Mass spectrometry based biomarker discovery, verification, and validation - Quality assurance and control of protein biomarker assays

Molecular Oncology

Volumn 8, Issue 4, 2014, Pages 840-858

  Parker, Carol E ^a   Borchers, Christoph H ^a,b  

^a UNIVERSITY OF VICTORIA   (Canada)

^b UNIVERSITY OF VICTORIA   (Canada)

Author keywords

Biomarker discovery; Biomarkers; Cancer; Mass spectrometry; Multiple reaction monitoring; Plasma or serum; Selected reaction monitoring; Targeted proteomics; Validation; Verification

Indexed keywords

BIOLOGICAL MARKER; ISOPROTEIN; PLASMA PROTEIN; PROTEIN; TUMOR MARKER; TUMOR PROTEIN;

ANALYTIC METHOD; BIOINFORMATICS; CANCER PATIENT; CORRELATIONAL STUDY; ENZYME LINKED IMMUNOSORBENT ASSAY; HUMAN; MASS SPECTROMETRY; MULTIPLE REACTION MONITORING; PROTEIN ANALYSIS; PROTEIN BLOOD LEVEL; PROTEIN DEPLETION; PROTEOMICS; QUALITY CONTROL; REVIEW; GENETIC ASSOCIATION; ISOLATION AND PURIFICATION; METABOLISM; PROCEDURES; STANDARDS; VALIDATION STUDY;

GENETIC ASSOCIATION STUDIES; HUMANS; MASS SPECTROMETRY; NEOPLASM PROTEINS; PROTEOMICS; QUALITY CONTROL; TUMOR MARKERS, BIOLOGICAL; VALIDATION STUDIES AS TOPIC;

EID: 84906716279     PISSN: 15747891     EISSN: 18780261     Source Type: Journal    
DOI: 10.1016/j.molonc.2014.03.006     Document Type: Review

References (142)

1. Abbatiello S.E., Mani D.R., Keshishian H., Carr S.A. Automated detection of inaccurate and imprecise transitions in peptide quantification by multiple reaction monitoring mass spectrometry. Clin. Chem. 2010, 56:291-305.
2. Abbatiello S.E., Mani D.R., Schilling B., Maclean B., Zimmerman L.J., Feng X., Cusack M.P., Sedransk N., Hall S.C., Addona T., Allen S., Dodder N.G., Ghosh M., Held J.M., V.H., Inerowicz H.D., Jackson A., Keshishian H., Kim J.W., Lyssand J.S., Riley C.P., Rudnick P., Sadowski P., Shaddox K., Smith D., Tomazela D., Wahlander A., Waldemarson S., Whitwell C.A., You J., Zhang S., Kinsinger C.R., Mesri M., Rodriguez H., Borchers C.H., Buck C., Fisher S.J., Gibson B.W., Liebler D., Maccoss M., Neubert T.A., Paulovich A., Regnier F., Skates S.J., Tempst P., Wang M., Carr S.A. 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.
3. Adachi J., Kumar C., Zhang Y., Olsen J.V., Mann M. The human urinary proteome contains more than 1500 proteins, including a large proportion of membrane proteins. Genome Biol. 2006, 7:R80.
4. Addona T.A., Abbatiello S.E., Schilling B., Skates S.J., Mani D.R., Bunk D.M., Spiegelman C.H., Zimmerman L.J., Ham A.-J.L., Keshishian H., Hall S.C., Allen S., Blackman R.K., Borchers C.H., Buck C., Cardasis H.L., Cusack M.P., Dodder N.G., Gibson B.W., Held J.M., Hiltke T., Jackson A., Johansen E.B., Kinsinger C.R., Li J., Mesri M., Neubert T.A., Niles R.K., Pulsipher T.C., Ransohoff D., Rodriguez H., Rudnick P.A., Smith D., Tabb D.L., Tegeler T.J., Variyath A.M., Vega-Montoto L.J., Wahlander A., Waldemarson S., Wang M., Whiteaker J.R., Zhao L., Anderson N.L., Fisher S.J., Liebler D.C., Paulovich A.G., Regnier F.E., Tempst P., Carr S.A. Multi-site assessment of the precision and reproducibility of multiple reaction monitoring-based measurements of proteins in plasma. Nat. Biotechnol. 2009, 27:633-641.
5. Addona T.A., Shi X., Keshishian H., Mani D.R., Burgess M., Gillette M.A., Clauser K.R., Shen D., Lewis G.D., Farrell L.A., Fifer M.A., Sabatine M.S., Gerszten R.E., Carr S.A. A pipeline that integrates the discovery and verification of plasma protein biomarkers reveals candidate markers for cardiovascular disease. Nat. Biotechnol. 2011, 29:635-643.
6. Adkins J.N., Monroe M.E., Auberry K.J., Shen Y., Jacobs J.M., Camp D.G., Vitzthum F., Rodland K.D., Zangar R.C., Smith R.D., Pounds J.G. A proteomic study of the HUPO Plasma Proteome Project's pilot samples using an accurate mass and time tag strategy. Proteomics 2005, 5:3454-3466.
7. Aguilar-Mahecha A., Kuzyk M.A., Domanski D., Borchers C.H., 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. [Epub 2012 Jun 6].
