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

doi:10.1016/j.euprot.2015.06.001

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 KopylovMiguel 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

Research output: Contribution to journal › Article › peer-review

30 Citations (Scopus)

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.

Original language	English
Pages (from-to)	6-15
Number of pages	10
Journal	EuPA Open Proteomics
Volume	8
DOIs	https://doi.org/10.1016/j.euprot.2015.06.001
Publication status	Published - 2015 Sep 1

Bibliographical note

Funding Information:
The UVic-Genome BC Proteomics Centre would like to thank Genome Canada and Genome British Columbia for STIC funding and support, as well as Western Economic Diversification of Canada for instrumentation support. All laboratories from Spain are members of ProteoRed (Plataforma de Recursos Biomoleculares y Bioinformáticos) and are supported by grant PT13/0001 funded by Instituto de Salud Carlos III (ISCIII) and the European Regional Development Fund (FEDER) . FC wishes to acknowledge support from Grant PRB2 (IPT13/0001 - ISCIII-SGEFI/FEDER). GD wishes to acknowledge support from grants FAPERJ E26-110.138/2013, FAPERJ E-26/111.697/2013, and FAPERJ E-26/0010.1582/2014. AK and VZ state that the Russian portion of the work was done in the framework of the State Academies Fundamental Research Program (2013-2020). Reynaldo Interior (Hospital for Sick Children; Toronto, ON, Canada), Jay Gambee (AAA Service Laboratory; Damascus, OR, USA), and David Chen (University of British Columbia; Vancouver, BC, Canada) are recognized for characterizing the 43 SIS peptides. PAH wishes to thank Ardeshir Amirkhani of the Australian Proteome Analysis Facility, Macquarie University, Sydney, Australia for assistance with sample preparation and data analysis.

Publisher Copyright:
© 2015 The Authors.

All Science Journal Classification (ASJC) codes

Biochemistry

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10.1016/j.euprot.2015.06.001

Cite this

Percy, A. J., Tamura-Wells, J., Albar, J. P., Aloria, K., Amirkhani, A., Araujo, G. D. T., Arizmendi, J. M., Blanco, F. J., Canals, F., Cho, J. Y., Colomé-Calls, N., Corrales, F. J., Domont, G., Espadas, G., Fernandez-Puente, P., Gil, C., Haynes, P. A., Hernáez, M. L., Kim, J. Y., ... Borchers, C. H. (2015). Inter-laboratory evaluation of instrument platforms and experimental workflows for quantitative accuracy and reproducibility assessment. EuPA Open Proteomics, 8, 6-15. https://doi.org/10.1016/j.euprot.2015.06.001

@article{3d316431a7234e1b8683677bcb11d969,

title = "Inter-laboratory evaluation of instrument platforms and experimental workflows for quantitative accuracy and reproducibility assessment",

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.",

author = "Percy, {Andrew J.} and Jessica Tamura-Wells and Albar, {Juan Pablo} and Kerman Aloria and Ardeshir Amirkhani and Araujo, {Gabriel D.T.} and Arizmendi, {Jesus M.} and Blanco, {Francisco J.} and Francesc Canals and Cho, {Jin Young} and N{\'u}ria Colom{\'e}-Calls and Corrales, {Fernando J.} and Gilberto Domont and Guadalupe Espadas and Patricia Fernandez-Puente and Concha Gil and Haynes, {Paul A.} and Hern{\'a}ez, {Maria Luisa} and Kim, {Jin Young} and Arthur Kopylov and Miguel Marcilla and McKay, {Mathew J.} and Mehdi Mirzaei and Molloy, {Mark P.} and Ohlund, {Leanne B.} and Paik, {Young Ki} and Alberto Paradela and Mark Raftery and Eduard Sabid{\'o} and Lekha Sleno and Daniel Wilffert and Wolters, {Justina C.} and Yoo, {Jong Shin} and Victor Zgoda and Parker, {Carol E.} and Borchers, {Christoph H.}",

note = "Funding Information: The UVic-Genome BC Proteomics Centre would like to thank Genome Canada and Genome British Columbia for STIC funding and support, as well as Western Economic Diversification of Canada for instrumentation support. All laboratories from Spain are members of ProteoRed (Plataforma de Recursos Biomoleculares y Bioinform{\'a}ticos) and are supported by grant PT13/0001 funded by Instituto de Salud Carlos III (ISCIII) and the European Regional Development Fund (FEDER) . FC wishes to acknowledge support from Grant PRB2 (IPT13/0001 - ISCIII-SGEFI/FEDER). GD wishes to acknowledge support from grants FAPERJ E26-110.138/2013, FAPERJ E-26/111.697/2013, and FAPERJ E-26/0010.1582/2014. AK and VZ state that the Russian portion of the work was done in the framework of the State Academies Fundamental Research Program (2013-2020). Reynaldo Interior (Hospital for Sick Children; Toronto, ON, Canada), Jay Gambee (AAA Service Laboratory; Damascus, OR, USA), and David Chen (University of British Columbia; Vancouver, BC, Canada) are recognized for characterizing the 43 SIS peptides. PAH wishes to thank Ardeshir Amirkhani of the Australian Proteome Analysis Facility, Macquarie University, Sydney, Australia for assistance with sample preparation and data analysis. Publisher Copyright: {\textcopyright} 2015 The Authors.",

