Mass-Coded Abundance Tagging for Protein Identification and Relative Abundance Determination in Proteomic Experiments

Abstract

Advances in mass spectrometry have led to the emergence of the distinct field of proteomics. One aim of proteomics, the identification of the protein components of complex biological mixtures, is now routinely realized, typically by peptide mass mapping following matrix-assisted laser desorption/ionization (MALDI) mass spectrometry (MS) or by peptide sequence determination from tandem mass spectra obtained by electrospray ionization followed by collision-induced dissociation (CID) (1). Both approaches rely on the identified proteins being present in DNA or protein sequence databases. This is because the behavior of ionized peptides in MS experiments is somewhat unpredictable and the resulting spectra are searched against “idealized” spectra generated from the sequence databases to find the nearest match. Nevertheless, both approaches have been highly successful, with thousands of proteins identified in a single large-scale analysis (reviewed in ref. 2). A method that is independent of databases would be useful in certain cases, however, especially for protein samples deriving from organisms whose genomes remain unsequenced, proteins with erroneous sequences deposited in the databases, or proteins whose splicing patterns or modification states are unknown. Another partially fulfilled goal of proteomics is to determine the quantities of each protein present in a mixture, or at least the relative abundance of proteins present in two different samples, such as a test sample and a reference control. Several approaches for determining relative abundance in proteomic experiments have involved differential incorporation of stable isotopes into one of the samples, using either labeled growth media (3) or postexperimental chemical labeling (4,5). At least two methods using nonisotopic reagents for purposes of proteomic quantification have recently been reported (6,7)