EasyProt - An easy-to-use graphical platform for proteomics data analysis

Gluck, Florent; Hoogland, Christine; Antinori Malaspina, Paola; Robin, Xavier Arnaud; Nikitin, Frédéric; Zufferey Bakos, Anne; Pasquarello Mosimann, Carla; Fétaud, Vanessa; Dayon, Loic; Müller, Markus; Lisacek, Frédérique; Geiser, Laurent; Hochstrasser, Denis; Sanchez, Jean-Charles; Scherl, Alexander

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Title		EasyProt - An easy-to-use graphical platform for proteomics data analysis
Authors		Gluck, Florent Hoogland, Christine Antinori Malaspina, Paola Robin, Xavier Arnaud Nikitin, Frédéric Zufferey Bakos, Anne Pasquarello Mosimann, Carla Fétaud, Vanessa Dayon, Loic Müller, Markus Lisacek, Frédérique Geiser, Laurent Hochstrasser, Denis Sanchez, Jean-Charles Scherl, Alexander show all authors [1 - 15]
Published in		Journal of Proteomics. 2013, vol. 79, p. 146-60
Abstract		High throughput protein identification and quantification analysis based on mass spectrometry are fundamental steps in most proteomics projects. Here, we present EasyProt (available at http://easyprot.unige.ch), a new platform for mass spectrometry data processing, protein identification, quantification and unexpected post-translational modification characterization. EasyProt provides a fully integrated graphical experience to perform a large part of the proteomic data analysis workflow. Our goal was to develop a software platform that would fulfill the needs of scientists in the field, while emphasizing ease-of-use for non-bioinformatician users. Protein identification is based on OLAV scoring schemes and protein quantification is implemented for both, isobaric labeling and label-free methods. Additional features are available, such as peak list processing, isotopic correction, spectra filtering, charge-state deconvolution and spectra merging. To illustrate the EasyProt platform, we present two identification and quantification workflows based on isobaric tagging and label-free methods.
Keywords		Protein identification — Protein quantification — Label-free — Isobaric labeling — Post-translational modifications — Mass spectrometry
Identifiers		DOI: 10.1016/j.jprot.2012.12.012 PMID: 23277275
Full text		Article (Published version) (3.1 MB) - Limited access to UNIGE
Structures		Faculté de médecine / Section de médecine fondamentale / Département de biologie structurale et bioinformatique
Research groups		Groupe de Protéomique biomédicale (635) Chimie et protéomique clinique (270)
Citation (ISO format)		GLUCK, Florent et al. EasyProt - An easy-to-use graphical platform for proteomics data analysis. In: Journal of Proteomics, 2013, vol. 79, p. 146-60. https://archive-ouverte.unige.ch/unige:26872