Proteomics quality and standard: From a regulatory perspective

Journal of Proteomics

Volumn 96, Issue , 2014, Pages 353-359

  Gu, Qiang ^a   Yu, Li Rong ^a  

^a NATIONAL CENTER FOR TOXICOLOGICAL RESEARCH   (United States)

Author keywords

Biomarker qualification; Mass spectrometry; Proteomics; Quality control; Regulatory decision; Standards

Indexed keywords

STABLE ISOTOPE;

EXTRACTION; GOOD LABORATORY PRACTICE; ISOTOPE LABELING; LIQUID CHROMATOGRAPHY; MASS SPECTROMETRY; METHODOLOGY; NANOFLOW LIQUID CHROMATOGRAPHY TANDEM MASS SPECTROMETRY; PRACTICE GUIDELINE; PRIORITY JOURNAL; PROTEIN CONTENT; PROTEIN DETERMINATION; PROTEIN ISOLATION; PROTEOMICS; QUALITY CONTROL; REVERSED PHASE LIQUID CHROMATOGRAPHY; REVIEW; SHOTGUN PROTEOMICS; TANDEM MASS SPECTROMETRY;

BIOMARKER QUALIFICATION; MASS SPECTROMETRY; PROTEOMICS; QUALITY CONTROL; REGULATORY DECISION; STANDARDS;

GUIDELINES AS TOPIC; PROTEOMICS; RESEARCH DESIGN; UNITED STATES; UNITED STATES FOOD AND DRUG ADMINISTRATION;

EID: 84890946839     PISSN: 18743919     EISSN: 18767737     Source Type: Journal    
DOI: 10.1016/j.jprot.2013.11.024     Document Type: Review

References (53)

