Retention Time Prediction with X!Tandem

Created: 2012-09-03 10:43:31      Last updated: 2012-09-03 10:44:33

This workflow identifies peptides from tandem mass spectra using X!Tandem as in a standard installation of the Trans-Proteomic Pipeline (TPP, version 4.6, but earlier versions should also work). The peptide-spectrum matches are validates using PeptideProphet (also from a standard installation of TPP) and peptides with at least a probability 0.95 are used to train a linear retention time predictor (Palmblad et al., 2002), whereby retention coefficients are also derived. These indirectly provide information on the chromatographic stationary and mobile phase (composition and pH) and the gradient. The two Rshell scrips visualize the prediction versus measured retention times and amino acid coefficients colored by physico-chemical properties (basic/acidic/polar etc.).

Information Preview

Information Run

Run this Workflow in the Taverna Workbench...

Option 1:

Copy and paste this link into File > 'Open workflow location...'
[ More InfoExpand ]

Information Workflow Components

Information Authors (1)
Information Titles (1)
Information Descriptions (1)
Information Dependencies (0)
Inputs (4)
Processors (10)
Beanshells (2)
Outputs (2)
Datalinks (21)
Coordinations (2)

Information Workflow Type

Taverna 2

Information Uploader

Information License

All versions of this Workflow are licensed under:

Information Version 1 (of 1)

Information Credits (3)


Information Attributions (1)


Information Tags (5)

Log in to add Tags

Information Shared with Groups (0)


Information Featured In Packs (0)


Log in to add to one of your Packs

Information Attributed By (3)


Information Favourited By (0)

No one

Information Statistics


Citations (0)


Version History

In chronological order:

Reviews Reviews (0)

No reviews yet

Be the first to review!

Comments Comments (1)

Log in to make a comment

  • Monday 03 September 2012 10:47:29 (UTC)

    This is the local-only version of the workflow. The Trans-Proteomic Pipeline needs to be installed in the standard directories and rt 3.0 should be available where specified in the rt component.

    A version with a Web service rt is also available.

Workflow Other workflows that use similar services (0)

There are no workflows in myExperiment that use similar services to this Workflow.