CoChat
Sign Up
Cited by 11Advanced Proteomics Techniques and ApplicationsClinical Laboratory Practices and Quality ControlMass Spectrometry Techniques and Applications

Quality requirements for quantitative clinical chemistry proteomics

Open access
·2014·Translational Proteomics
DOI 10.1016/j.trprot.2013.10.001
Open this paper in CoChat — free accountOpen PDF

Abstract

The great potential of mass spectrometry (MS)-based proteomics as a quantitative application in clinical chemistry has been explored and shown since more than a decade.As a result of maturation of strategies as well as MS-equipment, the field of quantitative proteomics now experiences a growing interest for implementation in the clinic.MS methods have the potential to outperform the currently applied clinical immunoassays and offer multiple opportunities to support standardization initiatives for the measurement of protein biomarkers in routine clinical practice.For successful introduction and broad use of MS-based quantitative protein assays in clinical chemistry, several important concepts for quality assurance generally accepted in the clinical chemistry community have to be borne in mind.To translate the quality specifications of routine clinical assays to newly developed MS-based methods, common knowledge of the underlying principles to define minimal, desirable and optimal analytical performance, such as those based on biological variation, is essential.In this review critical steps in the complete quantitative clinical chemistry proteomics (qCCP) workflow that may contribute to the total variation of the MS-procedure are outlined, in particular for applications that involve liquid chromatography in combination with stable-isotope dilution methodology and multiple reaction monitoring MS (LC-SID-MRM-MS).Furthermore, in this review well-known clinical chemistry concepts of metrological traceability and commutability of reference materials are introduced with regard to MS strategies, and the potential of qCCP in standardization of clinical protein assays is emphasized.Critical steps for safeguarding analytical performance at the pre-, and analytical phase,

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

A few free checks a day · papers already verified open instantly · results are public

Integrity signals

Registry

Crossref · 10.1016/j.trprot.2013.10.001

Cites

1 of 1 references verified0 citation errors · 0 not checkable

Statistics

Claims the paper makes

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

A few free checks a day · papers already verified open instantly · results are public

Claims other papers make about this one

Each is checked against this paper’s own text: does it say what the citing paper says it does?

Self-check

Percentages, sums and reported differences re-computed from the paper’s own numbers.

The self-check needs the paper’s full text.

