Quandenser condenses quantification data from label-free mass spectrometry experiments.
An installer for all major platforms (Windows, OS X, Ubuntu, etc.) can be found on the Release page. Furthermore, Java >=1.6 has to be installed.
If you prefer to compile from source, or are running on a different operating system, click here.
Note that we also provide Docker and Singularity support through the Quandenser-pipeline project.
Usage:
quandenser -b <batch_file_list> -f <output_directory>
<batch_file_list> is a flat text file with the absolute path to each of the mzML files (one per line). The mzML files should be peak picked on both MS1 and MS2 level.
If everything executed correctly, you will find a file with the quantified feature groups at <output_directory>/Quandenser.feature_groups.tsv and one or several files with consensus spectra in <output_directory>/consensus_spectra/MaRaCluster.consensus.part<x>.ms2. Different output formats for the consensus spectra files can be specified using the -o option and the consensus spectra can subsequently be searched by any search engine.
An example run including downstream analysis with Triqler can be found here: https://app.box.com/s/kp4219dc22l3gq27014nms8oco594c2i
The folder contains a ReadMe file with instructions on how to run the example.
Note that this same pipeline is also implemented in the Quandenser-pipeline project, which allows users to run the entire pipeline from RAW files to Triqler results using Nextflow with pre-built Singularity or Docker images.
First, clone the repository using git clone --recursive https://github.com/statisticalbiotechnology/quandenser.git. Note the --recursive flag which is needed to pull in the submodules.
Quandenser depends on the Proteowizard and Boost libraries, which are automatically installed by the builder scripts.
To install Quandenser, you can use the provided installation script ./quickbuild.sh (Unix) or ./quickbuild.bat/./quickbuild64.bat (Windows 32-bit and 64-bit respectively), which calls the appropriate build script for your platform located at admin/builders/<platform>_build.<ext>. By default, it will install the executables in the /usr/bin folder (needs superuser rights). If you do not have superuser rights or want to install the executable somewhere else, modify the script accordingly by setting the -DCMAKE_INSTALL_PREFIX flag to the desired location.