title: Multicenter experiment for quality control of peptide-centric LC-MS/MS analysis - A longitudinal performance assessment with nLC coupled to orbitrap MS analyzers.
abstract: Proteomic technologies based on mass spectrometry (MS) have greatly evolved in the past years, and nowadays it is possible to routinely identify thousands of peptides from complex biological samples in a single LC-MS/MS experiment. Despite the advancements in proteomic technologies, the scientific community still faces important challenges in terms of depth and reproducibility of proteomics analyses. Here, we present a multicenter study designed to evaluate long-term performance of LC-MS/MS platforms within the Spanish Proteomics Facilities Network (ProteoRed-ISCIII). The study was performed under well-established standard operating procedures, and demonstrated that it is possible to attain qualitative and quantitative reproducibility over time. Our study highlights the importance of deploying quality assessment metrics routinely in individual laboratories and in multi-laboratory studies. The mass spectrometry data have been deposited to the ProteomeXchange Consortium with the data set identifier PXD000205.This article is part of a Special Issue entitled: HUPO 2014.
authors.affiliation: ProteoRed-ISCIII, Proteomics Platform, Barcelona Science Park, Barcelona, Spain; Integromics, Madrid, Spain. Electronic address: alex.proteomics@gmail.com.
authors.forename: Alex
authors.initials: A
authors.lastname: Campos
authors.affiliation: ProteoRed-ISCIII, Proteomics Platform, Barcelona Science Park, Barcelona, Spain.
authors.forename: Ramón
authors.initials: R
authors.lastname: Díaz
authors.affiliation: ProteoRed-ISCIII, Proteomics Facility, Centro Nacional de Biotecnología - CSIC, Madrid, Spain.
authors.forename: Salvador
authors.initials: S
authors.lastname: Martínez-Bartolomé
authors.affiliation: Integromics, Madrid, Spain.
authors.forename: Jose
authors.initials: J
authors.lastname: Sierra
authors.affiliation: ProteoRed-ISCIII, CSIC/UAB Proteomics Laboratory, Instituto de Investigaciones Biomédicas de Barcelona, Spanish National Research Council, Barcelona, Spain.
authors.forename: Oscar
authors.initials: O
authors.lastname: Gallardo
authors.affiliation: ProteoRed-ISCIII, Proteomics Unit, Universitat Pompeu Fabra (UPF) and Centre de Regulació Genòmica (CRG), Barcelona, Spain.
authors.forename: Eduard
authors.initials: E
authors.lastname: Sabidó
authors.affiliation: ProteoRed-ISCIII, Proteomics Facility and Functional Proteomics Laboratory, Centro de Investigaciones, Biológicas, Madrid, Spain.
authors.forename: Maria
authors.initials: M
authors.lastname: López-Lucendo
authors.affiliation: ProteoRed-ISCIII, Proteomics Facility and Functional Proteomics Laboratory, Centro de Investigaciones, Biológicas, Madrid, Spain.
authors.forename: J
authors.initials: J
authors.lastname: Ignacio Casal
authors.affiliation: Proteomics Core Facility, CMU, University of Geneva, Switzerland.
authors.forename: Carla
authors.initials: C
authors.lastname: Pasquarello
authors.affiliation: Department of Human Protein Sciences, CMU, University of Geneva, Switzerland.
authors.forename: Alexander
authors.initials: A
authors.lastname: Scherl
authors.affiliation: ProteoRed-ISCIII, Proteomics Unit, Universitat Pompeu Fabra (UPF) and Centre de Regulació Genòmica (CRG), Barcelona, Spain.
authors.forename: Cristina
authors.initials: C
authors.lastname: Chiva
authors.affiliation: ProteoRed-ISCIII, Proteomics Unit, Universitat Pompeu Fabra (UPF) and Centre de Regulació Genòmica (CRG), Barcelona, Spain.
authors.forename: Eva
authors.initials: E
authors.lastname: Borras
authors.affiliation: ProteoRed-ISCIII, Proteomics Platform, Barcelona Science Park, Barcelona, Spain.
authors.forename: Antonia
authors.initials: A
authors.lastname: Odena
authors.affiliation: ProteoRed-ISCIII, Proteomics Platform, CIC bioGUNE, CIBERehd, Technology Park of Bizkaia, Derio, Spain.
authors.forename: Félix
authors.initials: F
authors.lastname: Elortza
authors.affiliation: ProteoRed-ISCIII, Proteomics Platform, CIC bioGUNE, CIBERehd, Technology Park of Bizkaia, Derio, Spain.
authors.forename: Mikel
authors.initials: M
authors.lastname: Azkargorta
authors.affiliation: ProteoRed-ISCIII, Centro de Investigación del Cáncer and Instituto de Biología Molecular y Celular del Cáncer, CSIC-University of Salamanca, Salamanca, Spain.
authors.forename: Nieves
authors.initials: N
authors.lastname: Ibarrola
authors.affiliation: ProteoRed-ISCIII, Proteomic Laboratory, Vall d'Hebron Institute of Oncology-VHIO, Vall d'Hebron University Hospital, Barcelona, Spain.
authors.forename: Francesc
authors.initials: F
authors.lastname: Canals
authors.affiliation: ProteoRed-ISCIII, Proteomics Facility, Centro Nacional de Biotecnología - CSIC, Madrid, Spain.
authors.forename: Juan P
authors.initials: JP
authors.lastname: Albar
authors.affiliation: ProteoRed-ISCIII, Proteomics Platform, Barcelona Science Park, Barcelona, Spain.
authors.forename: Eliandre
authors.initials: E
authors.lastname: Oliveira
mesh_terms: D002853:Chromatography, Liquid / Q000379:methods / Q000592:standards; D013058:Mass Spectrometry / Q000379:methods* / Q000592:standards*; D010455:Peptides / Q000032:analysis*; D011786:Quality Control; D012441:Saccharomyces cerevisiae / Q000737:chemistry*; D029701:Saccharomyces cerevisiae Proteins / Q000032:analysis*
chemical_list: D010455:Peptides; D029701:Saccharomyces cerevisiae Proteins
keywords: LC-MS/MS performance; Quality control; Reproducibility; Yeast