title: EasyProt--an easy-to-use graphical platform for proteomics data analysis.
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.
authors.affiliation: Swiss Center for Applied Human Toxicology (SCAHT), Geneva, Switzerland. florent.gluck@unige.ch
authors.forename: Florent
authors.initials: F
authors.lastname: Gluck
authors.forename: Christine
authors.initials: C
authors.lastname: Hoogland
authors.forename: Paola
authors.initials: P
authors.lastname: Antinori
authors.forename: Xavier
authors.initials: X
authors.lastname: Robin
authors.forename: Frederic
authors.initials: F
authors.lastname: Nikitin
authors.forename: Anne
authors.initials: A
authors.lastname: Zufferey
authors.forename: Carla
authors.initials: C
authors.lastname: Pasquarello
authors.forename: Vanessa
authors.initials: V
authors.lastname: Fétaud
authors.forename: Loïc
authors.initials: L
authors.lastname: Dayon
authors.forename: Markus
authors.initials: M
authors.lastname: Müller
authors.forename: Frederique
authors.initials: F
authors.lastname: Lisacek
authors.forename: Laurent
authors.initials: L
authors.lastname: Geiser
authors.forename: Denis
authors.initials: D
authors.lastname: Hochstrasser
authors.forename: Jean-Charles
authors.initials: JC
authors.lastname: Sanchez
authors.forename: Alexander
authors.initials: A
authors.lastname: Scherl
mesh_terms: D013058:Mass Spectrometry / Q000379:methods; D011499:Protein Processing, Post-Translational; D011506:Proteins / Q000032:analysis; D040901:Proteomics / Q000379:methods*; D020539:Sequence Analysis, Protein / Q000379:methods*; D012984:Software
chemical_list: D011506:Proteins