Strong cation exchange chromatography Isoelectric focusing SDS-PAGE Comparison Taverna Scientific workflows a b s t r a c t Multiple fractionation or separation methods are often combined in proteomics to improve signal-to-noise and proteome coverage and to reduce interference between peptides in quantitative proteomics. Furthermore, a given fractionation method provides additional information on the analytes, such as molecular weight, hydrophobicity or isoelectric point that can be used to

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... ove identification, and to discover protein splice variants or large post-translational modifications. Here we describe a Taverna scientific workflow for analysis and comparison between strong cation exchange (SCX) chromatography, peptide isoelectric focusing (pIEF) and SDS-PAGE performed using robust capillary LC and ion trap tandem mass spectrometry. (M. Palmblad). identification and possibly quantitation of more peptides and proteins, including those of lower abundance. At the same time, fractionation adds information about the analytes without any additional analytical effort. This information can be used together with the tandem mass spectrometry data in the validation of peptide-spectrum matches. A wide range of fractionation strategies for peptides and proteins are generally available, often combined in multidimensional methods or systems. Any type of chromatographic separation can be used at the protein level, including ion exchange [1], reversed phase [2], hydrophobic interaction 2212-9685