Correlation of acidic and basic carrier ampholyte and immobilized pH gradient two‐dimensional gel electrophoresis patterns based on mass spectrometric protein identification

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Abstract
Separation of proteins on either carrier ampholyte‐based or immobilized pH gradient‐based two‐dimensional (2‐D) gels gives rise to electrophoretic patterns that are difficult to compare visually. In this paper we have used matrix‐assisted laser desorption/ionization mass spectrometry (MALDI‐MS) to determine the identities of 335 protein spots in these two 2‐D gel systems, including a substantial number of basic proteins which had never been identified before. Proteins that were identified in both gel systems allowed us to cross‐reference the gel patterns. Vector analysis of these cross‐references demonstrated that there is no obvious pattern by which the mobility of a protein in one gel system can be used to predict its mobility in the other. Thus, as laboratories adopt the immobilized pH gradient‐based 2‐D gel systems, the only reliable means of translating the data gained with the carrier ampholyte‐based gel system is to positively identify the proteins in both 2‐D systems.