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ProteoWizard provides a modular and extensible set of open-source, cross-platform tools and libraries. The tools perform proteomics data analyses; the libraries enable rapid tool creation by providing a robust, pluggable development framework that simplifies and unifies data file access, and performs standard chemistry and LCMS dataset computations.

How to Use

Proteowizard uses environment modules. Type

module load proteowizard

at the prompt.

Proteowizard is a set of executables:

chainsaw   msaccess     msconvert  msistats   pepcat          sldout
idcat      msbenchmark  msdiff     mspicture  pepsum          txt2mzml
idconvert  mscat        msdir      peakaboo   qtofpeakpicker

For help, Run the command with no arguments.


msconvert data.RAW --32 --zlib --filter "peakPicking true 1-" --filter "zeroSamples removeExtra"

How to run on Biowulf

As a batch job

Create a batch script, for example:

# -- this file is pwiz.sh --
#PBS -N pwiz
#PBS -o pwiz.o
#PBS -e pwiz.e

module load proteowizard
msconvert data.RAW --zlib --filter "peakPicking true [2,3]"

Then submit it to an appropriate nodetype. For example,

qsub -l nodes=1:c16 pwiz.sh

As a swarm job

Create a swarmfile containing commandlines (for example, the file is named "swarmfile"):

msconvert data_1.RAW --mzXML
msconvert data_2.RAW --mzXML
msconvert data_3.RAW --mzXML
msconvert data_4.RAW --mzXML

Then submit it to swarm like this:

swarm --module proteowizard --file swarmfile