EuPA Open Proteomics (Sep 2015)
Inter-laboratory evaluation of instrument platforms and experimental workflows for quantitative accuracy and reproducibility assessment
- Andrew J. Percy,
- Jessica Tamura-Wells,
- Juan Pablo Albar,
- Kerman Aloria,
- Ardeshir Amirkhani,
- Gabriel D.T. Araujo,
- Jesus M. Arizmendi,
- Francisco J. Blanco,
- Francesc Canals,
- Jin-Young Cho,
- Núria Colomé-Calls,
- Fernando J. Corrales,
- Gilberto Domont,
- Guadalupe Espadas,
- Patricia Fernandez-Puente,
- Concha Gil,
- Paul A. Haynes,
- Maria Luisa Hernáez,
- Jin Young Kim,
- Arthur Kopylov,
- Miguel Marcilla,
- Mathew J. McKay,
- Mehdi Mirzaei,
- Mark P. Molloy,
- Leanne B. Ohlund,
- Young-Ki Paik,
- Alberto Paradela,
- Mark Raftery,
- Eduard Sabidó,
- Lekha Sleno,
- Daniel Wilffert,
- Justina C. Wolters,
- Jong Shin Yoo,
- Victor Zgoda,
- Carol E. Parker,
- Christoph H. Borchers
Affiliations
- Andrew J. Percy
- University of Victoria—Genome British Columbia Proteomics Centre, Vancouver Island Technology Park, #3101-4464 Markham St., Victoria, BC V8Z 7X8, Canada
- Jessica Tamura-Wells
- University of Victoria—Genome British Columbia Proteomics Centre, Vancouver Island Technology Park, #3101-4464 Markham St., Victoria, BC V8Z 7X8, Canada
- Juan Pablo Albar
- Proteomics Facility, Centro Nacional de Biotecnologia (CSIC), UAM Campus Cantoblanco, Darwin, 3, Madrid E-28049, Spain
- Kerman Aloria
- Proteomics Core Facility-SGIKER, University of the Basque Country (UPV/EHU), Leioa 48940, Spain
- Ardeshir Amirkhani
- Australian Proteome Analysis Facility, Macquarie University, Sydney, NSW 2109, Australia
- Gabriel D.T. Araujo
- Proteomics Unit of the Department of Biochemistry, Institute of Chemistry, Federal University of Rio de Janeiro, Rio de Janeiro 21941-909, Rio de Janeiro, Brazil
- Jesus M. Arizmendi
- Department of Biochemistry and Molecular Biology, University of the Basque Country (UPV/EHU), Barrio Sarriena s/n, Leioa 48940, Spain
- Francisco J. Blanco
- Grupo de Proteómica-ProteoRed/Plataforma PBR2-ISCIII, Servicio de Reumatología, Instituto de Investigación Biomédica de A Coruña (INIBIC), Complexo Hospitalario Universitario de A Coruña (CHUAC), Sergas, Universidade da Coruña, As Xubias, A Coruña 15006, Spain
- Francesc Canals
- Laboratori de Proteòmica, Institut de Recerca Hospital Univ. Vall d'Hebron. Edifici Collserola, Pg. Vall d'Hebron, 119-129, Barcelona 08035, Spain
- Jin-Young Cho
- Yonsei Proteome Research Center and Department of Biochemistry, College of Life Science and Biotechnology, Yonsei University, Seoul 120-749, South Korea
- Núria Colomé-Calls
- Laboratori de Proteòmica, Institut de Recerca Hospital Univ. Vall d'Hebron. Edifici Collserola, Pg. Vall d'Hebron, 119-129, Barcelona 08035, Spain
- Fernando J. Corrales
- Center for Applied Medical Research (CIMA), University of Navarra, ProteoRed-ISCIII, CIBERHED-ISCIII, IDISNA, Pío XII, 55; Ed. CIMA, Pamplona 31008, Spain
- Gilberto Domont
- Proteomics Unit of the Department of Biochemistry, Institute of Chemistry, Federal University of Rio de Janeiro, Rio de Janeiro 21941-909, Rio de Janeiro, Brazil
- Guadalupe Espadas
- Proteomics Unit, Center of Genomics Regulation (CRG), Carrer Dr. Aiguader 88, Barcelona 08003, Spain
- Patricia Fernandez-Puente
- Grupo de Proteómica-ProteoRed/Plataforma PBR2-ISCIII, Servicio de Reumatología, Instituto de Investigación Biomédica de A Coruña (INIBIC), Complexo Hospitalario Universitario de A Coruña (CHUAC), Sergas, Universidade da Coruña, As Xubias, A Coruña 15006, Spain
- Concha Gil
