Multi-laboratory experiment PME11 for the standardization of phosphoproteome analysis

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Colomé, NúriaProteoRed-ISCIII, Vall d'Hebron Institute of Oncology (VHIO), Barcelona 08035, Spain (author)

Multi-laboratory experiment PME11 for the standardization of phosphoproteome analysis

Article/chapterEnglish2022

Publisher, publication year, extent ...

Elsevier,2022
electronicrdacarrier

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LIBRIS-ID:oai:DiVA.org:umu-189495
https://urn.kb.se/resolve?urn=urn:nbn:se:umu:diva-189495URI
https://doi.org/10.1016/j.jprot.2021.104409DOI

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Language:English
Summary in:English

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Subject category:ref swepub-contenttype
Subject category:art swepub-publicationtype

Notes

Global analysis of protein phosphorylation by mass spectrometry proteomic techniques has emerged in the last decades as a powerful tool in biological and biomedical research. However, there are several factors that make the global study of the phosphoproteome more challenging than measuring non-modified proteins. The low stoichiometry of the phosphorylated species and the need to retrieve residue specific information require particular attention on sample preparation, data acquisition and processing to ensure reproducibility, qualitative and quantitative robustness and ample phosphoproteome coverage in phosphoproteomic workflows. Aiming to investigate the effect of different variables in the performance of proteome wide phosphoprotein analysis protocols, ProteoRed-ISCIII and EuPA launched the Proteomics Multicentric Experiment 11 (PME11). A reference sample consisting of a yeast protein extract spiked in with different amounts of a phosphomix standard (Sigma/Merck) was distributed to 31 laboratories around the globe. Thirty-six datasets from 23 laboratories were analyzed. Our results indicate the suitability of the PME11 reference sample to benchmark and optimize phosphoproteomics strategies, weighing the influence of different factors, as well as to rank intra and inter laboratory performance.

Subject headings and genre

NATURVETENSKAP Biologi Bioinformatik och systembiologi hsv//swe
NATURAL SCIENCES Biological Sciences Bioinformatics and Systems Biology hsv//eng
NATURVETENSKAP Biologi Biokemi och molekylärbiologi hsv//swe
NATURAL SCIENCES Biological Sciences Biochemistry and Molecular Biology hsv//eng
NATURVETENSKAP Biologi Cellbiologi hsv//swe
NATURAL SCIENCES Biological Sciences Cell Biology hsv//eng
Biochemistry
Biophysics
Biochemistry
biokemi
Analytical Chemistry
analytisk kemi

Added entries (persons, corporate bodies, meetings, titles ...)