8. Ahn Y.H., Shin P.M., Kim Y.S., Oh N.R., Ji E.S., Kim K.H., Lee Y.J., Kim S.H., Yoo J.S. Quantitative analysis of aberrant protein glycosylation in liver cancer plasma by AAL-enrichment and MRM mass spectrometry. Analyst 2013, 138:6454-6462.
9. Ahn Y.H., Shin P.M., Oh N.R., Park G.W., Kim H., Yoo J.S. A lectin-coupled, targeted proteomic mass spectrometry (MRM MS) platform for identification of multiple liver cancer biomarkers in human plasma. J.Proteomics 2012, 75:5507-5515.
10. Anderson L. Within sight of a rational pipeline for development of protein diagnostics. Clin. Chem. 2012, 58:28-30.
11. Anderson L., Pope M., Razavi M., Pearson T., Werner P., Waddell K., Miller C. High sensitivity SISCAPA-based peptide quantitation using UHPLC and the 6490 QQQ with iFunnel technology. Agilent Appl. Note 2011, http://www.chem.agilent.com/Library/applications/5990-8999en_lo.pdf.
12. Anderson N.L., Anderson N.G. The human plasma proteome: history, character, and diagnostic prospects. Mol. Cell Proteomics 2002, 1:845-867.
13. Anderson N.L., Anderson N.G., Haines L.R., Hardie D.B., Olafson R.W., Pearson T.W. Mass spectrometric quantitation of peptides and proteins using stable isotope standards and capture by anti-peptide antibodies (SISCAPA). J.Proteome Res. 2004, 3:235-244.
14. mTRAQ 2009, Applied Biosystems. http://www.sciex.com/products/standards-and-reagents/mtraq-reagents.xml?country=Canada.
15. Asara J.M., Christofk H.R., Freimark L.M., Cantley L.C. A label-free quantification method by MS/MS TIC compared to SILAC and spectral counting in a proteomics screen. Proteomics 2008, 8:994-999.
16. Aziz N., Nishanian P., Mitsuyasu R., Detels R., Fahey J.L. Variables that affect assays for plasma cytokines and soluble activation markers. Clin. Diagn. Lab. Immunol. 1999, 6:89-95.
17. Bellei E., Bergamini S., Monari E., Fantoni L.I., Cuoghi A., Ozben T., Tomasi A. High-abundance proteins depletion for serum proteomic analysis: concomitant removal of non-targeted proteins. Amino Acids 2011, 40:145-156.
18. Berna M., Ott L., Engle S., Watson D., Solter P., Ackermann B. Quantification of NTproBNP in rat serum using immunoprecipitation and LC/MS/MS: a biomarker of drug-induced cardiac hypertrophy. Anal. Chem. 2008, 80:561-566.
19. Berna M.J., Zhen Y., Watson D.E., Hale J.E., Ackermann B.L. Strategic use of immunoprecipitation and LC/MS/MS for trace-level protein quantification: myosin light chain 1, a biomarker of cardiac necrosis. Anal. Chem. 2007, 79:4199-4205.
20. Biognosys Indexed Retention Time (iRT) 2014, http://www.biognosys.ch/technology/irt.html.
21. Boja E.S., Jortani S.A., Ritchie J., Hoofnagle A.N., Težak Ž., Mansfield E., Keller P., Rivers R.C., Rahbar A., Anderson N.L., Srinivas P., Rodriguez H. The journey to regulation of protein-based multiplex quantitative assays. Clin. Chem. 2011, 57:560-567.
22. Boja E.S., Rodriguez H. Mass spectrometry-based targeted quantitative proteomics: achieving sensitive and reproducible detection of proteins. Proteomics 2012, 12:1093-1110.
23. Brock R., Xiong B., Li L., Vanbogelen R.A., Christman L. A multiplex serum protein assay for determining the probability of colorectal cancer. Am. J. Cancer Res. 2012, 2:598-605.
24. Calvo E., Camafeita E., Fernández-Gutiérrez B., López J.A. Applying selected reaction monitoring to targeted proteomics. Expert Rev. Proteomics 2011, 8:165-173.
25. Camenzind A.G., van der Gugten J.G., Popp R., Leurs U., Holmes D.T., Borchers C.H. Development and evaluation of an immuno-MALDI (iMALDI) Assay for Angiotensin I and the Diagnosis of Secondary Hypertension. Clin Proteomics 2013, 10:20.
26. Chambers A.G., Percy A.J., Simon R., Borchers C.H. MRM for the verification of Cancer biomarker proteins: recent applications to human plasma and serum. Expert Rev. Proteomics 2014, 11:137-148.
27. Chen Y.-T., Chen H.-W., Domanski D., Smith D.S., Liang K.-H., Wu C.-C., Chen C.-L., Chung T., Chen M.-C., Chang Y.-S., Parker C.E., Borchers C.H., Yu J.-S. Multiplexed quantification of 63 proteins in human urine by multiple reaction monitoring-based mass spectrometry for discovery of potential bladder Cancer biomarkers. J.Proteomics 2012, 75:3529-3545.
28. Chen Y.-T., Parker C.E., Chen H.-W., Chen C.-L., Domanski D., Smith D.S., Chih-Wu C.-C., Chung T., Liang K.-H., Chen M.-C., Chang Y.-S., Borchers C.H., Yu J.-S. A Pipeline That Integrates the Discovery and Verification Studies of Urinary Protein Biomarkers Reveals Candidate Markers for Bladder Cancer, in "Proteomics Biomarker Discovery and Validation for Clinical Applications" 2013, Royal Society of Chemistry (RSC). P. Horvatovich (Ed.).