1. Goodsaid F., Papaluca M. Evolution of biomarker qualification at the health authorities. Nat Biotechnol 2010, 28:441-443.
2. Goodsaid F.M., Mendrick D.L. Translational medicine and the value of biomarker qualification. Sci Transl Med 2010, 2. [47 ps4].
3. Taylor C.F., Paton N.W., Lilley K.S., Binz P.A., Julian R.K., Jones A.R., et al. The minimum information about a proteomics experiment (MIAPE). Nat Biotechnol 2007, 25:887-893.
4. Tao F. 1st NCI annual meeting on Clinical Proteomic Technologies for Cancer. Expert Rev Proteomics 2008, 5:17-20.
5. Taylor C.F., Binz P.A., Aebersold R., Affolter M., Barkovich R., Deutsch E.W., et al. Guidelines for reporting the use of mass spectrometry in proteomics. Nat Biotechnol 2008, 26:860-861.
6. Binz P.A., Barkovich R., Beavis R.C., Creasy D., Horn D.M., Julian R.K., et al. Guidelines for reporting the use of mass spectrometry informatics in proteomics. Nat Biotechnol 2008, 26:862.
7. Gibson F., Anderson L., Babnigg G., Baker M., Berth M., Binz P.A., et al. Guidelines for reporting the use of gel electrophoresis in proteomics. Nat Biotechnol 2008, 26:863-864.
8. Domann P.J., Akashi S., Barbas C., Huang L., Lau W., Legido-Quigley C., et al. Minimum Information About a Proteomics E. Guidelines for reporting the use of capillary electrophoresis in proteomics. Nat Biotechnol 2010, 28:654-655.
9. Jones A.R., Carroll K., Knight D., Maclellan K., Domann P.J., Legido-Quigley C., et al. Minimum Information About a Proteomics E. Guidelines for reporting the use of column chromatography in proteomics. Nat Biotechnol 2010, 28:654.
10. Hoogland C., O'Gorman M., Bogard P., Gibson F., Berth M., Cockell S.J., et al. Minimum Information About a Proteomics E. Guidelines for reporting the use of gel image informatics in proteomics. Nat Biotechnol 2010, 28:655-656.
11. Orchard S., Salwinski L., Kerrien S., Montecchi-Palazzi L., Oesterheld M., Stumpflen V., et al. The minimum information required for reporting a molecular interaction experiment (MIMIx). Nat Biotechnol 2007, 25:894-898.
12. Bourbeillon J., Orchard S., Benhar I., Borrebaeck C., de Daruvar A., Dubel S., et al. Minimum information about a protein affinity reagent (MIAPAR). Nat Biotechnol 2010, 28:650-653.
13. Montecchi-Palazzi L., Kerrien S., Reisinger F., Aranda B., Jones A.R., Martens L., et al. The PSI semantic validator: a framework to check MIAPE compliance of proteomics data. Proteomics 2009, 9:5112-5119.
14. Gloriam D.E., Orchard S., Bertinetti D., Bjorling E., Bongcam-Rudloff E., Borrebaeck C.A., et al. A community standard format for the representation of protein affinity reagents. Mol Cell Proteomics 2010, 9:1-10.
15. Gibson F., Hoogland C., Martinez-Bartolome S., Medina-Aunon J.A., Albar J.P., Babnigg G., et al. The gel electrophoresis markup language (GelML) from the Proteomics Standards Initiative. Proteomics 2010, 10:3073-3081.
16. Tabb D.L., Vega-Montoto L., Rudnick P.A., Variyath A.M., Ham A.J., Bunk D.M., et al. Repeatability and reproducibility in proteomic identifications by liquid chromatography-tandem mass spectrometry. J Proteome Res 2010, 9:761-776.
17. Mischak H., Apweiler R., Banks R.E., Conaway M., Coon J., Dominiczak A., et al. Clinical proteomics: a need to define the field and to begin to set adequate standards. Proteomics Clin Appl 2007, 1:148-156.
18. Bell A.W., Deutsch E.W., Au C.E., Kearney R.E., Beavis R., Sechi S., et al. A HUPO test sample study reveals common problems in mass spectrometry-based proteomics. Nat Methods 2009, 6:423-430.
19. Sabido E., Selevsek N., Aebersold R. Mass spectrometry-based proteomics for systems biology. Curr Opin Biotechnol 2012, 23:591-597.
20. Meng Z., Veenstra T.D. Targeted mass spectrometry approaches for protein biomarker verification. J Proteomics 2011, 74:2650-2659.
21. Gerszten R.E., Carr S.A., Sabatine M. Integration of proteomic-based tools for improved biomarkers of myocardial injury. Clin Chem 2010, 56:194-201.
22. Ning M.M., Lopez M., Sarracino D., Cao J., Karchin M., McMullin D., et al. Pharmaco-proteomics opportunities for individualizing neurovascular treatment. Neurol Res 2013, 35:448-456.
23. Yu L.R. Pharmacoproteomics and toxicoproteomics: the field of dreams. J Proteomics 2011, 74:2549-2553.
24. Michalski A., Damoc E., Lange O., Denisov E., Nolting D., Muller M., et al. Ultra high resolution linear ion trap Orbitrap mass spectrometer (Orbitrap Elite) facilitates top down LC MS/MS and versatile peptide fragmentation modes. Mol Cell Proteomics 2012, 11. [O111 013698].
25. Altelaar A.F., Heck A.J. Trends in ultrasensitive proteomics. Curr Opin Chem Biol 2012, 16:206-213.
26. Boja E.S., Rodriguez H. Mass spectrometry-based targeted quantitative proteomics: achieving sensitive and reproducible detection of proteins. Proteomics 2012, 12:1093-1110.
27. Shi T., Sun X., Gao Y., Fillmore T.L., Schepmoes A.A., Zhao R., et al. Targeted quantification of low ng/mL level proteins in human serum without immunoaffinity depletion. J Proteome Res 2013, 12:3353-3361.
28. Nagaraj N., Kulak N.A., Cox J., Neuhauser N., Mayr K., Hoerning O., et al. System-wide perturbation analysis with nearly complete coverage of the yeast proteome by single-shot ultra HPLC runs on a bench top Orbitrap. Mol Cell Proteomics 2012, 11. [M111 013722].
