About: 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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About: 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 Goto Sponge NotDistinct Permalink

An Entity of Type : http://linked.opendata.cz/ontology/domain/vavai/Vysledek, within Data Space : linked.opendata.cz associated with source document(s)

Attributes	Values
rdf:type	skos:Concept http://linked.opendata.cz/ontology/domain/vavai/Vysledek
rdfs:seeAlso	http://onlinelibrary.wiley.com/doi/10.1002/pmic.201200121/pdf
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. 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. (en)
Title	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 (en)
skos:prefLabel	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 (en)
skos:notation	RIV/00209805:_____/13:#0000401!RIV14-GA0-00209805
http://linked.open...avai/riv/aktivita	I P S
http://linked.open...avai/riv/aktivity	I, P(ED2.1.00/03.0101), P(GAP304/10/0868), S
http://linked.open...iv/cisloPeriodika	7
http://linked.open...vai/riv/dodaniDat	2014
http://linked.open...aciTvurceVysledku	Vojtěšek, Bořivoj Bouchal, Pavel Dvořáková, Monika Nenutil, Rudolf
http://linked.open.../riv/druhVysledku	J - Článek v odborném periodiku
http://linked.open...iv/duvernostUdaju	S - Úplné a pravdivé údaje nepodléhající ochraně podle zvláštních právních předpisů
http://linked.open...titaPredkladatele	Masarykův onkologický ústav
http://linked.open...dnocenehoVysledku	80488
http://linked.open...ai/riv/idVysledku	RIV/00209805:_____/13:#0000401
http://linked.open...riv/jazykVysledku	eng - angličtina
http://linked.open.../riv/klicovaSlova	breast cancer; FT-MS; MALDI-TOF MS; SELDI-TOF MS; technology (en)
http://linked.open.../riv/klicoveSlovo	FT-MS breast cancer technology SELDI-TOF MS MALDI-TOF MS
http://linked.open...odStatuVydavatele	DE - Spolková republika Německo
http://linked.open...ontrolniKodProRIV	[01768F427FA6]
http://linked.open...i/riv/nazevZdroje	Proteomics
http://linked.open...in/vavai/riv/obor	FD
http://linked.open...ichTvurcuVysledku	4 (xsd:int)
http://linked.open...cetTvurcuVysledku	6 (xsd:int)
http://linked.open...vavai/riv/projekt	Regional Centre for Applied Molecular Oncology (RECAMO) The proteomics-based study on molecular mechanisms of early lymph node metastases formation in low-grade breast cancer
http://linked.open...UplatneniVysledku	2013
http://linked.open...v/svazekPeriodika	13
http://linked.open...iv/tvurceVysledku	Vojtěšek, Bořivoj Bouchal, Pavel Dvořáková, Monika Nenutil, Rudolf
http://linked.open...ain/vavai/riv/wos	000317290000001
issn	1615-9853
number of pages	6 (xsd:int)
http://bibframe.org/vocab/doi	10.1002/pmic.201200121

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