- Department of Microbiology II and Proteomics Unit UCM-PCM Complutense Unversity of Madrid, Plaza Ramón y Cajal s/n, Madrid 28040, Spain
- Paul A. Haynes
- Department of Chemistry and Biomolecular Sciences, Macquarie University, North Ryde, NSW 2109, Australia
- Maria Luisa Hernáez
- Department of Microbiology II and Proteomics Unit UCM-PCM Complutense Unversity of Madrid, Plaza Ramón y Cajal s/n, Madrid 28040, Spain
- Jin Young Kim
- Division of Mass Spectrometric Analysis, Korea Basic Science Institute, Cheongwon, South Korea
- Arthur Kopylov
- Institute of Biomedical Chemistry, Pogodinskaya Street 10, Moscow 119121, Russian Federation
- Miguel Marcilla
- Proteomics Facility, Centro Nacional de Biotecnologia (CSIC), UAM Campus Cantoblanco, Darwin, 3, Madrid E-28049, Spain
- Mathew J. McKay
- Australian Proteome Analysis Facility, Macquarie University, Sydney, NSW 2109, Australia
- Mehdi Mirzaei
- Department of Chemistry and Biomolecular Sciences, Macquarie University, North Ryde, NSW 2109, Australia
- Mark P. Molloy
- Australian Proteome Analysis Facility, Macquarie University, Sydney, NSW 2109, Australia
- Leanne B. Ohlund
- Université du Québec à Montréal, CP 8888 Succ. Centre-Ville Montreal QC H3P 3P8, Canada
- Young-Ki Paik
- Yonsei Proteome Research Center and Department of Biochemistry, College of Life Science and Biotechnology, Yonsei University, Seoul 120-749, South Korea
- Alberto Paradela
- Proteomics Facility, Centro Nacional de Biotecnologia (CSIC), UAM Campus Cantoblanco, Darwin, 3, Madrid E-28049, Spain
- Mark Raftery
- Bioanalytical Mass Spectrometry, Wallace Wurth Building, University of New South Wales, Sydney NSW 2052, Australia
- Eduard Sabidó
- Proteomics Unit, Center of Genomics Regulation (CRG), Carrer Dr. Aiguader 88, Barcelona 08003, Spain
- Lekha Sleno
- Université du Québec à Montréal, CP 8888 Succ. Centre-Ville Montreal QC H3P 3P8, Canada
- Daniel Wilffert
- Department of Pharmacy, Analytical Biochemistry, University of Groningen, Antonius Deusinglaan 1, 9713 AV Groningen, The Netherlands
- Justina C. Wolters
- Department of Pharmacy, Analytical Biochemistry, University of Groningen, Antonius Deusinglaan 1, 9713 AV Groningen, The Netherlands
- Jong Shin Yoo
- Division of Mass Spectrometric Analysis, Korea Basic Science Institute, Cheongwon, South Korea
- Victor Zgoda
- Institute of Biomedical Chemistry, Pogodinskaya Street 10, Moscow 119121, Russian Federation
- Carol E. Parker
- University of Victoria—Genome British Columbia Proteomics Centre, Vancouver Island Technology Park, #3101-4464 Markham St., Victoria, BC V8Z 7X8, Canada
- Christoph H. Borchers
- University of Victoria—Genome British Columbia Proteomics Centre, Vancouver Island Technology Park, #3101-4464 Markham St., Victoria, BC V8Z 7X8, Canada
- DOI
- https://doi.org/10.1016/j.euprot.2015.06.001
- Journal volume & issue
-
Vol. 8,
no. C
pp. 6 – 15
Abstract
The reproducibility of plasma protein quantitation between laboratories and between instrument types was examined in a large-scale international study involving 16 laboratories and 19 LC–MS/MS platforms, using two kits designed to evaluate instrument performance and one kit designed to evaluate the entire bottom-up workflow. There was little effect of instrument type on the quality of the results, demonstrating the robustness of LC/MRM-MS with isotopically labeled standards. Technician skill was a factor, as errors in sample preparation and sub-optimal LC–MS performance were evident. This highlights the importance of proper training and routine quality control before quantitation is done on patient samples.
Keywords
