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

EuPA Open Proteomics

Volumn 8, Issue , 2015, Pages 6-15

  Percy, Andrew J ^a   Tamura Wells, Jessica ^a   Albar, Juan Pablo ^b   Aloria, Kerman ^c   Amirkhani, Ardeshir ^d   Araujo, Gabriel D T ^e   Arizmendi, Jesus M ^c   Blanco, Francisco J ^f,g   Canals, Francesc ^h   Cho, Jin Young ⁱ   Colomé Calls, Núria ^h   Corrales, Fernando J ^j   Domont, Gilberto ^e   Espadas, Guadalupe ^k,l   Fernandez Puente, Patricia ^f   Gil, Concha ^m   Haynes, Paul A ^d   Hernáez, Maria Luisa ^m   Kim, Jin Young ⁿ   Kopylov, Arthur ^o   Marcilla, Miguel ^b   McKay, Mathew J ^d   Mirzaei, Mehdi ^d   Molloy, Mark P ^d   Ohlund, Leanne B ^p   Paik, Young Ki ⁱ   Paradela, Alberto ^b   Raftery, Mark ^q   Sabidó, Eduard ^k,l   Sleno, Lekha ^p   Wilffert, Daniel ^r   Wolters, Justina C ^r   Yoo, Jong Shin ⁿ   Zgoda, Victor ^o   Parker, Carol E ^a   Borchers, Christoph H ^a,s   more..

^a UNIVERSITY OF VICTORIA   (Canada)

^b CENTRO NACIONAL DE BIOTECNOLOGÍA   (Spain)

^c UNIVERSITY OF THE BASQUE COUNTRY UPV EHU   (Spain)

^d MACQUARIE UNIVERSITY   (Australia)

^e FEDERAL UNIVERSITY OF RIO DE JANEIRO   (Brazil)

^f HOSPITAL JUAN CANALEJO   (Spain)

^g UNIVERSITY OF A CORUÑA   (Spain)

^h HOSPITAL UNIVERSITARI VALL D HEBRON   (Spain)

ⁱ Yonsei University   (South Korea)

^j INSTITUTO DE SALUD CARLOS III   (Spain)

^k CENTRE FOR GENOMIC REGULATION CRG   (Spain)

^l UNIVERSITAT POMPEU FABRA   (Spain)

^m UNIVERSIDAD COMPLUTENSE DE MADRID   (Spain)

ⁿ Korea Basic Science Institute (KBSI)   (South Korea)

^o INSTITUTE OF BIOMEDICAL CHEMISTRY   (Russian Federation)

^p UNIVERSITÉ DU QUÉBEC À MONTRÉAL   (Canada)

^q UNIVERSITY OF NEW SOUTH WALES   (Australia)

^r UNIVERSITY OF GRONINGEN   (Netherlands)

^s UNIVERSITY OF VICTORIA   (Canada)

more..

Author keywords

Accuracy; Human plasma; Quality control; Quantitative proteomics; Reproducibility; Workflow validation

Indexed keywords

PLASMA PROTEIN; TRYPSIN;

ARTICLE; CONTROLLED STUDY; ERROR; ISOTOPE LABELING; LABORATORY; LIQUID CHROMATOGRAPH; PARAMEDICAL PERSONNEL; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEOMICS; QUALITY CONTROL; QUANTITATIVE ANALYSIS; REPRODUCIBILITY; SKILL; STANDARD; STANDARDIZATION; TANDEM MASS SPECTROMETRY;

EID: 84940917784     PISSN: 22129685     EISSN: 22129685     Source Type: Journal    
DOI: 10.1016/j.euprot.2015.06.001     Document Type: Article

References (23)

