
-sN <arg> binary library batch size (# spectra)
-sO <arg> binary library out directory
-v verbose mode
To increase memory of JVM try java -Xmx2048M -jar QM-x.x.jar
The latest version is v1.03 - Download app with
the default properties file
or access the
||The dependencies for MzML reader were missing!
||java.lang.NumberFormatException thrown while flushing
results. QM was crashing when decimal separator was not '.' (i.e. LANG=fr_FR.utf8).
support zip and tar.gz type files in "libraryPath" and "expDataPath" params
now generates only one pepxml file
|Bug Fixed||QM was crashing due to an internal error in PepXML exporter
(threw java.lang.illegalArgumentException - bad format <mzdata-filename.start-scan.end-scan.charge>)
|New||Add PepXML format export
(set new tag 'pepXmlExport=true' in parameters file).