Optimization of plasma sample pretreatment for quantitative analysis using iTRAQ labeling and LC-MALDI-TOF/TOF.

Shotgun proteomic methods involving iTRAQ (isobaric tags for relative and absolute quantitation) peptide labeling facilitate quantitative analyses of proteomes and searches for useful biomarkers. However, the plasma proteome's complexity and the highly dynamic plasma protein concentration range...

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Autores principales:	Magdalena Luczak, Lukasz Marczak, Maciej Stobiecki
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2014
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/86907b7beea74f658bd408ce85ec31d2
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spelling	oai:doaj.org-article:86907b7beea74f658bd408ce85ec31d22021-11-25T06:09:57ZOptimization of plasma sample pretreatment for quantitative analysis using iTRAQ labeling and LC-MALDI-TOF/TOF.1932-620310.1371/journal.pone.0101694https://doaj.org/article/86907b7beea74f658bd408ce85ec31d22014-01-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/24988083/?tool=EBIhttps://doaj.org/toc/1932-6203Shotgun proteomic methods involving iTRAQ (isobaric tags for relative and absolute quantitation) peptide labeling facilitate quantitative analyses of proteomes and searches for useful biomarkers. However, the plasma proteome's complexity and the highly dynamic plasma protein concentration range limit the ability of conventional approaches to analyze and identify a large number of proteins, including useful biomarkers. The goal of this paper is to elucidate the best approach for plasma sample pretreatment for MS- and iTRAQ-based analyses. Here, we systematically compared four approaches, which include centrifugal ultrafiltration, SCX chromatography with fractionation, affinity depletion, and plasma without fractionation, to reduce plasma sample complexity. We generated an optimized protocol for quantitative protein analysis using iTRAQ reagents and an UltrafleXtreme (Bruker Daltonics) MALDI TOF/TOF mass spectrometer. Moreover, we used a simple, rapid, efficient, but inexpensive sample pretreatment technique that generated an optimal opportunity for biomarker discovery. We discuss the results from the four sample pretreatment approaches and conclude that SCX chromatography without affinity depletion is the best plasma sample preparation pretreatment method for proteome analysis. Using this technique, we identified 1,780 unique proteins, including 1,427 that were quantified by iTRAQ with high reproducibility and accuracy.Magdalena LuczakLukasz MarczakMaciej StobieckiPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 9, Iss 7, p e101694 (2014)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Magdalena Luczak Lukasz Marczak Maciej Stobiecki Optimization of plasma sample pretreatment for quantitative analysis using iTRAQ labeling and LC-MALDI-TOF/TOF.
description	Shotgun proteomic methods involving iTRAQ (isobaric tags for relative and absolute quantitation) peptide labeling facilitate quantitative analyses of proteomes and searches for useful biomarkers. However, the plasma proteome's complexity and the highly dynamic plasma protein concentration range limit the ability of conventional approaches to analyze and identify a large number of proteins, including useful biomarkers. The goal of this paper is to elucidate the best approach for plasma sample pretreatment for MS- and iTRAQ-based analyses. Here, we systematically compared four approaches, which include centrifugal ultrafiltration, SCX chromatography with fractionation, affinity depletion, and plasma without fractionation, to reduce plasma sample complexity. We generated an optimized protocol for quantitative protein analysis using iTRAQ reagents and an UltrafleXtreme (Bruker Daltonics) MALDI TOF/TOF mass spectrometer. Moreover, we used a simple, rapid, efficient, but inexpensive sample pretreatment technique that generated an optimal opportunity for biomarker discovery. We discuss the results from the four sample pretreatment approaches and conclude that SCX chromatography without affinity depletion is the best plasma sample preparation pretreatment method for proteome analysis. Using this technique, we identified 1,780 unique proteins, including 1,427 that were quantified by iTRAQ with high reproducibility and accuracy.
format	article
author	Magdalena Luczak Lukasz Marczak Maciej Stobiecki
author_facet	Magdalena Luczak Lukasz Marczak Maciej Stobiecki
author_sort	Magdalena Luczak
title	Optimization of plasma sample pretreatment for quantitative analysis using iTRAQ labeling and LC-MALDI-TOF/TOF.
title_short	Optimization of plasma sample pretreatment for quantitative analysis using iTRAQ labeling and LC-MALDI-TOF/TOF.
title_full	Optimization of plasma sample pretreatment for quantitative analysis using iTRAQ labeling and LC-MALDI-TOF/TOF.
title_fullStr	Optimization of plasma sample pretreatment for quantitative analysis using iTRAQ labeling and LC-MALDI-TOF/TOF.
title_full_unstemmed	Optimization of plasma sample pretreatment for quantitative analysis using iTRAQ labeling and LC-MALDI-TOF/TOF.
title_sort	optimization of plasma sample pretreatment for quantitative analysis using itraq labeling and lc-maldi-tof/tof.
publisher	Public Library of Science (PLoS)
publishDate	2014
url	https://doaj.org/article/86907b7beea74f658bd408ce85ec31d2
work_keys_str_mv	AT magdalenaluczak optimizationofplasmasamplepretreatmentforquantitativeanalysisusingitraqlabelingandlcmalditoftof AT lukaszmarczak optimizationofplasmasamplepretreatmentforquantitativeanalysisusingitraqlabelingandlcmalditoftof AT maciejstobiecki optimizationofplasmasamplepretreatmentforquantitativeanalysisusingitraqlabelingandlcmalditoftof
_version_	1718414112428392448

Optimization of plasma sample pretreatment for quantitative analysis using iTRAQ labeling and LC-MALDI-TOF/TOF.

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