Cites

Flagged first, then by citations

Research works printed but not linked: 97

  1. Hoofnagle AN, Wener MH. The fundamental flaws of immunoassays and potential solutions using tandem mass spectrometry. J Immunol Methods 2009;347:3-11.
  2. Stenman UH. Immunoassay standardization: is it possible, who is responsible, who is capable? Clin Chem 2001;47:815-20.
  3. Gillette MA, Carr SA. Quantitative analysis of peptides and proteins in biomedicine by targeted mass spectrometry. Nat Methods 2013;10:28-34.
  4. Lehmann S, Hoofnagle A, Hochstrasser D, Brede C, Glueckmann M, Cocho JA, et al. Quantitative Clinical Chemistry Proteomics (qCCP) using mass spectrometry: general characteristics and application. Clin Chem Lab Med 2013;51:919-35.
  5. Horvath AR, Lord SJ, St John A, Sandberg S, Cobbaert C, Lorenz S, et al. From biomarker to medical tests: the changing landscape of test evaluation. Clin Chim Acta 2013, http://dx.doi.org/10.1016/j.cca.2013.09.018. · DOI · Paper page
  6. Gillery P, Young IS. Progress towards standardization: an IFCC Scientific Division Perspective. Clin Chem Lab Med 2013;51:915-8.
  7. Vesper HW, Miller WG, Myers GL. Reference materials and commutability. Clin Biochem Rev 2007;28:139-47.
  8. Lange V, Picotti P, Domon B, Aebersold R. Selected reaction monitoring for quantitative proteomics: a tutorial. Mol Syst Biol 2008;4:222.
  9. Gallien S, Duriez E, Domon B. Selected reaction monitoring applied to proteomics. J Mass Spectrom 2011;46:298-312.
  10. Wasinger VC, Zeng M, Yau Y. Current status and advances in quantitative proteomic mass spectrometry. Int J Proteomics 2013;2013:180605.
  11. Pan S, Aebersold R, Chen R, Rush J, Goodlett DR, McIntosh MW, et al. Mass spectrometry based targeted protein quantification: methods and applications. J Proteome Res 2009;8:787-97.
  12. Domon B, Aebersold R. Options and considerations when selecting a quantitative proteomics strategy. Nat Biotechnol 2010;28:710-21.
  13. Duncan MW, Aebersold R, Caprioli RM. The pros and cons of peptide-centric proteomics. Nat Biotechnol 2010;28:659-64.
  14. Barr JR, Maggio VL, Patterson Jr DG, Cooper GR, Henderson LO, Turner WE, et al. Isotope dilution-mass spectrometric quantification of specific proteins: model application with apolipoprotein A-I. Clin Chem 1996;42:1676-82.
  15. Bantscheff M, Schirle M, Sweetman G, Rick J, Kuster B. Quantitative mass spectrometry in proteomics: a critical review. Anal Bioanal Chem 2007;389:1017-31.
  16. van den Broek I, Niessen WM, van Dongen WD. Bioanalytical LC-MS/MS of protein-based biopharmaceuticals. J Chromatogr B Analyt Technol Biomed Life Sci 2013;929:161-79.
  17. Lehmann S, Poinot P, Tiers L, Junot C, Becher F, Hirtz C. From "Clinical Proteomics" to "Clinical Chemistry Proteomics": considerations using quantitative mass-spectrometry as a model approach. Clin Chem Lab Med 2012;50:235-42.
  18. Bansal S, DeStefano A. Key elements of bioanalytical method validation for small molecules. AAPS J 2007;9:E109-14.
  19. Kushnir MM, Rockwood AL, Bergquist J. Liquid chromatography-tandem mass spectrometry applications in endocrinology. Mass Spectrom Rev 2010;29:480-502.
  20. Honour JW. Development and validation of a quantitative assay based on tandem mass spectrometry. Ann Clin Biochem 2011;48:97-111.
  21. Novakova L. Challenges in the development of bioanalytical liquid chromatography-mass spectrometry method with emphasis on fast analysis. J Chromatogr A 2013;1292:25-37.
  22. Taverniers I, De Loose M, Van Bockstaele E. Trends in quality in the analytical laboratory. II. Analytical method validation and quality assurance. Trends Anal Chem 2004;23:535-52.
  23. Bozovic A, Kulasingam V. Quantitative mass spectrometry-based assay development and validation: from small molecules to proteins. Clin Biochem 2012;46:444-55.
