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
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
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.
1053-1058
Bouchal, P.
858de967-6994-44df-8b31-acd1e8999427
Dvorakova, M.
fdb209f9-60fc-4b1b-8317-712c562e7221
Scherl, A.
63a09e54-a1ed-4ec6-9f5d-07777e4eb511
Garbis, S.D.
7067fd19-50c9-4d42-9611-f370289470bd
Nenutil, R.
77b3603d-7076-4ae8-b539-2a6b2e6e4802
Vojtesek, B.
72fdb292-02f2-47b2-9eae-0fe256520bf4
April 2013
Bouchal, P.
858de967-6994-44df-8b31-acd1e8999427
Dvorakova, M.
fdb209f9-60fc-4b1b-8317-712c562e7221
Scherl, A.
63a09e54-a1ed-4ec6-9f5d-07777e4eb511
Garbis, S.D.
7067fd19-50c9-4d42-9611-f370289470bd
Nenutil, R.
77b3603d-7076-4ae8-b539-2a6b2e6e4802
Vojtesek, B.
72fdb292-02f2-47b2-9eae-0fe256520bf4
Bouchal, P., Dvorakova, M., Scherl, A., Garbis, S.D., Nenutil, R. and Vojtesek, B.
(2013)
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.
Proteomics, 13 (7), .
(doi:10.1002/pmic.201200121).
(PMID:23303686)
Abstract
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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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.pdf
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Accepted/In Press date: 17 December 2012
e-pub ahead of print date: 8 February 2013
Published date: April 2013
Organisations:
Cancer Sciences
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Local EPrints ID: 395408
URI: http://eprints.soton.ac.uk/id/eprint/395408
ISSN: 1615-9853
PURE UUID: a6be458e-87c7-479b-9086-1d51dca64152
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Date deposited: 15 Jul 2016 14:34
Last modified: 15 Mar 2024 00:40
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Author:
P. Bouchal
Author:
M. Dvorakova
Author:
A. Scherl
Author:
S.D. Garbis
Author:
R. Nenutil
Author:
B. Vojtesek
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