Protein and Metabolite Identification - Proteomic and Metabolomic Approaches to Biomarker Discovery - page 238

CHAPTER
16

Protein a nd Metabolite Ide nti cation

Timothy D. Veenstra, Que N. Van, Stephen D. Fox,
Haleem J. Issaq
Laboratory of Proteomics and Analytical Technologies, Advanced Technology Program,
SAIC-Frederick, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD, USA

OUTLINE

Protein Identi cation 245 Metabolite Identi cation in Global

Introduction 245 Metabolomics 250

Peptide Mapping 245 MS Metabolite Identi cation 251

Tandem Mass Spectrometry 247 NMR Metabolite Identi cation 253

Protein Databases 249

References 257

Top-Down Mass Spectrometry 249

P ROTEIN IDENTIFICATION

proteins that have been predigested into
peptide fragments. In top-down MS, the intact
protein is identi

Introduction
In proteomics, protein identi

cation
is more common than top-down, which still
has signi

ed. Bottom-up identi

cation is the
bread and butter of mass spectrometry (MS).
One of the most basic tasks performed using
MS is protein identi

cant technological hurdles to over-
come before it becomes mainstream within MS
laboratories. In this chapter, we describe the
tools required for peptide mapping and MS 2
identi

cation. Approximately
90% of experiments submitted for MS analysis
request protein identi

cation as well as progress in top-down

cation. There are two
major types of MS experiments for protein iden-
ti

identi cation.

cation: peptide mapping and tandem MS
(MS 2 ). There are also two different means of
identifying proteins: bottom-up and top-down.
Bottom-up MS refers to the identi

Peptide Mapping
Peptide mapping is usually performed on an
isolated protein or a protein mixture. Identifying

cation of