29. Choa C.-K.J., Drabovich A.P., Batruch I., Diamandis E.P. Verification of a biomarker discovery approach for detection of Down syndrome in amniotic fluid via multiplex selected reaction monitoring (SRM) assay. J.Proteomics 2011, 74:2052-2059.
30. Cima I., Schiess R., Wild P., Kaelin M., Schuffler P., Lange V., Picotti P., Ossola R., Templeton A., Schubert O., Fuchs T., Leippold T., Wyler S., Zehetner J., Jochum W., Buhmann J., Cerny T., Moch H., Gillessen S., Aebersold R., Krek W. Cancer genetics-guided discovery of serum biomarker signatures for diagnosis and prognosis of prostate cancer. Proc. Natl. Acad. Sci. U S a 2011, 108:3342-3347.
31. Cohen Freue G.V., Borchers C.H. Multiple reaction monitoring (MRM) - principles and application to coronary artery disease. Circ. Cardiovasc. Genet. 2012, 5:378.
32. Cohen Freue G.V., Meredith A., Smith D., Bergman A., Sasaki M., Lam K.K.Y., Hollander Z., Opushneva N., Takhar M., Lin D., Wilson-McManus J., Balshaw R., Keown P.A., Borchers C.H., McManus B., Ng* R.T., McMaster W.R. Computational biomarker pipeline from discovery to clinical implementation: plasma proteomic biomarkers for cardiac transplantation. PLoS Comput. Biol. 2013, 9:e1002963. for the Biomarkers in Transplantation and the NCE CECR Prevention of Organ Failure Centre of Excellence Teams.
33. Craven R.A., Vasudev N.S., Banks R.E. Proteomics and the search for biomarkers for renal cancer. Clin. Biochem. 2013, 46:456-465.
34. de Wit M., Fijneman R.J., Verheul H.M., Meijer G.A., Jimenez C.R. Proteomics in colorectal cancer translational research: biomarker discovery for clinical applications. Clin. Biochem. 2013, 46:466-479.
35. Domanski D., Murphy L.C., Borchers C.H. Assay development for the determination of phosphorylation stoichiometry using multiple reaction monitoring methods with and without phosphatase treatment: application to breast cancer signaling pathways. Anal. Chem. 2010, 82:5610-5620.
36. Domanski D., Percy A.J., Yang J., Chambers A.G., Hill J.S., Cohen Freue G.V., Borchers C.H. MRM-based multiplexed quantitation of 67 putative cardiovascular disease biomarkers in human plasma. Proteomics 2012, 12:1222-1243.
37. Editor Nature Methods Method of the year 2012. Nat. Methods 2013, 10:1.
38. Elliott M., Smith D., Kuzyk M., Parker C.E., Borchers C.H. Recent Trends in quantitative proteomics. J.Mass Spectrom. 2009, 44:1637-1660.
39. Escher C., Reiter L., MacLean B., Ossola R., Herzog F., Chilton J., MacCoss M.J., Rinner O. Using iRT, a normalized retention time for more targeted measurement of peptides. Proteomics 2012, 12:1111-1121.
40. Evanko D. A different kind of method of the year for 2012. Nat. Methods Methagora 2012, http://blogs.nature.com/methagora/2012/12/a-different-kind-of-method-of-the-year-for-2012.html.
41. Farrah T., Deutsch E.W., Kreisberg R., Sun Z., Campbell D.S., Mendoza L., Kusebauch U., Brusniak M.Y., Hüttenhain R., Schiess R., Selevsek N., Aebersold R., Moritz R.L. PASSEL: the PeptideAtlas SRM experiment library. Proteomics 2012, 12:1170-1175.
42. Farrah T., Deutsch E.W., Omenn G.S., Campbell D.S., Sun Z., Bletz J.A., Mallick P., Katz J.E., Malmström J., Ossola R., Watts J.D., Lin B., Zhang H., Moritz R.L., Aebersold R. A high-confidence human plasma proteome reference set with estimated concentrations in PeptideAtlas. Mol. Cell Proteomics 2011, 10. M110.006353.
43. Fuzery A.K., Levin J., Chan M.M., Chan D.W. Translation of proteomic biomarkers into FDA approved cancer diagnostics: issues and challenges. Clin. Prot. 2013, 10:13. [Epub ahead of print].
44. Gallien S., Duriez E., Domon B. Selected reaction monitoring applied to proteomics. J.Mass Spectrom. 2011, 46:298-312.
45. Gelfand C.A., Omenn G.S. Preanalytical variables for plasma and serum proteome analyses. Sample Preparation in Biological Mass Spectrometry 2011, 269-290. Springer, Heidelberg, London, New York. A.R. Ivanov, A.V. Lazarev (Eds.).
46. Goo Y.A., Goodlett D.R. Advances in proteomic prostate cancer biomarker discovery. J.Proteomics 2010, 73:1839-1850.
47. Haab B.B., Paulovich A.G., Anderson N.L., Clark A.M., Downing G.J., Hermjakob H., Labaer J., Uhlen M. A reagent resource to identify proteins and peptides of interest for the cancer community: a workshop report. Mol. Cell Proteomics 2006, 5:1996-2007.