1. Ong S., Mann M. Mass spectrometry-based proteomics turns quantitative. Nat. Chem. Biol. 2005, 1:252-262.
2. Chace D.H., Kalas T.A. A biochemical perspective on the use of tandem mass spectrometry for newborn screening and clinical testing. Clin. Biochem. 2005, 38:296-309.
3. Want E.J., Cravatt B.F., Siuzdak G. The expanding role of mass spectrometry in metabolite profiling and characterization. Chembiochem 2005, 6:1941-1951.
4. Rai A.J., Vitzthum F. Effects of preanalytical variables on peptide and protein measurements in human serum and plasma: implications for clinical proteomics. Expert Rev. Proteomics 2006, 3:409-426.
5. Rai A.J., Gelfand C.A., Haywood B.C., Warunek D.J., Yi J., Schuchard M.D., et al. HUPO Plasma Proteome Project specimen collection and handling: Towards the standardization of parameters for plasma proteome samples. Proteomics 2005, 5:3262-3277.
6. Malm J., Fehniger T.E., Danmyr P., Végvári A., Welinder C., Lindberg H., et al. Developments in biobanking workflow standardization providing sample integrity and stability. J. Proteomics 2013, 95:38-45.
7. Marko-Varga G., Végvári A., Welinder C., Lindberg H., Rezeli M., Edula G., et al. Standardization and utilization of biobank resources in clinical protein science with examples of emerging applications. J. Proteome Res. 2012, 11:5124-5134.
8. Addona T.A., Abbatiello S.E., Schilling B., Skates S.J., Mani D.R., Bunk D.M., et al. Multi-site assessment of the precision and reproducibility of multiple reaction monitoring-based measurements of proteins in plasma. Nat. Biotechnol. 2009, 27:633-641.
9. Anderson N.L., Anderson N.G., Pearson T.W., Borchers C.H., Paulovich A.G., Patterson S.D., et al. A human proteome detection and quantitation project. Mol. Cell Proteomics 2009, 8:883-886.
10. Abbatiello S.E., Mani D.R., Schilling B., Maclean B., Zimmerman L.J., Feng X., et al. Design, implementation, and multi-site evaluation of a system suitability protocol for the quantitative assessment of instrument performance in LC-MRM-MS. Mol. Cell Proteomics 2013, 12:2623-2639.
11. Paulovich A.G., Billheimer D.D., Ham A.-J.L., Vega-Montoto L., Rudnick P.A., Tabb D.L., et al. A CPTAC inter-laboratory study characterizing a yeast performance standard for benchmarking LC-MS platform performance. Mol. Cell Proteomics 2010, 9:242-254.
12. CPTAC. 2010. http://proteomicscancergov/programs/CPTAC/.
13. Percy A.J., Chambers A.G., Yang J., Jackson A.M., Domanski D., Burkhart J., et al. Method and platform standardization in MRM-based quantitative plasma proteomics. J. Proteomics 2013, 95:66-76.
14. Percy A.J., Chambers A.G., Smith D.S., Borchers C.H. Standardized protocols for quality control of MRM-based plasma proteomic workflow. J. Proteome Res. 2013, 12:222-233.
15. Peterson A.C., Russell J.D., Bailey D.J., Westphall M.S., Coon J.J. Parallel reaction monitoring for high resolution and high mass accuracy quantitative, targeted proteomics. Mol. Cell Proteomics 2012, 11:1475-1488.
16. Abbatiello S.E., Schilling B., Mani D.R., Zimmerman L.J., Hall S.C., MacLean B., et al. Large-scale inter-laboratory study to develop, analytically validate and apply highly multiplexed, quantitative peptide assays to measure cancer-relevant proteins in plasma. Mol. Cell Proteomics 2015, pii: mcp.M114.047050.
17. Kuzyk M.A., Smith D., Yang J., Cross T.J., Jackson A.M., Hardie D.B., et al. Multiple reaction monitoring-based, multiplexed, absolute quantitation of 45 proteins in human plasma. Mol. Cell. Proteomics 2009, 8:1860-1877.
18. SIB_Swiss_Institute_of_Bioinformatics. Compute pI/Mw. http://web.expasy.org/compute_pi/.
19. Mohammed Y., Percy A.J., Chambers A.G., Borchers C.H. Qualis-SIS. Automated standard curve generation and quality assessment for multiplexed targeted quantitative proteomic experiments with labeled standards. J. Proteome Res. 2015, 14:1137-1146.
20. Percy A.J., Yang J., Chambers A.G., Simon R., Hardie D.B., Borchers C.H. Multiplexed MRM with internal standards for cerebrospinal fluid candidate protein biomarker quantitation. J. Proteome Res. 2014, 13:3733-3747.
21. Grubbs F.E., Beck G. Extension of sample sizes and percentage points for significance tests of outlying observations. Technometrics 1972, 14:847-854.
22. Percy A.J., Simon R., Chambers A.G., Borchers C.H. Enhanced sensitivity and multiplexing with 2D LC/MRM-MS and labeled standards for deeper and more comprehensive protein quantitation. J. Proteomics 2014, 106:113-124.
23. Percy A.J., Chambers A.G., Yang J., Hardie D.B., Borchers C.H. Advances in multiplexed MRM-based protein biomarker quantitation toward clinical utility. Biochim. Biophys. Acta 2014, 1844:917-926.