  24. Mani DR, Abbatiello SE, Carr SA. Statistical characterization of multiple-reaction monitoring mass spectrometry (MRM-MS) assays for quantitative proteomics. BMC Bioinformatics 2012;13(16):S9.
  25. Abbatiello SE, Mani DR, Schilling B, Maclean B, Zimmerman LJ, 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;12:2623-39.
  26. Mann M. Comparative analysis to guide quality improvements in proteomics. Nat Methods 2009;6:717-9.
  27. Tholen D. CLSI evaluation protocols. MLO Med Lab Obs 2006;38:39-41.
  28. Kenny D, Fraser CG, Petersen PH, Kallner A. Consensus agreement. Scand J Clin Lab Invest 1999;59:585.
  29. Ricos C, Alvarez V, Cava F, Garcia-Lario JV, Hernandez A, Jimenez CV, et al. Current databases on biological variation: pros, cons and progress. Scand J Clin Lab Invest 1999;59:491-500.
  30. Sikaris K. Analytical quality -what should we be aiming for? Clin Biochem Rev 2008;29(1):S5-10.
  31. Thienpont LM, van Uytfanghe K, De Leenheer AP. Reference measurement systems in clinical chemistry. Clin Chim Acta 2002;323:73-87.
  32. Panteghini M. Traceability, reference systems and result comparability. Clin Biochem Rev 2007;28:97-104.
  33. Miller WG, Meyers GL, Gantzer ML, Kahn SE, Schonbrunner ER, Thienpont LM, et al. Roadmap for harmonization of clinical laboratory measurement procedures. Clin Chem 2011;57:1108-17.
  34. Bunk DM. Reference materials and reference measurement procedures: an overview from a national metrology institute. Clin Biochem Rev 2007;28:131-7.
  35. Brownridge P, Beynon RJ. The importance of the digest: proteolysis and absolute quantification in proteomics. Methods 2011;54:351-60.
  36. Cobbaert C, Weykamp C, Baadenhuijsen H, Kuypers A, Lindemans J, Jansen R. Selection, preparation, and characterization of commutable frozen human serum pools as potential secondary reference materials for lipid and apolipoprotein measurements: study within the framework of the Dutch project "Calibration 2000". Clin Chem 2002;48:1526-38.
  37. Armbruster D, Miller RR. The Joint Committee for Traceability in Laboratory Medicine (JCTLM): a global approach to promote the standardisation of clinical laboratory test results. Clin Biochem Rev 2007;28:105-13.
  38. Kushnir MM, Rockwood AL, Roberts WL, Abraham D, Hoofnagle AN, Meikle AW. Measurement of thyroglobulin by liquid chromatography-tandem mass spectrometry in serum and plasma in the presence of antithyroglobulin autoantibodies. Clin Chem 2013;59:982-90.
  39. Neubert H, Muirhead D, Kabir M, Grace C, Cleton A, Arends R. Sequential protein and peptide immunoaffinity capture for mass spectrometry-based quantification of total human beta-nerve growth factor. Anal Chem 2013;85:1719-26.
  40. Beynon RJ, Doherty MK, Pratt JM, Gaskell SJ. Multiplexed absolute quantification in proteomics using artificial QCAT proteins of concatenated signature peptides. Nat Methods 2005;2:587-9.
  41. Kito K, Ota K, Fujita T, Ito T. A synthetic protein approach toward accurate mass spectrometric quantification of component stoichiometry of multiprotein complexes. J Proteome Res 2007;6:792-800.
  42. Brun V, Dupuis A, Adrait A, Marcellin M, Thomas D, Court M, et al. Isotope-labeled protein standards: toward absolute quantitative proteomics. Mol Cell Proteomics 2007;6:2139-49.
  43. Brun V, Masselon C, Garin J, Dupuis A. Isotope dilution strategies for absolute quantitative proteomics. J Proteomics 2009;72:740-9.
  44. Agger SA, Marney LC, Hoofnagle AN. Simultaneous quantification of apolipoprotein A-I and apolipoprotein B by liquid-chromatography-multiple-reaction-monitoring mass spectrometry. Clin Chem 2010;56:1804-13.
  45. Hoofnagle AN, Roth MY. Clinical review: improving the measurement of serum thyroglobulin with mass spectrometry. J Clin Endocrinol Metab 2013;98:1343-52.
  46. Plebani M. Quality indicators to detect pre-analytical errors in laboratory testing. Clin Biochem Rev 2012;33:85-8.