48. Hanash S.M., Baik C.S., Kallioniemi O. Emerging molecular biomarkers-blood-based strategies to detect and monitor cancer. Nat. Rev. Clin. Oncol. 2011, 8:142-150.
49. Hoofnagle A.N., Wener M.H. The fundamental flaws of immunoassays and potential solutions using tandem mass spectrometry. J.Immunol. Methods 2009, 347:3-11.
50. Hu S., Loo J.A., Wong D.T. Human body fluid proteome analysis. Proteomics 2006, 6:6326-6353.
51. Hulmes J.D., Bethea D., Ho K., Huang S.-P., Ricci D.L., Opiteck G.J., Hefta S.A. An investigation of plasma collection, stabilization, and storage procedures for proteomic analysis of clinical samples. Clin. Proteomics 2004, 1:17-31.
52. HUPO Human Standards Initiative 2010, HUPO. http://www.hupo.org/research/psi/.
53. Huttenhain R., Soste M., Selevsek N., Rost H., Sethi A., Carapito C., Farrah T., Deutsch E.W., Kusebauch U., Moritz R.L., Nimeus-Malmstrom E., Rinner O., Aebersold R. Reproducible quantification of cancer-associated proteins in body fluids using targeted proteomics. Sci. Translational Med. 2012, 4:142ra194.
54. Huttenhain R., Surinova S., Ossola R., Sun Z., Campbell D., Cerciello F., Schiess R., Bausch-Fluck D., Rosenberger G., Chen J., Rinner O., Kusebauch U., Hajduch M., Moritz R.L., Wollscheid B., Aebersold R. N-glycoprotein SRMAtlas: a resource of mass spectrometric assays for N-glycosites enabling consistent and multiplexed protein quantification for clinical applications. Mol. Cell. Prot. 2013, 12:1005-1016.
55. Ito Y., Nakachi K., Imai K., Hashimoto S., Watanabe Y., Inaba Y., Tamakoshi A., Yoshimura T. Stability of frozen serum levels of insulin-like growth factor-I, insulin-like growth factor-II, insulin-like growth factor binding protein-3, transforming growth factor beta, soluble Fas, and superoxide dismutase activity for the JACC study. J.Epidemiol. 2005, 15:S67-S73. JACC Study Group.
56. Jiang J., Parker C.E., Fuller J.R., Kawula T.H., Borchers C.H. An immunoaffinity tandem mass spectrometry (iMALDI) assay for detection of Francisella tularensis. Anal. Chim. Acta 2007, 605:70-79.
57. Jiang J., Parker C.E., Hoadley K.A., Perou C.M., Boysen G., Borchers C.H. Development of an immuno tandem mass spectrometry (iMALDI) assay for EGFR diagnosis. Proteomics Clin. Appl. 2007, 1:1651-1659.
58. Kalin M., Cima I., Schiess R., Fankhauser N., Powles T., Wild P., Templeton A., Cerny T., Aebersold R., Krek W., Gillessen S. Novel prognostic markers in the serum of patients with castration-resistant prostate cancer derived from quantitative analysis of the pten conditional knockout mouse proteome. Eur. Urol. 2011, 60:1235-1243.
59. Kim H., Kim K., Yu S.J., Jang E.S., Yu J., Cho G., Yoon J.H., Kim Y. Development of biomarkers for screening hepatocellular carcinoma using global data mining and multiple reaction monitoring. PLoS One. 2013, 8:e63468.
60. Krastins B., Prakash A., Sarracino D.A., Nedelkov D., Niederkofler E.E., Kiernan U.A., Nelson R., Vogelsang M.S., Vadali G., Garces A., Sutton J.N., Peterman S., Byram G., Darbouret B., Pérusse J.R., Seidah N.G., Coulombe B., Gobom J., Portelius E., Pannee J., Blennow K., Kulasingam V., Couchman L., Moniz C., Lopez M.F. Rapid development of sensitive, high-throughput, quantitative and highly selective mass spectrometric targeted immunoassays for clinically important proteins in human plasma and serum. Clin. Biochem. 2013, 46:399-410.
61. 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 13C-labeled peptide standards. Proteomics 2004, 4:1175-1186.
62. Kuzyk M.A., Parker C.E., Domanski D., Borchers C.H. Development of MRM-based assays for the absolute quantitation of plasma proteins. Methods Mol. Biol. 2013, 1023:53-82.
63. Kuzyk M.A., Smith D., Yang J., Cross T.J., Jackson A.M., Hardie D.B., Anderson N.L., Borchers C.H. Multiple reaction monitoring-based, multiplexed, absolute quantitation of 45 proteins in human plasma. Mol. Cell Proteomics 2009, 8:1860-1877.
64. Lee J.Y., Kim J.Y., Park G.W., Cheon M.H., Kwon K.H., Ahn Y.H., Moon M.H., Lee H.J., Paik Y.K., Yoo J.S. Targeted mass spectrometric approach for biomarker discovery and validation with nonglycosylated tryptic peptides from N-linked glycoproteins in human plasma. Mol. Cell. Prot. 2011, 10. M111.009290. [Epub 002011].
65. Liebler D.C., Zimmerman L.J. Targeted quantitation of proteins by mass spectrometry. Biochemistry 2013, 52:3797-3806.
66. Lin D., Alborn W.E., Slebos R.J., Liebler D.C. Comparison of protein immunoprecipitation-multiple reaction monitoring with ELISA for assay of biomarker candidates in plasma. J.Proteome Res. 2013, 12:5996-6003.
