Introduction

A variety of stable isotope reagents have been developed for relative quantification in proteomics, including ICAT,® SILAC, 18O, AQUA,™ and iTRAQ.™1,2,3 Most methods enable quantification in the full MS scan and peptide identification based on subsequent fragmentation (MS/MS) of precursor ions, with the exception of iTRAQ where both the identification and quantification is performed in the MS/MS scan. This requirement was thought to make the iTRAQ reagent incompatible with ion traps which, upon MS/MS analysis of large m/z iTRAQ-labeled peptides, would suffer from the “1/3 Rule” and be unable to effectively analyze the iTRAQ reporter ions at m/z 114–117. However, the LTQ can perform additional scans beyond just MS/MS which allows quantification of iTRAQ reporter ions in a subsequent scan.

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