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J Biomol Tech. 2010 September; 21(3 Suppl): S38–S39.
PMCID: PMC2918103

Ion Funnel Transmission Increases Number of Protein Identifications in Complex Proteomic Samples

M. Lubeck,2 R. Hartmer,2 C. Gebhardt,2 and A. Schneider2
1Bruker Daltonics Inc., Fremont, CA, United States;
2Bruker Daltonik GmbH, Bremen, Germany



Although ion traps are used as workhorses in life science due to their high spectral rate and unmatched MS/MS sensitivity, there is a high demand to further push their limits. An improved ion transfer by funnel-ion guides allows for a substantial increase of ion flux. However, as the benefit of the higher ion flux depends strongly on the ratio of accumulation time and scan duration, it is crucial to couple funnel inlets with fast scan rates to achieve best performance. To test this approach, peptide identification from complex mixtures using LC-autoMSn is investigated as key application. All measurements were carried out on a Bruker amazon ion trap equipped with a two-stage funnel ion-guide. Via an improved control of the non-linear ejection process and the trap environment faster scan rates as well as a higher mass resolution are readily achieved. As a sample of high complexity digests of Escherichia coli cells were analyzed using 90 min nanoLC gradients at a flow rate of 300nl/min. Depending on fragmentation type (CID or ETD) trypsin or Lys-C were used to obtain peptides most suitable for the respective technique. Peptide identification was performed with Mascot search algorithm and results validated using decoy searches. For MSMS signals a 10fold better signal to noise could be obtained. Several concentrations of the complete e.coli digest from 5-500 ng protein on column were investigated: The combination of ion-funnel interface and fast scan rates allows for more information from limited sample amounts. If sample availability is less critical the increased MSMS sensitivity enables further fractionation of the sample or repeated investigations using information from previous runs.

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