67. Lin L.L., Huang H.C., Juan H.F. Discovery of biomarkers for gastric cancer: a proteomics approach. J.Proteomics 2012, 75:3081-3097.
68. Lista S., Faltraco F., Hampel H. Biological and methodical challenges of blood-based proteomics in the field of neurological research. Prog. Neurobiol. 2013, 101-102:18-34.
69. Liu Y., Luo X., Hu H., Wang R., Sun Y., Zeng R., Chen H. Integrative proteomics and tissue microarray profiling indicate the association between overexpressed serum proteins and non-small cell lung cancer. PLoS One 2012, 7:e51748.
70. Lundblad R.L. Considerations for the Use of Blood Plasma and Serum for Proteomic Analysis 2005, http://archive.ispub.com/journal/the-internet-journal-of-genomics-and-proteomics/volume-1-number-2/considerations-for-the-use-of-blood-plasma-and-serum-for-proteomic-analysis.html.
71. Makawita S., Diamandis E.P. The bottleneck in the Cancer biomarker pipeline and protein quantification through mass spectrometry-based approaches: current strategies for candidate verification. Clin. Chem. 2010, 56:212-222.
72. Mannello F. Serum or plasma samples? the "Cinderella" role of blood collection procedures: preanalytical methodological issues influence the release and activity of circulating matrix metalloproteinases and their tissue inhibitors, hampering diagnostic trueness and leading to misinterpretation. Arterioscler. Thromb. Vasc. Biol. 2008, 28:611-614.
73. Manrow R., Chasan R. Fact Sheet - Cancer 2013, http://report.nih.gov/nihfactsheets/viewfactsheet.aspx?csid=75.
74. Meng Z., Veenstra T.D. Targeted mass spectrometry approaches for protein biomarker verification. J.Proteomics 2011, 74:2650-2659.
75. Mohammed Y., Domanski D., Jackson A.M., Smith D.S., Deelder A.M., Palmblad M., Borchers C.H. PeptidePicker: a scientific workflow with web interface for selecting appropriate peptides for targeted proteomics experiments. J.Proteomics 2014, (submitted for publication).
76. Nicol G.R., Han M., Kim J., Birse C.E., Brand E., Nguyen A., Mesri M., FitzHugh W., Kaminker P., Moore P.A., Ruben S.M., He T. Use of an immunoaffinity-mass spectrometry-based approach for the quantification of protein biomarkers from serum samples of lung Cancer patients. Mol. Cell Proteomics 2008, 7:1974-1982.
77. Ohlund L.B., Hardie D.B., Elliott M.H., Smith D.S., Reid J.D., Cohen-Freue G.V., Bergman A.P., Sasaki M., Robertson L., Balshaw R.F., Ng R.T., Mui A., McManus B.M., Keown P.A., McMaster W.R., Parker C.E., Borchers C.H. Standard operating procedures and protocols for the preparation and analysis of plasma samples using the iTRAQ methodology. Sample Preparation in Biological Mass Spectrometry 2011, 575-624. Springer, New York. A. Ivanov, A. Lazarev (Eds.).
78. Omenn G.S. Advancement of biomarker discovery and validation through the HUPO plasma proteome project. Dis. Markers 2004, 20:131-134.
79. Omenn G.S. The Human Proteome Organization Plasma Proteome Project pilot phase: reference specimens, technology platform comparisons, and standardized data submissions and analyses. Proteomics 2004, 4:1235-1240.
80. Omenn G.S. The HUPO human plasma proteome project. Proteomics Clin. Appl. 2007, 1:769-779.
81. Omenn G.S., States D.J., Adamski M., Blackwell T.W., Menon R., Hermjakob H., Apweiler R., Haab B.B., Simpson R.J., Eddes J.S., Kapp E.A., Moritz R.L., Chan D.W., Rai A.J., Admon A., Aebersold R., Eng J., Hancock W.S., Hefta S.A., Meyer H., Paik Y.-K., Yoo J.-S., Ping P., Pounds J., Adkins J., Qian X., Wang R., Wasinger V., Wu C.Y., Zhao X., Zeng R., Archakov A., Tsugita A., Beer I., Pandey A., Pisano M., Andrews P., Tammen H., Speicher D.W., Hanash S.M. Overview of the HUPO Plasma Proteome Project: results from the pilot phase with 35 collaborating laboratories and multiple analytical groups, generating a core dataset of 3020 proteins and a publicly-available database. Proteomics 2005, 5:3226-3245.
82. Ong S., Mann M. Mass Spectrometry-based proteomics turns quantitative. Nat. Chem. Biol. 2005, 1:252-262.
83. Ostroff R., Foreman T., Keeney T.R., Stratford S., Walker J.J., Zichi D. The stability of the circulating human proteome to variations in sample collection and handling procedures measured with an aptamer-based proteomics array. J.Proteomics 2010, 73:649-666.
84. Pan S., Chen R., Brand R.E., Hawley S., Tamura Y., Gafken P.R., Milless B.P., Goodlett D.R., Rush J., Brentnall T.A. Multiplex targeted proteomic assay for biomarker detection in plasma: a pancreatic cancer biomarker case study. J.Proteome Res. 2012, 11:1937-1948.