Abian, JoaquínProteoRed-ISCIII, Instituto de Investigaciones Biomédicas de Barcelona, IIBB-CSIC/IDIBAPS, 08036 Barcelona, Spain (author)
Aloria, KermanProteoRed-ISCIII, Proteomics Core Facility-SGIKER, University of the Basque Country (UPV/EHU), Leioa, Spain (author)
Arizmendi, Jesús M.Department of Biochemistry and Molecular Biology, Faculty of Science and Technology, University of the Basque Country (UPV/EHU), Leioa, Spain (author)
Barceló-Batllori, SilviaProteoRed-ISCIII, Bellvitge Biomedical Research Institute (IDIBELL), Barcelona, Spain (author)
Braga-Lagache, SophieDepartment for BioMedical Research (DBMR), Proteomics and Mass Spectrometry Core Facility, University of Bern, CH-3010 Bern, Switzerland (author)
Burlet-Schiltz, OdileProteomics and Mass Spectrometry of Biomolecules, Proteomics Infrastructure of Toulouse, Proteomics French Infrastructure, ProFI. Institut de Pharmacologie et Biologie Structurale (IPBS), Université de Toulouse, UPS, CNRS, Toulouse, France (author)
Carrascal, MontseProteoRed-ISCIII, Instituto de Investigaciones Biomédicas de Barcelona, IIBB-CSIC/IDIBAPS, 08036 Barcelona, Spain (author)
Casal, J. IgnacioProteoRed-ISCIII, Centro de Investigaciones Biológicas-CSIC, Madrid 28040, Spain (author)
Chicano-Gálvez, EduardProteoRed-ISCIII, Proteomics Unit, IMIBIC/UCO/HURS, IMIBIC Building Fl.3, 14004 Córdoba, Spain (author)
Chiva, CristinaProteomics Unit, Center for Genomics Regulation, Barcelona Institute of Science and Technology (BIST), Barcelona, Spain (author)
Clemente, Luis FelipeProteoRed-ISCIII, Proteomics Unit, Complutense University, 28040 Madrid, Spain (author)
Elortza, FelixProteoRed-ISCIII, CIC bioGUNE, Proteomics Platform, Basque Research & Technology Alliance (BRTA), CIBERehd,Bizkaia Science and Technology Park, 48160 Derio, Spain (author)
Estanyol, Josep M.ProteoRed-ISCIII, Scientific and Technological Centers (CCiTUB), University of Barcelona, 08036 Barcelona, Spain (author)
Fernandez-Irigoyen, JoaquínProteored-ISCIII. Proteomics Unit, Clinical Neuroproteomics Group, Navarrabiomed, Complejo Hospitalario de Navarra (CHN), Universidad Pública de Navarra (UPNA), IdiSNA, 31008 Pamplona, Spain (author)
Fernández-Puente, PatriciaGrupo de Investigación de Reumatología (GIR), Agrupación CICA-INIBIC, Universidad de A Coruña, A Coruña, Spain (author)
Fidalgo, María JoséProteoRed-ISCIII, Scientific and Technological Centers (CCiTUB), University of Barcelona, 08036 Barcelona, Spain (author)
Froment, CarineProteomics and Mass Spectrometry of Biomolecules, Proteomics Infrastructure of Toulouse, Proteomics French Infrastructure, ProFI. Institut de Pharmacologie et Biologie Structurale (IPBS), Université de Toulouse, UPS, CNRS, Toulouse, France (author)
Fuentes, ManuelDepartment of Medicine and General Cytometry Service-Nucleus, Proteomics Unit, CIBERONC, Cancer Research Center (IBMCC/CSIC/USAL/IBSAL), Universidad de Salamanca, Spain (author)
Fuentes-Almagro, CarlosProteomics Unit, SCAI, University of Córdoba, Ramón y Cajal Building, Rabanales Campus, 14071, Córdoba, Spain (author)
Gay, MarinaProteoRed-ISCIII, Institute for Research in Biomedicine (IRB Barcelona), BIST (The Barcelona Institute of Science and Technology), Baldiri i Reixac 10, 08028 Barcelona, Spain (author)
Hainard, AlexandreProteomics Core Facility, CMU, University of Geneva, Switzerland (author)
Heller, ManfredDepartment for BioMedical Research (DBMR), Proteomics and Mass Spectrometry Core Facility, University of Bern, CH-3010 Bern, Switzerland (author)
Hernández, María LuisaProteoRed-ISCIII, Proteomics Unit, Complutense University, 28040 Madrid, Spain (author)
Ibarrola, NievesProteoRed-ISCIII, Proteomics Unit. Cancer Research Center (IBMCC/CSIC/USAL/IBSAL), Universidad de Salamanca-CSIC, Salamanca, Spain (author)
Iloro, IbonProteoRed-ISCIII, CIC bioGUNE, Proteomics Platform, Basque Research & Technology Alliance (BRTA), CIBERehd,Bizkaia Science and Technology Park, 48160 Derio, Spain (author)
Kieselbach, ThomasUmeå universitet,Kemiska institutionen,Thomas Kieselbach(Swepub:umu)thskih04 (author)
Lario, AntonioProteoRed-ISCIII, IPBLN -CSIC, 18016 Granada, Spain (author)
Locard-Paulet, MarieProteomics and Mass Spectrometry of Biomolecules, Proteomics Infrastructure of Toulouse, Proteomics French Infrastructure, ProFI. Institut de Pharmacologie et Biologie Structurale (IPBS), Université de Toulouse, UPS, CNRS, Toulouse, France (author)
Marina-Ramírez, AnabelProteoRed-ISCIII, CBM Severo Ochoa (CSIC-UAM), Madrid 28049, Spain (author)
Martín, LunaProteoRed-ISCIII, Vall d'Hebron Institute of Oncology (VHIO), Barcelona 08035, Spain (author)
Morato-López, EsperanzaProteoRed-ISCIII, CBM Severo Ochoa (CSIC-UAM), Madrid 28049, Spain (author)
Muñoz, JavierProteoRed-ISCIII, Spanish National Cancer Research Centre (CNIO), Madrid 28029, Spain (author)
Navajas, RosanaProteoRed-ISCIII, Centro Nacional de Biotecnologia (CSIC), 28049, Madrid, Spain (author)
Odena, M. AntoniaProteoRed-ISCIII, Proteomics Platform, Barcelona Science Park, 08028, Barcelona, Spain (author)
Odriozola, LeticiaProteoRed-ISCIII, CIMA, University of Navarra, 31008, Pamplona, Spain (author)
de Oliveira, EliandreProteoRed-ISCIII, Proteomics Platform, Barcelona Science Park, 08028, Barcelona, Spain (author)
Paradela, AlbertoProteoRed-ISCIII, Centro Nacional de Biotecnologia (CSIC), 28049, Madrid, Spain (author)
Pasquarello, CarlaProteomics Core Facility, CMU, University of Geneva, Switzerland (author)
de los Rios, VivianProteoRed-ISCIII, Centro de Investigaciones Biológicas-CSIC, Madrid 28040, Spain (author)
Ruiz-Romero, CristinaGrupo de Investigación de Reumatología (GIR) - ProteoRed-ISCIII, Unidad de Proteómica, INIBIC–Complejo Hospitalario Universitario de A Coruña, SERGAS, A Coruña, Spain (author)
Sabidó, EduardProteoRed ISCIII, Proteomics Unit, Universitat Pompeu Fabra, Barcelona, Spain (author)
Sánchez del Pino, ManuelBiotechnology and Biomedicine Interdisciplinary Research Unit (ERI BIOTECMED), University of Valencia, 46100 Burjassot, Spain (author)
Sancho, JaimeProteoRed-ISCIII, IPBLN -CSIC, 18016 Granada, Spain (author)
Santamaría, EnriqueProteored-ISCIII. Proteomics Unit, Clinical Neuroproteomics Group, Navarrabiomed, Complejo Hospitalario de Navarra (CHN), Universidad Pública de Navarra (UPNA), IdiSNA, 31008 Pamplona, Spain (author)
Schaeffer-Reiss, ChristineLaboratoire de Spectrométrie de Masse BioOrganique, Université de Strasbourg, CNRS, IPHC UMR 7178, 67000, Strasbourg, France (author)
Schneider, JustineLaboratoire de Spectrométrie de Masse BioOrganique, Université de Strasbourg, CNRS, IPHC UMR 7178, 67000, Strasbourg, France (author)
de la Torre, CarolinaProteoRed-ISCIII, Bellvitge Biomedical Research Institute (IDIBELL), Barcelona, Spain (author)
Valero, M. LuzProteoRed-ISCIII, Proteomics Unit, Central Service for Experimental Research (SCSIE), University of Valencia, 46100, Burjassot, Spain (author)
Vilaseca, MartaProteoRed-ISCIII, Institute for Research in Biomedicine (IRB Barcelona), BIST (The Barcelona Institute of Science and Technology), Baldiri i Reixac 10, 08028 Barcelona, Spain (author)
Wu, ShuaiProteoRed-ISCIII, Vall d’Hebron Institute of Oncology (VHIO), Barcelona 08035, Spain; Proteomics and Mass Spectrometry of Biomolecules, Proteomics Infrastructure of Toulouse, Proteomics French Infrastructure, ProFI. Institut de Pharmacologie et Biologie Structurale (IPBS), Universit´e de Toulouse, UPS, CNRS, Toulouse, France (author)
Wu, LinfegProteoRed-ISCIII, Vall d’Hebron Institute of Oncology (VHIO), Barcelona 08035, Spain; Proteomics and Mass Spectrometry of Biomolecules, Proteomics Infrastructure of Toulouse, Proteomics French Infrastructure, ProFI. Institut de Pharmacologie et Biologie Structurale (IPBS), Universit´e de Toulouse, UPS, CNRS, Toulouse, France (author)
de Embún, Pilar XiménezProteoRed-ISCIII, Spanish National Cancer Research Centre (CNIO), Madrid 28029, Spain (author)
Canals, FrancescProteoRed-ISCIII, Vall d’Hebron Institute of Oncology (VHIO), Barcelona 08035, Spain (author)
Corrales, Fernando J.ProteoRed-ISCIII, Centro Nacional de Biotecnologia (CSIC), 28049, Madrid, Spain; ProteoRed-ISCIII, CIMA, University of Navarra, 31008, Pamplona, Spain (author)
ProteoRed-ISCIII, Vall d'Hebron Institute of Oncology (VHIO), Barcelona 08035, SpainProteoRed-ISCIII, Instituto de Investigaciones Biomédicas de Barcelona, IIBB-CSIC/IDIBAPS, 08036 Barcelona, Spain (creator_code:org_t)

