Taverna Workflows for Proteomics

Copyright Notice

These Taverna workflows, pepAlign, pepWarp, msHybrid, and msRecal are Copyright (C) 2006-2011 Jeroen de Bruin and Magnus Palmblad. They are free software; you can redistribute them and/or modify them under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version.

These programs and workflows are distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.

You should have received a copy of the GNU General Public License along with any of these program; if not, write to the Free Software Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.

The Copyright of the incorporated tools such as CompassXport, X!Tandem and PeptideProphet™ are the properties of third parties. Please see their corresponding official websites for more details.

Getting the Workflows and Components

All workflows and components can be downloaded as a package, installed and configured using the provided installer as described.

In the paper by de Bruin et al, four workflows are described:

Workflow 1 (with embedded Workflow 1a)
Workflow 2 (with embedded Workflow 2a)
Workflow 3
Workflow 4

These workflows incorporate CompassXport from Bruker Daltonics, X!Tandem, PeptideProphet and other tools of the Trans-Proteomics Pipeline.

They also deploy four specialized programs:


These programs in turn make use the mzXMLLib and pepXMLLib libraries for reading and writing mzXML and pepXML files respectively. (Left-click or right-click and choose "Save Link As..." to download them.)

To use the latter tools, or any external program or utility, these first need to be acquired, installed and (optionally but ideally) tested before being used in a Taverna workflow that assumes these are running on the local machine. For external tools and Web Services, only the workflows are needed.

Taverna can be downloaded here.

Executing the Workflows

To run the workflows, a parameter set specifying input files and processing options is also required. Examples of such parameter sets for Workflow 1 to Workflow 4 in the paper, that were also used to generate the data in the paper, can be found here.

Taverna workflows can be run through the graphical workflow interface, or on the command line. Please see the Taverna documentation for more information on how to execute workflows.


We strongly encourage feedback, positive or negative, questions, comments and suggestions for improvement. If you need help adapting the workflows for similar analytical tasks, feel free to contact Magnus Palmblad or Jeroen de Bruin.