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

Chromatography and Mass Spectrometry Application Note

Melissa Chen, Diane Cho, Thermo Electron Corporation, San Jose, CA

Introduction
Rapid identification of low abundance proteins in complex mixtures is one of the key objectives for the use of mass spectrometry in proteomics research. Traditionally, this approach has utilized 3-dimensional quadrupole ion trap systems, such as the Finnigan LCQ Deca XP Plus and the Finnigan ProteomeX. Recent developments in ion trap mass spectrometry, and the introduction of the Finnigan LTQ linear ion trap mass spectrometer provide further tools to boost sample throughput, and produce higher peptide coverage with a higher degree of confidence for protein identification.

Goal
This study demonstrates how the fast cycle time and unparalleled MS/MS sensitivity of the high performance Finnigan LTQ linear ion trap mass spectrometer result in increased coverage, and faster and more confident protein identification.

Experimental
LC/MS/MS analysis of enzymatically modified human plasma samples was performed using NanoSpray ionization. The TurboSEQUEST algorithm was used for data analysis and protein identification.

Sample Preparation
A whole human plasma sample (5 mg, Sigma) was reduced, alkylated, and enzymatically digested. A total of 3 uL of the digested mixture (1 ug/uL) was loaded onto a reversed-phase (RP) C18 column for LC/MS analysis.

LC Separation and MS Analysis
HPLC
HPLC system: Finnigan Surveyor MS pump with a flow splitter.
Column: 0.15100 mm C18 (Thermo Electron)
Flow rate: 600 nL/min
Mobile phase A: Water with 0.1% Formic Acid
B: Acetonitrile with 0.1% Formic Acid

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