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J Biomol Tech. 2010 September; 21(3 Suppl): S50.
PMCID: PMC2918192

Comparison of Multi-Dimensional Separation of Peptides Using Traditional MudPIT and Parallel Isoelectric Focusing

B.S. Phinney
University of California, Davis, CA, United States



Bottom up proteomics analysis of complex mixtures of proteins commonly begin with either a protein-level separation (i.e. SDS-PAGE, iso-electric focusing) or a peptide level separation (Mudpit) before the proteins are identified by LC-MS/MS. Here we will compare the efficiency of two different types of two-dimensional peptide-level separations. We will compare the total proteins identified by liquid chromatography tandem mass spectrometry, sequence coverage and dynamic range. The two techniques differ only in the 1st dimension: the first being iso-electric focusing of peptides in pH range 4.2-6.2 (Protein Forest dPC peptide chip) and the second being strong cation exchange (SCX) chromatography and timed fraction collection of peptides.

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