Quantification of Proteins by Label-Free LC-MS/MS - LC-MS/MS in Proteomics: Methods and Applications - page 215

Chapter 13

Quantification of Proteins by Label-Free LC-MS/MS

Yishai Levin and Sabine Bahn

Abstract

Quantitative proteomic profiling is becoming a widely used approach in systems biology and biomarker
discovery. There is a growing realization that quantitative studies require high numbers of non-pooled
samples for increased statistical power. We present a descriptive protocol for label-free quantitation of
proteins by LC-MS/MS that enables to obtain both quantitative and qualitative information in one
study without the need to pool samples or label them.

Key words: Label free, proteomics, LC-MS, MSE, time alignment, nanoLC-MS/MS, quantitation,
relative quantitation.

1. Introduction

Proteomics is an evolving field mostly due to new technolo-
gies advancing at a rapid rate. These new technologies enable
researchers to break new frontiers and reach uncharted territo-
ries in the investigation of biological systems. In Clinical Pro-
teomics, for example, these advances are increasingly exploited
for the purpose of disease biomarker discovery. Few will doubt
that the proteome holds the key to unravelling disease mecha-
nisms, thereby enabling the development of improved diagnos-
tics, the assessment of drug response, drug efficacy, and drug tox-
icity ( 1 ) . The discovery of novel biomarkers involves profiling of
biological samples in search for disease- or drug-related qualitative
and quantitative changes of proteins. Recent advances in analyt-
ical instrumentation and bioinformatics now enable the relative
quantitation of hundreds of proteins across dozens of samples