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.).

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  • 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.




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