Multiple ion/ion reactions in the 3D ion trap: Selective reagent anion production for ETD and PTR from a single compound

Electron transfer dissociation (ETD) is dedicated for the sequence analysis of larger peptides and proteins. It is particularly suited for the identification of post-translational modifications (PTMs), as weakly bonded PTMs like phosphorylation or glycosilation survive the electron-induced fragmentation of the backbone of the amino acid chain. A drawback however is that ETD MS/MS-data of proteins are typically highly complex because a large number of multiply charged fragment ions are obtained. This complexity of the ETD MS/MS-data is significantly reduced when the initial electron-induced fragmentation is followed by a subsequent proton transfer reaction (PTR) to reduce the charge states of the multiple charge fragments. Traditionally ETD and PTR are accomplished using different reagent ions generated from different neutral compounds. Here we show that the formation of reagent anions dedicated for either ETD or PTR can be accomplished from only one neutral compound. By altering the voltage of the negative chemical ionization source (nCl-source) either the odd electron anion (appropriate for ETD) or the even electron anion (appropriate for PTR) is extracted. The PTR-reagent as well as the ETD-reagent are exclusively generated at an appropriate ionization chamber voltage and no further mass selection of the reagent anion is needed. The voltage of the ionization chamber can be switched within milliseconds allowing applications for rapid sequential ion/ion reactions. One of the more interesting sequential ion/ion reactions is the combination of ETD followed by PTR, which make top-down sequencing of intact proteins possible for ion trap instruments. (C) 2008 Elsevier B.V. All rights reserved.