year = "2015",

month = sep,

day = "1",

doi = "10.1016/j.euprot.2015.06.001",

language = "English",

volume = "8",

pages = "6--15",

journal = "EuPA Open Proteomics",

issn = "2212-9685",

publisher = "Elsevier BV",

}

Percy, AJ, Tamura-Wells, J, Albar, JP, Aloria, K, Amirkhani, A, Araujo, GDT, Arizmendi, JM, Blanco, FJ, Canals, F, Cho, JY, Colomé-Calls, N, Corrales, FJ, Domont, G, Espadas, G, Fernandez-Puente, P, Gil, C, Haynes, PA, Hernáez, ML, Kim, JY, Kopylov, A, Marcilla, M, McKay, MJ, Mirzaei, M, Molloy, MP, Ohlund, LB, Paik, YK, Paradela, A, Raftery, M, Sabidó, E, Sleno, L, Wilffert, D, Wolters, JC, Yoo, JS, Zgoda, V, Parker, CE & Borchers, CH 2015, 'Inter-laboratory evaluation of instrument platforms and experimental workflows for quantitative accuracy and reproducibility assessment', EuPA Open Proteomics, vol. 8, pp. 6-15. https://doi.org/10.1016/j.euprot.2015.06.001

TY - JOUR

T1 - Inter-laboratory evaluation of instrument platforms and experimental workflows for quantitative accuracy and reproducibility assessment

AU - Percy, Andrew J.

AU - Tamura-Wells, Jessica

AU - Albar, Juan Pablo

AU - Aloria, Kerman

AU - Amirkhani, Ardeshir

AU - Araujo, Gabriel D.T.

AU - Arizmendi, Jesus M.

AU - Blanco, Francisco J.

AU - Canals, Francesc

AU - Cho, Jin Young

AU - Colomé-Calls, Núria

AU - Corrales, Fernando J.

AU - Domont, Gilberto

AU - Espadas, Guadalupe

AU - Fernandez-Puente, Patricia

AU - Gil, Concha

AU - Haynes, Paul A.

AU - Hernáez, Maria Luisa

AU - Kim, Jin Young

AU - Kopylov, Arthur

AU - Marcilla, Miguel

AU - McKay, Mathew J.

AU - Mirzaei, Mehdi

AU - Molloy, Mark P.

AU - Ohlund, Leanne B.

AU - Paik, Young Ki

AU - Paradela, Alberto

AU - Raftery, Mark

AU - Sabidó, Eduard

AU - Sleno, Lekha

AU - Wilffert, Daniel

AU - Wolters, Justina C.

AU - Yoo, Jong Shin

AU - Zgoda, Victor

AU - Parker, Carol E.

AU - Borchers, Christoph H.

N1 - Funding Information: The UVic-Genome BC Proteomics Centre would like to thank Genome Canada and Genome British Columbia for STIC funding and support, as well as Western Economic Diversification of Canada for instrumentation support. All laboratories from Spain are members of ProteoRed (Plataforma de Recursos Biomoleculares y Bioinformáticos) and are supported by grant PT13/0001 funded by Instituto de Salud Carlos III (ISCIII) and the European Regional Development Fund (FEDER) . FC wishes to acknowledge support from Grant PRB2 (IPT13/0001 - ISCIII-SGEFI/FEDER). GD wishes to acknowledge support from grants FAPERJ E26-110.138/2013, FAPERJ E-26/111.697/2013, and FAPERJ E-26/0010.1582/2014. AK and VZ state that the Russian portion of the work was done in the framework of the State Academies Fundamental Research Program (2013-2020). Reynaldo Interior (Hospital for Sick Children; Toronto, ON, Canada), Jay Gambee (AAA Service Laboratory; Damascus, OR, USA), and David Chen (University of British Columbia; Vancouver, BC, Canada) are recognized for characterizing the 43 SIS peptides. PAH wishes to thank Ardeshir Amirkhani of the Australian Proteome Analysis Facility, Macquarie University, Sydney, Australia for assistance with sample preparation and data analysis. Publisher Copyright: © 2015 The Authors.

PY - 2015/9/1

Y1 - 2015/9/1

N2 - 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.

AB - 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.

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U2 - 10.1016/j.euprot.2015.06.001

DO - 10.1016/j.euprot.2015.06.001

M3 - Article

AN - SCOPUS:84940917784

VL - 8

SP - 6

EP - 15

JO - EuPA Open Proteomics

JF - EuPA Open Proteomics

SN - 2212-9685

ER -

Inter-laboratory evaluation of instrument platforms and experimental workflows for quantitative accuracy and reproducibility assessment

Abstract

Bibliographical note

All Science Journal Classification (ASJC) codes

Access to Document

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