Ewa Gubb

CIC bioGUNE

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Rune Matthiesen

Universidade Nova de Lisboa

Eva Rodríguez‐Suárez

AstraZeneca (United Kingdom)

Juan Manuel Falcón‐Pérez

Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas

Félix Elortza

CIC bioGUNE

Itziar Frades

Icahn School of Medicine at Mount Sinai

António Amorim

i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto

José M. Mato

CIC bioGUNE

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CIC bioGUNE

Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas

Instituto de Salud Carlos III

Euskadiko Parke Teknologikoa

Centro de Investigación Biomédica en Red

Universidade do Porto

Ikerbasque

Hospital de Basurto

Medical Research Network

Universidade Nova de Lisboa

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VEMS: s tool to quantify iTRAQ labeled samples

Proteómica: revista de la Sociedad Española de Proteómica (2009)

Eva Rodríguez‐Suárez Ewa Gubb Juan Manuel Falcón‐Pérez José M. Mato Félix Elortza

Introduction: The goal of many MS-based proteomics experiments nowadays is to quantify changes in the abundance of the proteomes across several samples of biological interest. The iTRAQ labeling method is a powerful relative quantitation technique that combined with liquid chromatography coupled to tandem mass spectrometry allows quantify up to eight different samples simultaneously. The transformation of the multiple spectra containing different protein expression values is a challenging task. We have developed an integrated tool for database dependent interpretation, quantitation and database storage for iTRAQ labeled samples able to handle various input data formats from instruments from different manufacturers. Users can download the Web Server from http://personal.cic.biogune.es/rmatthiesen/.

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Virtual Expert Mass Spectrometrist: iTRAQ tool for database‐dependent search, quantitation and result storage

PROTEOMICS (2010)

Eva Rodríguez‐Suárez Ewa Gubb Itziar Frades Juan Manuel Falcón‐Pérez António Amorim

Abstract A frequent goal of MS‐based proteomics experiments nowadays is to quantify changes in the abundance of proteins across several biological samples. The iTRAQ labeling method is a powerful technique; when combined with LC coupled to MS/MS it allows relative quantitation of up to eight different samples simultaneously. Despite the usefulness of iTRAQ current software solutions have limited functionality and require the combined use of several software programs for analysis of the data from different MS vendors. We developed an integrated tool, now available in the virtual expert mass spectrometrist (VEMS) program, for database‐dependent search of MS/MS spectra, quantitation and database storage for iTRAQ‐labeled samples. VEMS also provides useful alternative report types for large‐scale quantitative experiments. The implemented statistical algorithms build on quantitative algorithms previously used in proposed iTRAQ tools as described in detail herein. We propose a new algorithm, which provides more accurate peptide ratios for data that show an intensity‐dependent saturation. The accuracy of the proposed iTRAQ algorithm and the performance of VEMS are demonstrated by comparing results from VEMS, MASCOT and PEAKS Q obtained by analyzing data from a reference mixture of six proteins. Users can download VEMS and test data from “ http://www.portugene.com/software.html ”.

10.1002/pmic.200900255

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Introduction to Omics

Methods in molecular biology (2009)

Ewa Gubb Rune Matthiesen

Omics

10.1007/978-1-60327-194-3_1

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Citations (11)