85. Parker C.E., Pearson T.W., Anderson N.L., Borchers C.H. Mass-spectrometry-based clinical proteomics - a review and prospective. Analyst 2010, 135:1830-1838.
86. The PeptideAtLas SRM Experiment Library (PASSEL) 2012, PASSEL. http://www.peptideatlas.org/passel/.
87. Patel B.B., Barrero C.A., Braverman A., Kim P.D., Jones K.A., Chen D.E., Bowler R.P., Merali S., Kelsen S.G., Yeung A.T. Assessment of two immunodepletion methods: off-target effects and variations in immunodepletion efficiency may confound plasma proteomics. J.Proteome Res. 2012, 11:5947-5958.
88. Paulovich A.G., Billheimer D.D., Ham A.-J.L., Vega-Montoto L., Rudnick P.A., Tabb D.L., Wang P., Blackman R.K., Bunk D.M., Cardasis H.L., Clauser K.R., Kinsinger C.R., Schilling B., Tegeler T.J., Variyath A.M., Wang M., Whiteaker J.R., Zimmerman L.J., Carr S.A., Fisher S.J., Gibson B.W., Mesri M., Neubert T.A., Regnier F.E., Rodriguez H., Spiegelman C., Stein S.E., Tempst P., Liebler D.C. A CPTAC inter-laboratory study characterizing a yeast performance standard for benchmarking LC-MS platform performance. Mol. Cell Proteomics 2010, 9:242-254. NCI Clinical Proteomic Technology Assessment for Cancer (CPTAC) Network.
89. Paulovich A.G., Whiteaker J.R., Hoofnagle A.N., Wang P. The interface between biomarker discovery and clinical validation: the tar pit of the protein biomarker pipeline. Proteomics Clin. Appl. 2008, 2:1386-1402.
90. PepFly PepFly - Peptide Flyability Prediction 2013, http://www.mybiosoftware.com/protein-sequence-analysis/11826.
91. PeptideAtlas, 2010. http://www.peptideatlas.org.
92. Percy A.J., Chambers A.G., Parker C.E., Borchers C.H. Absolute quantitation of proteins in human blood by multiplexed multiple reaction monitoring mass spectrometry. Methods Mol. Biol. 2013, 1000.
93. 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.
94. Percy A.J., Chambers A.G., Yang J., Borchers C.H. Multiplexed MRM-based quantitation of candidate Cancer biomarker proteins in undepleted and non-enriched human plasma. Proteomics 2013, 13:2202-2215.
95. Percy A.J., Chambers A.G., Yang J., Domanski D., Borchers C.H. Comparison of standard- and nano-flow liquid chromatography platforms for MRM-based quantitation of putative plasma biomarker proteins. Anal. Bioanal. Chem. 2012, 404:1089-1101.
96. Percy A.J., Chambers A.G., Yang J., Hardie D., Borchers C.H. Advances in multiplexed MRM-based protein biomarker quantitation toward clinical utility. Biochim. Biophys. Acta 2013, 13:239-242. pii: S1570-9639.
97. Percy A.J., Chambers A.G., Yang J., Jackson A.M., Domanski D., Burkhart J., Sickmann A., Borchers C.H. Method and platform standardization in MRM-based quantitative plasma proteomics. J.Proteomics 2013, 95:66-76.
98. Percy A.J., Parker C.E., Borchers C.H. Pre-analytical and analytical variability in absolute quantitative MRM-based plasma proteomic studies. Bioanalysis 2013, 5:2837-2856.
99. Picotti P., Aebersold R. Selected reaction monitoring-based proteomics: workflows, potential, pitfalls and future directions. Nat. Methods 2012, 9:555-566.
100. Picotti P., Rinner O., Stallmach R., Dautel F., Farrah T., Domon B., Wenschuh H., Aebersold R. High-throughput generation of selected reaction-monitoring assays for proteins and proteomes. Nat. Meth. 2010, 7:43-46.
101. Polanski M., Anderson N.L. A list of candidate Cancer biomarkers for targeted proteomics. Biomarker Insights 2007, 2:1-48.
102. Rai A.J., Gelfand C.A., Haywood B.C., Warunek D.J., Yi J., Schuchard M.D., Mehigh R.J., Cockrill S.L., Scott G.B.I., Tammen H., Schulz-Knappe P., Speicher D.W., Vitzthum F., Haab B.B., Siest G., Chan D.W. HUPO Plasma Proteome Project specimen collection and handling: towards the standardization of parameters for plasma proteome samples. Proteomics 2005, 5:3262-3277.
103. 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.
104. Randall S.A., McKay M.J., Pascovici D., Mahon K., Horvath L., Clarke S.J., Molloy M.P. Remarkable temporal stability of high-abundance human plasma proteins assessed by targeted mass spectrometry. Proteomics Clin. Appl. 2012, 6:626-634.
105. Razavi M., Pope M., Soste M.V., Eyford B.A., Jackson A.M., Anderson N.L., Pearson T.W. MALDI immunoscreening (MiSCREEN): a method for selection of anti-peptide monoclonal antibodies for use in immunoproteomics. J.Immunol. Methods 2011, 364:50-64.