  47. Elliott P, Peakman TC. The UK Biobank sample handling and storage protocol for the collection, processing and archiving of human blood and urine. Int J Epidemiol 2008;37:234-44.
  48. Malm J, Fehniger TE, Danmyr P, Vegvari A, Welinder C, Lindberg H, et al. Developments in biobanking workflow standardization providing sample integrity and stability. J Proteomics 2013, http://dx.doi.org/10.1016/j.jprot.2013.06.035. · DOI
  49. Hulmes JD, Bethea D, Ho K, Huang S-P, Ricci DL, Opiteck GJ, et al. An investigation of plasma collection, stabilization and storage procedures for proteomic analysis of clinical samples. Clin Proteomics 2004;1:17-31.
  50. Rai AJ, Gelfand CA, Haywood BC, Warunek DJ, Yi J, Schuchard MD, et al. HUPO Plasma Proteome Project specimen collection and handling: towards the standardization of parameters for plasma proteome samples. Proteomics 2005;5:3262-77.
  51. Tammen H, Schulte I, Hess R, Menzel C, Kellmann M, Mohring T, et al. Peptidomic analysis of human blood specimens: comparison between plasma specimens and serum by differential peptide display. Proteomics 2005;5:3414-22.
  52. O'Keane MP, Cunningham SK. Evaluation of three different specimen types (serum, plasma lithium heparin and serum gel separator) for analysis of certain analytes: clinical significance of differences in results and efficiency in use. Clin Chem Lab Med 2006;44:662-8.
  53. Lundblad RL. Considerations for the use of blood plasma and serum for proteomic analysis. Internet J Genom Proteom 2005;1, http://dx.doi.org/10.5580/26e. · DOI
  54. van den Broek I, Sparidans RW, Schellens JH, Beijnen JH. Specific investigation of sample handling effects on protease activities and absolute serum concentrations of various putative peptidome cancer biomarkers. Clin Proteomics 2010;6:115-27.
  55. Aguilar-Mahecha A, Kuzyk MA, Domanski D, Borchers CH, Basik M. The effect of pre-analytical variability on the measurement of MRM-MS-based mid-to high-abundance plasma protein biomarkers and a panel of cytokines. PLoS ONE 2012;7:e38290.
  56. Tuck MK, Chan DW, Chia D, Godwin AK, Grizzle WE, Krueger KE, et al. Standard operating procedures for serum and plasma collection: early detection research network consensus statement standard operating procedure integration working group. J Proteome Res 2009;8:113-7.
  57. Parker CE, Domanski D, Percy AJ, Chambers AG, Camenzind AG, Smith DS, et al. Mass spectrometry in high-throughput clinical biomarker assays: multiple reaction monitoring. In: Topics in current chemistry. Berlin Heidelberg: Springer; 2012, http://dx.doi.org/10.1007/128 2012 353. · DOI
  58. Dimeski G, Masci PP, Trabi M, Lavin MF, de JJ. Evaluation of the Becton-Dickinson rapid serum tube: does it provide a suitable alternative to lithium heparin plasma tubes? Clin Chem Lab Med 2010;48:651-7.
  59. Randall SA, McKay MJ, Baker MS, Molloy MP. Evaluation of blood collection tubes using selected reaction monitoring MS: implications for proteomic biomarker studies. Proteomics 2010;10:2050-6.
  60. Wildes D, Wells JA. Sampling the N-terminal proteome of human blood. Proc Natl Acad Sci U S A 2010;107:4561-6.
  61. Rezeli M, Vegvari A, Marko-Varga G, Laurell T. Isotope labeled internal standards (ILIS) as a basis for quality control in clinical studies using plasma samples. J Proteomics 2010;73:1219-29.
  62. Kelleher NL. Top-down proteomics. Anal Chem 2004;76:197A-203A.
  63. Kay RG, Gregory B, Grace PB, Pleasance S. The application of ultra-performance liquid chromatography/tandem mass spectrometry to the detection and quantitation of apolipoproteins in human serum. Rapid Commun Mass Spectrom 2007;21:2585-93.
  64. Campbell JL, Le Blanc JC. Peptide and protein drug analysis by MS: challenges and opportunities for the discovery environment. Bioanalysis 2011;3:645-57.
