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Complex Peptide Mixture Analysis on the Finnigan LTQ Linear Ion Trap Mass Spectrometer

cycle on the Finnigan LTQ, more experiments and thus more information is obtained from each sample, and in less time. Figure 4 illustrates the Triple Play feature, with a sequence setup to perform one full-scan, one zoom scan, and one MS/MS scan every 1.5 sec.

The zoom scan capability (Figure 4B) is used to determine the charge state of each peptide in order to improve data analysis speed. For example, the zoom scan of the m/z 418 peptide determined that this peptide is doubly charged based on the mass difference of 0.5 for each sequential peak from the zoom scan. This figure also demonstrates the high quality MS/MS spectra (Figure 4C) produced from a low abundant ion in the MS spectrum (Figure 4A). This added performance provides additional structural information and added confidence in the identification of minor components in a complex mixture.

Increased peptide coverage is also achieved with this higher performance. An example is shown in Table 1, illustrating a two-fold increase in coverage for four proteins. Percentage is based on the number of amino acids matched in this protein.

A dramatic increase (>5 times) in protein identification is summarized in Table 2. A comparison of results from the two different gradients also illustrates that use of a faster gradient on the LTQ still yields a significantly greater number of protein identifications.

Conclusions
Speed to results, and increased confidence in the results are important factors in advancing an investigation or research project.

These examples illustrate the benefits resulting from some of the key performance attributes of the Finnigan LTQ. Increased peptide coverage and protein identification, along with increased confidence in results are achieved in less time. The rapid scanning and unmatched fast cycle time, in combination with unprecedented high
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