Biology Reference
In-Depth Information
Chapter 22
Medicago truncatula
Proteomics for Systems Biology:
Novel Rapid Shotgun LC-MS Approach for Relative
Quantifi cation Based on Full-Scan Selective Peptide
Extraction (Selpex)
M. Angeles Castillejo , Christiana Staudinger , Volker Egelhofer ,
and Stefanie Wienkoop
Abstract
Medicago truncatula
has become the focus of systems biology research for improved legume crop breeding.
In plant systems biology, several comparative studies have been carried out using liquid chromatography
shotgun mass spectrometry (LC-MS/MS) and database-dependent protein identifi cation analyses in
combination with the spectral count for relative quantifi cation. In order to receive optimal protein identi-
fi cation rates and spectral count quantifi cation, data-dependent tandem mass spectrometry with LC sepa-
ration of more than 1 h is required. Thus LC-MS/MS analyses time is the bottleneck for high-throughput
research of experiments with high sample number.
We describe a novel method, called full-scan (FS) selective peptide extraction, that allows for com-
parative quantifi cation of target peptides combined with a signifi cant reduction in LC-MS analysis time. In
future, it will be a useful tool to detect
15
N-labeled selected peptide patterns for the targeted analysis of
protein turnover and synthesis. We provide a fi rst reference library of selected target peptides generated for
M. truncatula
leaf tissue. These peptides are also suitable candidates for selective reaction monitoring
approaches.
Key words
Medicago, Selpex, Target peptides, Peptide quantifi cation
Abbreviations
ACN Acetonitrile
DDP Data-dependent
FA Formic acid
FS Full-scan
LC-MS/MS Liquid chromatography mass spectrometry
MAPA
Mass accuracy precursor alignment
SC
Spectral count
Selpex
Selective peptide extraction
SRM
Selective reaction monitoring