  65. Keshishian H, Addona T, Burgess M, Kuhn E, Carr SA. Quantitative, multiplexed assays for low abundance proteins in plasma by targeted mass spectrometry and stable isotope dilution. Mol Cell Proteomics 2007;6:2212-29.
  66. Anderson NL, Anderson NG, Haines LR, Hardie DB, Olafson RW, Pearson TW. Mass spectrometric quantitation of peptides and proteins using Stable Isotope Standards and Capture by Anti-Peptide Antibodies (SISCAPA). J Proteome Res 2004;3:235-44.
  67. Mason DR, Reid JD, Camenzind AG, Holmes DT, Borchers CH. Duplexed iMALDI for the detection of angiotensin I and angiotensin II. Methods 2012;56:213-22.
  68. Addona TA, Abbatiello SE, Schilling B, Skates SJ, Mani DR, Bunk DM, et al. Multi-site assessment of the precision and reproducibility of multiple reaction monitoring-based measurements of proteins in plasma. Nat Biotechnol 2009;27:633-41.
  69. Hoofnagle AN. Quantitative clinical proteomics by liquid chromatography-tandem mass spectrometry: assessing the platform. Clin Chem 2010;56:161-4.
  70. Vandermarliere E, Mueller M, Martens L. Getting intimate with trypsin, the leading protease in proteomics. Mass Spectrom Rev 2013, http://dx.doi.org/10.1002/mas.21376. · DOI
  71. Burkhart JM, Schumbrutzki C, Wortelkamp S, Sickmann A, Zahedi RP. Systematic and quantitative comparison of digest efficiency and specificity reveals the impact of trypsin quality on MS-based proteomics. J Proteomics 2012;75:1454-62.
  72. Rice RH, Means GE, Brown WD. Stabilization of bovine trypsin by reductive methylation. Biochim Biophys Acta 1977;492:316-21.
  73. Proc JL, Kuzyk MA, Hardie DB, Yang J, Smith DS, Jackson AM, et al. A quantitative study of the effects of chaotropic agents, surfactants, and solvents on the digestion efficiency of human plasma proteins by trypsin. J Proteome Res 2010;9:5422-37.
  74. Kuhn E, Wu J, Karl J, Liao H, Zolg W, Guild B. Quantification of C-reactive protein in the serum of patients with rheumatoid arthritis using multiple reaction monitoring mass spectrometry and 13 C-labeled peptide standards. Proteomics 2004;4:1175-86.
  75. Arsene CG, Ohlendorf R, Burkitt W, Pritchard C, Henrion A, O'Connor G, et al. Protein quantification by isotope dilution mass spectrometry of proteolytic fragments: cleavage rate and accuracy. Anal Chem 2008;80:4154-60.
  76. Picotti P, Aebersold R, Domon B. The implications of proteolytic background for shotgun proteomics. Mol Cell Proteomics 2007;6:1589-98.
  77. Lawless C, Hubbard SJ. Prediction of missed proteolytic cleavages for the selection of surrogate peptides for quantitative proteomics. OMICS 2012;16:449-56.
  78. Razavi M, Frick LE, Lamarr WA, Pope ME, Miller CA, Anderson NL, et al. High-throughput SISCAPA quantitation of peptides from human plasma digests by ultrafast, liquid chromatography-free mass spectrometry. J Proteome Res 2012;11:5642-9.
  79. Westgard JO. Internal quality control: planning and implementation strategies. Ann Clin Biochem 2003;40:593-611.
  80. Gras JM, Philippe M. Application of the Six Sigma concept in clinical laboratories: a review. Clin Chem Lab Med 2007;45:789-96.
  81. Miller WG, Jones GR, Horowitz GL, Weykamp C. Proficiency testing/external quality assessment: current challenges and future directions. Clin Chem 2011;57:1670-80.
  82. Cobbaert C, Weykamp C, Franck P, de Jonge R, Kuypers A, Steigstra H, et al. Systematic monitoring of standardization and harmonization status with commutable EQA-samples -five year experience from the Netherlands. Clin Chim Acta 2012;414:234-40.
  83. Prakash A, Rezai T, Krastins B, Sarracino D, Athanas M, Russo P, et al. Platform for establishing interlaboratory reproducibility of selected reaction monitoring-based mass spectrometry peptide assays. J Proteome Res 2010;9:6678-88.
  84. Marin SJ, Jones BA, Felix WD, Clark J. Effect of high-temperature on high-performance liquid chromatography column stability and performance under temperature-programmed conditions. J Chromatogr A 2004;1030:255-62.