29. Hebert A.S., Merrill A.E., Stefely J.A., Bailey D.J., Wenger C.D., Westphall M.S., et al. Amine-reactive neutron-encoded labels for highly plexed proteomic quantitation. Mol Cell Proteomics 2013, 12:3360-3369.
30. Ding C., Jiang J., Wei J., Liu W., Zhang W., Liu M., et al. A fast workflow for identification and quantification of proteomes. Mol Cell Proteomics 2013, 12:2370-2380.
31. Hebert A.S., Richards A.L., Bailey D.J., Ulbrich A., Coughlin E.E., Westphall M.S., et al. The one hour yeast proteome. Mol Cell Proteomics 2013, 12. [M113.034769].
32. Kuhn E., Whiteaker J.R., Mani D.R., Jackson A.M., Zhao L., Pope M.E., et al. Interlaboratory evaluation of automated, multiplexed peptide immunoaffinity enrichment coupled to multiple reaction monitoring mass spectrometry for quantifying proteins in plasma. Mol Cell Proteomics 2012, 11. [M111 013854].
33. Abbatiello S.E., Mani D.R., Schilling B., Maclean B., Zimmerman L.J., Feng X., et al. Design, implementation and multisite evaluation of a system suitability protocol for the quantitative assessment of instrument performance in liquid chromatography-multiple reaction monitoring-MS (LC-MRM-MS). Mol Cell Proteomics 2013, 12:2623-2639.
34. Eisenacher M., Schnabel A., Stephan C. Quality meets quantity - quality control, data standards and repositories. Proteomics 2011, 11:1031-1036.
35. Wiener M.C., Sachs J.R., Deyanova E.G., Yates N.A. Differential mass spectrometry: a label-free LC-MS method for finding significant differences in complex peptide and protein mixtures. Anal Chem 2004, 76:6085-6096.
36. Wang M., You J., Bemis K.G., Tegeler T.J., Brown D.P. Label-free mass spectrometry-based protein quantification technologies in proteomic analysis. Brief Funct Genomic Proteomic 2008, 7:329-339.
37. Ong S.E., Blagoev B., Kratchmarova I., Kristensen D.B., Steen H., Pandey A., et al. Stable isotope labeling by amino acids in cell culture, SILAC, as a simple and accurate approach to expression proteomics. Mol Cell Proteomics 2002, 1:376-386.
38. Gygi S.P., Rist B., Gerber S.A., Turecek F., Gelb M.H., Aebersold R. Quantitative analysis of complex protein mixtures using isotope-coded affinity tags. Nat Biotechnol 1999, 17:994-999.
39. Yu L.R., Conrads T.P., Uo T., Issaq H.J., Morrison R.S., Veenstra T.D. Evaluation of the acid-cleavable isotope-coded affinity tag reagents: application to camptothecin-treated cortical neurons. J Proteome Res 2004, 3:469-477.
40. Ross P.L., Huang Y.N., Marchese J.N., Williamson B., Parker K., Hattan S., et al. Multiplexed protein quantitation in Saccharomyces cerevisiae using amine-reactive isobaric tagging reagents. Mol Cell Proteomics 2004, 3:1154-1169.
41. Thompson A., Schafer J., Kuhn K., Kienle S., Schwarz J., Schmidt G., et al. Tandem mass tags: a novel quantification strategy for comparative analysis of complex protein mixtures by MS/MS. Anal Chem 2003, 75:1895-1904.
42. Schnolzer M., Jedrzejewski P., Lehmann W.D. Protease-catalyzed incorporation of 18O into peptide fragments and its application for protein sequencing by electrospray and matrix-assisted laser desorption/ionization mass spectrometry. Electrophoresis 1996, 17:945-953.
43. Yao X., Freas A., Ramirez J., Demirev P.A., Fenselau C. Proteolytic 18O labeling for comparative proteomics: model studies with two serotypes of adenovirus. Anal Chem 2001, 73:2836-2842.
44. Gao Y., Gopee N.V., Howard P.C., Yu L.R. Proteomic analysis of early response lymph node proteins in mice treated with titanium dioxide nanoparticles. J Proteomics 2011, 74:2745-2759.
45. Anderson L., Hunter C.L. Quantitative mass spectrometric multiple reaction monitoring assays for major plasma proteins. Mol Cell Proteomics 2006, 5:573-588.
46. Levin Y., Schwarz E., Wang L., Leweke F.M., Bahn S. Label-free LC-MS/MS quantitative proteomics for large-scale biomarker discovery in complex samples. J Sep Sci 2007, 30:2198-2203.
47. Rudnick P.A., Clauser K.R., Kilpatrick L.E., Tchekhovskoi D.V., Neta P., Blonder N., et al. Performance metrics for liquid chromatography-tandem mass spectrometry systems in proteomics analyses. Mol Cell Proteomics 2010, 9:225-241.
48. Callister S.J., Barry R.C., Adkins J.N., Johnson E.T., Qian W.J., Webb-Robertson B.J., et al. Normalization approaches for removing systematic biases associated with mass spectrometry and label-free proteomics. J Proteome Res 2006, 5:277-286.
49. Balgley B.M., Laudeman T., Yang L., Song T., Lee C.S. Comparative evaluation of tandem MS search algorithms using a target-decoy search strategy. Mol Cell Proteomics 2007, 6:1599-1608.
50. Gao Y., Holland R.D., Yu L.R. Quantitative proteomics for drug toxicity. Brief Funct Genomic Proteomic 2009, 8:158-166.
51. Nesvizhskii A.I. A survey of computational methods and error rate estimation procedures for peptide and protein identification in shotgun proteomics. J Proteomics 2010, 73:2092-2123.
52. Beasley-Green A., Bunk D., Rudnick P., Kilpatrick L., Phinney K. A proteomics performance standard to support measurement quality in proteomics. Proteomics 2012, 12:923-931.
53. Vizcaino J.A., Cote R.G., Csordas A., Dianes J.A., Fabregat A., Foster J.M., et al. The PRoteomics IDEntifications (PRIDE) database and associated tools: status in 2013. Nucleic Acids Res 2013, 41:D1063-D1069.