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J Biomol Tech. 2010 September; 21(3 Suppl): S36–S37.
PMCID: PMC2918044

An Ion Trap with Increased Resolution and Scan Speed for Top-Down Proteomics with ETD/PTR

C. Albers,2 A. Brekenfeld,2 C. Gebhardt,2 and R. Hartmer2
1Bruker Daltonics Inc., Fremont, CA, United States;
2Bruker Daltonik GmbH, Bremen, Germany



MS/MS-techniques for top-down proteomics are electron-induced fragmentation processes like ECD or ETD. However, the analysis of ETD data of highly charged proteins is complicated because of multiply charged and overlaid fragment ions. The complexity of the ETD MS/MS-data is reduced when the initial ETD step is followed by proton transfer reaction (PTR) reducing the charge states of the multiple charge fragments. However, even following PTR a resolving power for ETD-fragments of z > 4 is demanded. We investigate the role of the increased resolution of a modified ion trap on top-down sequencing of larger peptides and proteins with ETD/PTR. An ion trap with improved control of the non-linear ejection process and faster scan modes as well as a higher mass resolution was used. ETD/PTR of isolated proteins is performed with reagent anions dedicated for either ETD or PTR. The formation of the different reagent anion is accomplished from only one neutral compound by altering the voltage of the negative chemical ionization source. The resolution of the used traps at a scan speed of 4,600 Th/sec is ideal for the identification of fragment ions with charge states up to 6+. Since with each proton transfer the m/z of an ETD-fragment will be shifted towards higher masses, the used high m/z range up to 3000u is essential for sufficient sequence coverage of intact proteins. We will present the impact of the increased resolution on the sequence analysis of intact proteins with a molecular weight up to 35kDa. With the increased resolution we were able to sequence a purified biomarker protein which has been previously discovered via MALDI imaging of breast cancer tissues.

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