  85. Briscoe CJ, Stiles MR, Hage DS. System suitability in bioanalytical LC/MS/MS. J Pharm Biomed Anal 2007;44:484-91.
  86. van den Broek I, Sparidans RW, Schellens JH, Beijnen JH. Quantitative bioanalysis of peptides by liquid chromatography coupled to (tandem) mass spectrometry. J Chromatogr B Analyt Technol Biomed Life Sci 2008;872:1-22.
  87. Matuszewski BK, Constanzer ML, Chavez-Eng CM. Strategies for the assessment of matrix effect in quantitative bioanalytical methods based on HPLC-MS/MS. Anal Chem 2003;75:3019-30.
  88. Jemal M, Ouyang Z, Xia YQ. Systematic LC-MS/MS bioanalytical method development that incorporates plasma phospholipids risk avoidance, usage of incurred sample and well thought-out chromatography. Biomed Chromatogr 2010;24:2-19.
  89. Xia YQ, Jemal M. Phospholipids in liquid chromatography/mass spectrometry bioanalysis: comparison of three tandem mass spectrometric techniques for monitoring plasma phospholipids, the effect of mobile phase composition on phospholipids elution and the association of phospholipids with matrix effects. Rapid Commun Mass Spectrom 2009;23:2125-38.
  90. Sherman J, McKay MJ, Ashman K, Molloy MP. How specific is my SRM? The issue of precursor and product ion redundancy. Proteomics 2009;9:1120-3.
  91. Rost H, Malmstrom L, Aebersold R. A computational tool to detect and avoid redundancy in selected reaction monitoring. Mol Cell Proteomics 2012;11:540-9.
  92. Kushnir MM, Rockwood AL, Nelson GJ, Yue B, Urry FM. Assessing analytical specificity in quantitative analysis using tandem mass spectrometry. Clin Biochem 2005;38:319-27.
  93. Abbatiello SE, Mani DR, Keshishian H, Carr SA. Automated detection of inaccurate and imprecise transitions in peptide quantification by multiple reaction monitoring mass spectrometry. Clin Chem 2010;56:291-305.
  94. Fortin T, Salvador A, Charrier JP, Lenz C, Bettsworth F, Lacoux X, et al. Multiple reaction monitoring cubed for protein quantification at the low nanogram/milliliter level in nondepleted human serum. Anal Chem 2009;81:9343-52.
  95. Horowitz GL, Altaie S, Boyd JC, Ceriotti F, Garg U, Horn P, et al. Defining, establishing, and verifying reference intervals in the clinical laboratory: approved guideline - third edition C28-A3c, vol. 28. CLSI; 2008. p. 1-61.
  96. Panteghini M. Implementation of standardization in clinical practice: not always an easy task. Clin Chem Lab Med 2012;50:1237-41.
  97. Anderson NL. The clinical plasma proteome: a survey of clinical assays for proteins in plasma and serum. Clin Chem 2010;56:177-85.

Cited by

Sorted by citations

Venue
Translational Proteomics
Publisher
Elsevier BV
Published
2014-03
Volume
2
Pages
1-13
ISSN
2212-9626 (ISSN-L)
DOI
10.1016/j.trprot.2013.10.001
OpenAlex
W4210970776
Cited by
11
References
1
Citations by year
2024: 1 · 2022: 1 · 2020: 2 · 2018: 2 · 2017: 1 · 2015: 2 · 2014: 2
Type
other
Language
en
Open access
Licence
Locations
Translational Proteomics (publishedVersion, cc-by-nc-nd)
Topics
  • Physical Sciences › Chemistry › Spectroscopy › Advanced Proteomics Techniques and Applications
  • Health Sciences › Medicine › Physiology › Clinical Laboratory Practices and Quality Control
  • Physical Sciences › Chemistry › Spectroscopy › Mass Spectrometry Techniques and Applications
Keywords
quality assurance, protein biomarkers, biological variation, analytical performance, liquid chromatography, stable isotope dilution, multiple reaction monitoring, measurement traceability

About these checks

Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.

Statistics and arithmetic are recomputed, not judged.

Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.

What counts as a claim ›How we measure confidence ›How we check this ›

Are you an author, or do you see a problem with this page? Request a review