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

ents: Normal gradient: 2-65% B in 180 min., 65-80% B in 5 min and hold for 5 min, 80-2% B in 0.5 min
Fast gradient: 2-65% B in 120 min, 65-80% B in 5 min and hold for 5 min, 80-2% B in 0.5 min.

Mass Spectrometers Finnigan LTQ, and Finnigan LCQ Deca XP Plus
Ionization mode: NanoSpray, positive ion
Scan sequence: Full-scan MS, Zoom scan, MS/MS scan
Acquisitionmodes: Normal, Data Dependent and Dynamic Exclusion

The zoom scan was used to determine the charge state of each peptide, therefore shortening the time required for data searching analysis. Results were compared to those obtained from the same experiment performed using a conventional 3D ion trap.

Results and Discussions

Data Analysis
Protein identification was performed using the Turbo- SEQUEST algorithm in the BioWorks 3.1 software package (Thermo Electron) and the Swiss-Prot human database (Swiss Institute of Bioinformatics, Geneva, Switzerland). The identified peptides were further evaluated using charge state versus cross-correlation number (XCorr). The criteria for positive identification of peptides was XCorr > 1.5 for singly charged ions, XCorr > 2.0 for doubly charged ions, and XCorr > 2.5 for triply charged ions.

Results

The plasma peptide mixture was analyzed under two different LC gradients on the Finnigan LTQ and Finnigan LCQ Deca XP Plus. Figure 1 shows a four-fold increase in the number of scans acquired on the Finnigan LTQ in comparison to the Finnigan LCQ Deca XP Plus. This fast scan speed capability, in combination with the unparalleled high sensitivity on the Finnigan LTQ, produces extremely high quality MS/MS spectra, which in turn results in increased confidence of analyte identification. Figures 2 and 3 compare the MS/MS spectra obtained on the two instruments. Moreover, with the rapid duty
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