106. Remily-Wood E.R., Liu R.Z., Xiang Y., Chen Y., Thomas C.E., Rajyaguru N., Kaufman L.M., Ochoa J.E., Hazlehurst L., Pinilla-Ibarz J., Lancet J., Zhang G., Haura E., Shibata D., Yeatman T., Smalley K.S.M., Dalton W.S., Huang E., Scott E., Bloom G.C., Eschrich S.A., Koomen J.M. A database of reaction monitoring mass spectrometry assays for elucidating therapeutic response in cancer. Proteomics Clin. Appl. 2011, 5:383-396.
107. Rifai N., Gillette M.A., Carr S.A. Protein biomarker discovery and validation: the long and uncertain path to clinical utility. Nat. Biotechnol. 2006, 24:971-983.
108. Rodriguez H., Rivers R., Kinsinger C., Mesri M., Hiltke T., Rahbar A., Boja E. Reconstructing the pipeline by introducing multiplexed multiple reaction monitoring mass spectrometry for cancer biomarker verification: an NCI-CPTC initiative perspective. Proteomics Clin. Appl. 2010, 4:904-914.
109. Rodriguez H., Težak Z., Mesri M., Carr S.A., Liebler D.C., Fisher S.J., Tempst P., Hiltke T., Kessler L.G., Kinsinger C.R., Philip R., Ransohoff D.F., Skates S.J., Regnier F.E., Anderson N.L. Analytical validation of protein-based multiplex assays: a workshop report by the NCI-FDA Interagency Oncology Task Force on molecular diagnostics. Clin. Chem. 2010, 56:237-243. Mansfield on behalf of the Workshop Participants, E.
110. Ross P.L., Huang Y.N., Marchese J.N., Williamson B., Parker K., Hattan S., Khainovski N., Pillai S., Dey S., Daniels S., Purkayastha S., Juhasz P., Martin S., Bartlet-Jones M., He F., Jacobson A., Pappin D.J. Multiplexed protein quantitation in Saccharomyces cerevisiae using amine-reactive isobaric tagging reagents. Mol. Cell Proteomics 2004, 3:1154-1169.
111. Rudnick P.A., Clauser K.R., Kilpatrick L.E., Tchekhovskoi D.V., Neta P., Blonder N., Billheimer D.D., Blackman R.K., Bunk D.M., Cardasis H.L., Ham A.-J.L., Jaffe J.D., Kinsinger C.R., Mesri M., Neubert T.A., Schilling B., Tabb D.L., Tegeler T.J., Vega-Montoto L., Variyath A.M., Wang M., Wang P., Whiteaker J.R., Zimmerman L.J., Carr S.A., Fisher S.J., Gibson B.W., Paulovich A.G., Regnier F.E., Rodriguez H., Spiegelman C., Tempst P., Liebler D.C., Stein S.E. Performance Metrics for evaluating liquid chromatography-tandem mass spectrometry systems in shotgun proteomics. Mol. Cell Proteomics 2010, 9:225-241.
112. Sanders W.S., Bridges S.M., McCarthy F.M., Nanduri B., Burgess S.C. Prediction of peptides observable by mass spectrometry applied at the experimental set level. BMC Bioinformatics 2007, 1:S23.
113. Schulze W.X., Usadel B. Quantitation in mass-spectrometry-based proteomics. Annu. Rev. Plant Biol. 2010, 61:491-516.
114. Shah B., Borchers C.H. iMALDI: a Targeted Proteomics Approach to the Differentiation of EGFR and its Isoforms, Presented at the 57th ASMS Conference on Mass Spectrometry and Allied Topics 2009, Philadelphia, PA, May 31-June 4.
115. Sherman J., McKay M.J., Ashman K., Molloy M.P. How specific is my SRM?: the issue of precursor and product ion redundancy. Proteomics 2009, 9:1120-1123.
116. Sherry S.T., Ward M., Sirotkin K. dbSNP-database for single nucleotide polymorphisms and other classes of minor genetic variation. Genome Res. 1999, 9:677-679.
117. Siegel R., Naishadham D., Jemal A. Cancer statistics, 2013. CA: A Cancer J. Clinicians 2013, 63:11-30.
118. Skyline_SRM/MRM_Builder Skyline Targeted Proteomics Environment 2011, update v0.7. http://brendanx-uw1.gs.washington.edu/labkey/wiki/home/software/Skyline/page.view?name=default.
119. Sung H.J., Jeon S.A., Ahn J.M., Seul K.J., Kim J.Y., Lee J.Y., Yoo J.S., Lee S.Y., Kim H., Cho J.Y. Large-scale isotype-specific quantification of Serum amyloid A 1/2 by multiple reaction monitoring in crude sera. J.Proteomics 2012, 75:2170-2180.
120. Surinova S., Schiess R., Hüttenhain R., Cerciello F., Wollscheid B., Aebersold R. On the development of plasma protein biomarkers. J.Proteome Res. 2011, 10:5-16.
121. Tan H.T., Lee Y.H., Chung M.C. Cancer proteomics. Mass Spectrom. Rev. 2012, 31:583-605.
122. Tang H.Y., Beer L.A., Tanyi J.L., Zhang R., Liu Q., Speicher D.W. Protein isoform-specific validation defines multiple chloride intracellular channel and tropomyosin isoforms as serological biomarkers of ovarian cancer. J.Proteomics 2013, 89c:165-178.
123. Tanner G.J., Colgrave M.L., Blundell M.J., Goswami H.P., Howitt C.A. Measuring hordein (gluten) in beer-a comparison of ELISA and mass spectrometry. PLoS One 2013, 8:e56452.
