Intact protein profiling in breast cancer biomarker discovery: Protein identification issue and the solutions based on 3D protein separation, bottom-up and top-down mass spectrometry

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Authors

BOUCHAL Pavel DVOŘÁKOVÁ Monika SCHERL Alexander GARBIS Spiros D. NENUTIL Rudolf VOJTĚŠEK Bořivoj

Year of publication 2013
Type Article in Periodical
Magazine / Source Proteomics
MU Faculty or unit

Faculty of Science

Citation
Web Full text
Doi http://dx.doi.org/10.1002/pmic.201200121
Field Biochemistry
Keywords Breast cancer; FT MS; MALDI TOF MS; SELDI TOF MS; Technology
Attached files
Description Proteomics profiling of intact proteins based on MALDI-TOF MS and derived platforms has been used in cancer biomarker discovery studies. This approach suffers from a number of limitations such as low resolution, low sensitivity, and that no knowledge is available on the identity of the respective proteins in the discovery mode. Nevertheless, it remains the most high-throughput, untargeted mode of clinical proteomics studies to date. Here we compare key protein separation and MS techniques available for protein biomarker identification in this type of studies and define reasons of uncertainty in protein peak identity. As a result of critical data analysis, we consider 3D protein separation and identification workflows as optimal procedures. Subsequently, we present a new protocol based on 3D LC-MS/MS with top-down at high resolution that enabled the identification of HNRNP A2/B1 intact peptide as correlating with the estrogen receptor expression in breast cancer tissues. Additional development of this general concept toward next generation, top-down based protein profiling at high resolution is discussed.
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