Targeted biomarker detection via whole protein ion trap tandem mass spectrometry: thymosin β4 in a human lung cancer cell line

N‐Terminally acetylated thymosin β4, a species implicated for use as a cancer biomarker, was identified in a human lung cancer cell line using ion trap tandem mass spectrometry at the whole protein level. Ion–ion proton transfer reactions were used for parent ion concentration/manipulation and to simplify interpretation of product ion spectra. Dissociation data for the +6 to +3 charge states are reported. As is usually the case, structural information available from the ion trap collisional activation of the protein is sensitive to parent ion charge state. Each parent ion charge state selected, however, provided sufficient information to make a confident identification. Furthermore, each charge state provided relatively rich fragmentation. Therefore, any of the charge states can be used to detect with high specificity thymosin β4 in a complex protein mixture. There are advantages associated with the rapid detection of protein biomarkers at the whole protein level, as opposed to the peptide level following protein digestion, particularly for relatively small protein and polypeptide biomarkers. Having identified and characterized the protein, product ion spectra obtained directly, without recourse to ion–ion proton transfer reactions, can be used for library matching. However, ion–ion proton transfer reactions for parent ion concentration and charge state purification are advantageous in addressing relatively complex mixtures. Copyright © 2005 John Wiley & Sons, Ltd.