281Alfred K. Lam (ed.), Esophageal Adenocarcinoma: Methods and Protocols, Methods in Molecular Biology, vol. 1756,
https://doi.org/10.1007/978-1-4939-7734-5_24, © Springer Science+Business Media, LLC 2018
Chapter 24
Proteomic Protocol in Esophageal Adenocarcinoma
Peter Kelly
Abstract
The technique of surface-enhanced laser desorption/ionization time-of-flight SELDI-TOF mass spec-
trometry could be used to establish serum or plasma proteomic profiles in esophageal adenocarcinoma.
The protein profiles in patients may be used to predict survival and monitor response to chemotherapy in
patients with esophageal adenocarcinoma. Here, a protocol for sample preparation from esophageal ade-
nocarcinoma, analysis of proteomic profiles, and collection of protein fractions for identification of signifi-
cant peaks is presented.
Key words Proteomic profile, Mass spectrometry, Protein chips, SELDI-TOF MS, Protein
fractionation1 Introduction
There has been growing interest in the use of methods for rapidly
profiling protein markers by mass spectrometry (MS) as a tech-
nique for discovery of novel biomarkers for medical applications,
particularly in the cancer field [ 1 ]. Proteomics can be defined as
the measurement of the proteins present in a given genome, tissue,
or cell type and as such represents the link between the genome,
proteins, and disease [ 2 ]. The key elements needed for successful
proteomics are: (1) A database of protein sequences; (2) a protein
separation technique; (3) mass spectrometry; and (4) software for
relating mass spectra to sequence data.
Early work was based on protein separation by two- dimensional
electrophoresis (SDS-PAGE) but developments in the technology
have been driven by the need for higher throughput and better
sensitivity [ 2 ]. Liquid chromatography methods such as high-
performance liquid chromatography (HPLC) and two- dimensional
liquid chromatography have been increasingly employed for pro-
tein separation and MS techniques used to analyze the proteins.
The MS techniques used include electrospray ionization (ESI) MS,
in which the sample in a polar volatile solvent is passed through a