Instrumentation for LC-MS/MS in Proteomics - LC-MS/MS in Proteomics: Methods and Applications - page 46

Chapter 3

Instrumentation for LC-MS/MS in Proteomics

Robert Chalkley

Abstract

Mass spectrometers now have sufficient sensitivity and acquisition rates to allow analysis of complex
proteomic samples on a chromatographic timescale. In this chapter the different instrument options for
protein and peptide analysis will be presented, along with their relative strengths and weaknesses for
producing different types of information, such as protein identification, modification characterization, or
reporting quantitative measurements.

Key words: Quadrupole, Orbitrap, Fourier transform, mass spectrometry, proteomics, meta-
bolomics.

1. Introduction

The two major types of ionization for analysis of biomolecules
are electrospray ionization (ESI) ( 1 ) and matrix-assisted laser des-
orption/ionization (MALDI) ( 2 ) . One of the fundamental dif-
ferences between these methods is that MALDI is employed on
samples in a solid state, whereas ESI is employed on samples in a
liquid state. Hence, interfacing liquid chromatography with ESI
is relatively straightforward, whereas LC-MALDI analysis is an
offline process, where fractions are collected and then analyzed
by MALDI at a later stage. Partly as a result of this, ESI is the
dominant ionization process for analysis of samples separated by
liquid chromatography and will be the emphasis of instrumenta-
tion discussed from hereon.