124. Thadikkaran L., Siegenthaler M.A., Crettaz D., Queloz P.A., Schneider P., Tissot J.D. Recent advances in blood-related proteomics. Proteomics 2005, 5:3019-3034.
125. The Global Proteome Machine Organization The Global Proteome Machine 2004-2011, http://www.thegpm.org/.
126. Thermo_TMT Tandem Mass Tag (TMT) 2008, http://www.piercenet.com/products/browse.cfm?fldID=C5A5F2FF-5056-8A76-4E4C-971BF496D176.
127. Toyama A., Nakagawa H., Matsuda K., Ishikawa N., Kohno N., Daigo Y., Sato T.A., Nakamura Y., Ueda K. Deglycosylation and label-free quantitative LC-MALDI MS applied to efficient serum biomarker discovery of lung cancer. Proteome Science 2011, 9:18.
128. Tu C., Rudnick P.A., Martinez M.Y., Cheek K.L., Stein S.E., Slebos R.J.C., Liebler D.C. Depletion of abundant plasma proteins and limitations of PlasmaProteomics. J.Proteome Res. 2010, 9:4982-4991.
129. Tuck M.K., Chan D.W., Chia D., Godwin A.K., Grizzle W.E., Krueger K.E., Rom W., Sanda M., Sorbara L., Stass S., Wang W., Brenner D.E. Standard operating procedures for serum and plasma collection: early detection research network consensus statement standard operating procedure integration working group. J.Proteome Res. 2009, 8:113-117.
130. UniProt Consortium The Universal protein resource (UniProt) 2009. Nucleic Acids Res. 2009, 37:D169-D174.
131. Vegvari A., Sjodin K., Rezeli M., Malm J., Lilja H., Laurell T., Marko-Varga G. Identification of a novel proteoform of prostate specific antigen (SNP-L132I) in clinical samples by multiple reaction monitoring. Mol. Cell Proteomics 2013, 12:2761-2773.
132. Wang P., Whiteaker J.R., Paulovich A.G. The evolving role of mass spectrometry in cancer biomarker discovery. Cancer Biol. Ther. 2009, 8:1083-1094.
133. Wehr A.Y., Hwang W.T., Blair I.A., Yu K.H. Relative quantification of serum proteins from pancreatic ductal adenocarcinoma patients by stable isotope dilution liquid chromatography-mass spectrometry. J. Proteome Res. 2012, 11:1749-1758.
134. Whiteaker J.R., Lin C., Kennedy J., Hou L., Trute M., Sokal I., Yan P., Schoenherr R.M., Zhao L., Voytovich U.J., Kelly-Spratt K.S., Krasnoselsky A., Gafken P.R., Hogan J.M., Jones L.A., Wang P., Amon L., Chodosh L.A., Nelson P.S., McIntosh M.W., Kemp C.J., Paulovich A.G. A targeted proteomics-based pipeline for verification of biomarkers in plasma. Nat. Biotechnol. 2011, 29:625-634.
135. Whiteaker J.R., Zhang H., Zhao L., Wang P., Kelly-Spratt K.S., Ivey R.G., Piening B.D., Feng L.-C., Kasarda E., Gurley K.E., Eng J.K., Chodosh L.A., Kemp C.J., McIntosh M.W., Paulovich A.G. Integrated pipeline for mass spectrometry-based discovery and confirmation of biomarkers demonstrated in a mouse model of breast Cancer. J.Proteome Res. 2007, 6:3962-3975.
136. Yang X., Lazar I.M. MRM screening/biomarker discovery with linear ion trap MS: a library of human cancer-specific peptides. BMC Cancer 2009, 96.
137. Yi J., Craft D., Gelfand C.A. Minimizing preanalytical variation of plasma samples by proper blood collection and handling. Methods Mol. Biol. 2011, 728:137-149.
138. Yocum A.K., Gratsch T.E., Leff N., Strahler J.R., Hunter C.L., Walker A.K., Michailidis G., Omenn G.S., O'Shea K.S., Andrews P.C. Coupled global and targeted proteomics of human embryonic stem cells during induced differentiation. Mol. Cell Proteomics 2008, 7:750-767.
139. Yoneyama T., Ohtsuki S., Ono M., Ohmine K., Uchida Y., Yamada T., Tachikawa M., Terasaki T. Quantitative targeted absolute proteomics-based large-scale quantification of proline-hydroxylated alpha-fibrinogen in plasma for pancreatic cancer diagnosis. J.Proteome Res. 2013, 12:753-762.
140. Zhao X., Qureshi F., Eastman P.S., Manning W.C., Alexander C., Robinson W.H., Hesterberg L.K. Pre-analytical effects of blood sampling and handling in quantitative immunoassays for rheumatoid arthritis. J.Immunol. Methods 2012, 378:72-80.
141. Zhao Y., Jia W., Sun W., Jin W., Guo L., Wei J., Ying W., Zhang Y., Xie Y., Jiang Y., He F., Qian X. Combination of improved (18)O incorporation and multiple reaction monitoring: a universal strategy for absolute quantitative verification of serum candidate biomarkers of liver cancer. J.Proteome Res. 2010, 9:3319-3327.
142. Zimmerman L.J., Li M., Yarbrough W.G., Slebos R.J., Liebler D.C. Global stability of plasma proteomes for mass spectrometry-based analyses. Mol. Cell Proteomics 2012, 11. M111.014340.