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By the author/editor: Colomé, Núria; Abian, Joaquín; Aloria, Kerman; Arizmendi, Jesús ...; Barceló-Batllori ...; Braga-Lagache, S ...; show more...; Burlet-Schiltz, ...; Carrascal, Monts ...; Casal, J. Ignaci ...; Chicano-Gálvez, ...; Chiva, Cristina; Clemente, Luis F ...; Elortza, Felix; Estanyol, Josep ...; Fernandez-Irigoy ...; Fernández-Puente ...; Fidalgo, María J ...; Froment, Carine; Fuentes, Manuel; Fuentes-Almagro, ...; Gay, Marina; Hainard, Alexand ...; Heller, Manfred; Hernández, María ...; Ibarrola, Nieves; Iloro, Ibon; Kieselbach, Thom ...; Lario, Antonio; Locard-Paulet, M ...; Marina-Ramírez, ...; Martín, Luna; Morato-López, Es ...; Muñoz, Javier; Navajas, Rosana; Odena, M. Antoni ...; Odriozola, Letic ...; de Oliveira, Eli ...; Paradela, Albert ...; Pasquarello, Car ...; de los Rios, Viv ...; Ruiz-Romero, Cri ...; Sabidó, Eduard; Sánchez del Pino ...; Sancho, Jaime; Santamaría, Enri ...; Schaeffer-Reiss, ...; Schneider, Justi ...; de la Torre, Car ...; Valero, M. Luz; Vilaseca, Marta; Wu, Shuai; Wu, Linfeg; de Embún, Pilar ...; Canals, Francesc; Corrales, Fernan ...; show less...

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