Plasma Precipitation Analysis

ABOUT THE WORKFLOW This workflow was used to analyze the data in a manuscript by Mostovenko et al. (2012, submitted), comparing proteins in the precipitate with those left in solution after organic solvent precipitation. However, the workflow is generally applicable in comparisons of any binary fractionation method in proteomics, where the fractions are analyzed by liquid chromatography-tandem mass spectrometry. The workflow identifies proteins by SpectraST spectral library search and X!Tandem database search, validates the results using PeptideProphet and combines them with InterProphet. The proteins are quantified by spectral counting and the fractions compared with respect to protein molecular weight, isoelectric point and GRAVY hydrophobicity score. In the end, an Rshell script produces the figures as presented in the manuscript. Executing the workflow requires Rserve running and the Trans-Proteomic Pipeline (http://tools.proteomecenter.org/wiki/index.php?title=Software:TPP) installed with default settings and in the default location. The Rshell script contains the location where the figures will be generated. All other output files are stored in the input data folders by default. The version of X!Tandem called from this workflow is separate from the one installed with the Trans-Proteomic Pipeline (the location specified in the Tandem components). COPYRIGHT NOTICE This workflow is based on open software and the workflow itself is shared under the Creative Commons Attribution-ShareAlike 3.0 Unported License (CC BY-SA) (see http://creativecommons.org/licenses/by-sa/3.0/) Copyright© 2012 Ekaterina Mostovenko, Jeroen de Bruin, Yassene Mohammed and Magnus Palmblad