Protocol

Tandem Mass Spectrometry Analysis Using the ThermoFinnigan LCQ System

This protocol was adapted from "The Use of Mass Spectrometry in Proteomics," Chapter 8 in Proteins and Proteomics (ed. Simpson). Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY, USA, 2003.

INTRODUCTION

This protocol provides guidance for setting the parameters for a typical data-dependent MS/MS acquisition analysis using the ThermoFinnigan LCQ system. The method consists of a continual cycle beginning with one scan of MS (scan one), which records all of the m/z values of the ions present at that moment in the gradient, followed by two rounds of MS/MS. The initial MS/MS scan is of the first most-intense ion recorded from the MS scan. The second MS/MS scan is of the second most-intense ion recorded from scan one. Dynamic exclusion is activated to improve the protein identification capacity during the analysis.