Cancer biomarker discovery via low molecular weight serum profiling - Are we following circular paths?

Clinical Chemistry

Volumn 56, Issue 2, 2010, Pages 244-247

  Davis, Michael T ^a   Auger, Paul L ^a   Patterson, Scott D ^a  

^a AMGEN INC   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

SERUM AMYLOID A; TUMOR MARKER;

BREAST CANCER; HUMAN; LIQUID CHROMATOGRAPHY; MATRIX ASSISTED LASER DESORPTION IONIZATION TIME OF FLIGHT MASS SPECTROMETRY; MOLECULAR WEIGHT; NOTE; PROTEIN ANALYSIS; PROTEIN EXPRESSION; TANDEM MASS SPECTROMETRY;

HUMANS; MOLECULAR WEIGHT; NEOPLASMS; SPECTROMETRY, MASS, MATRIX-ASSISTED LASER DESORPTION-IONIZATION; TUMOR MARKERS, BIOLOGICAL;

EID: 75749149788     PISSN: 00099147     EISSN: 15308561     Source Type: Journal    
DOI: 10.1373/clinchem.2009.127951     Document Type: Note

References (24)

1. Aebersold R. A stress test for mass spectrometry-based proteomics. Nat Methods 2009;6:411-2.
2. Davis MT, Auger P, Spahr C, Patterson SD. Cancer biomarker discovery via low molecular weight serum proteome profiling - Where is the tumor? Proteomics Clin Appl 2007;1:1545-58.
3. Anderson NL. Clinical proteomics heads into real world. Improved instrumentation and unbiased samples renew promise of biomarker pipeline. Genet Eng BiotechnolNews2009;29(5). http://www.genengnews. com/articles/chitem.aspx? aid=2822&chid=4 (Accessed June 2009).
4. Petricoin EF, Ardekani AM, Hitt BA, Levine PJ, Fusaro VA, Steinberg SM, et al. Use of proteomic patterns in serum to identify ovarian cancer. Lancet 2002;359:572-7.
5. Baggerly KA, Morris JS, Coombes KR. Reproducibility of SELDI-TOF protein patterns in serum: comparing datasets from different experiments. Bioinformatics 2004;20:777-85.
6. Koomen JM, Li D, Xia LC, Coombes KR, Abbruzzese J, Kobayashi R. Direct tandem mass spectrometry reveals limitations in protein profiling Proteome Res 2005;4:972-81.
7. Villanueva J, Nazarian A, Lawlor K, Yi SS, Robbins RJ, Tempst P. A sequence-specific exopeptidase activity test (SSEAT) for "functional" biomarker discovery. Mol Cell Proteomics 2008;7:509-18.
8. Hortin GL. The MALDI-TOF mass spectrometric view of the plasma proteome and peptidome. Clin Chem 2006;52:1223-37.
9. Bakun M, Karczmarski J, Poznanski J, Rubel T, Rozga M, Malinowska A, et al. An integrated LC-ESI-MS platform for quantitation of serum peptide ladders. Application for colon carcinoma study. Proteomics Clin Appl 2009;3:932-46.
10. Hortin GL, Sviridov D, Anderson NL. High-abundance polypeptides of the human plasma proteome compromising the top 4 logs of polypeptide abundance. Clin Chem 2008;54: 1608-16.
11. Han KQ, Huang G, Gao CF, Wang XL, Ma B, Sun LQ, Wei ZJ. Identification of lung cancer patients by serum protein profiling using surface-enhanced laser desorption/ionization time-offlight mass spectrometry. Am J Clin Oncol 2008; 31:133-9.
12. Shi L, Zhang J, Wu P, Feng K, Li J, Xie Z, et al. Discovery and identification of potential biomarkers of pediatric acute lymphoblastic leukemia. Proteome Sci 2009;7:7.
13. Fiedler GM, Leichtle AB, Kase J, Baumann S, Ceglarek U, Felix K, et al. Serum peptidome profiling revealed platelet factor 4 as a potential discriminating peptide associated with pancreatic cancer. Clin Cancer Res 2009;15:3812-9.
14. Villanueva J, Philip J, Entenberg D, Chaparro CA, Tanwar MK, Holland EC, Tempst P. Serum peptide profiling by magnetic particle-assisted, automated sample processing and MALDI-TOF mass spectrometry. Anal Chem 2004;76:1560-70.
15. Callesen AK, Vach W, Jorgenson PE, Cold S, Mogensen O, Kruse TA, et al. Reproducibility of mass spectrometry based protein profiles for diagnosis of breast cancer across clinical studies: a systematic review. J Proteome Res 2008;7:1395-402.
16. Freed GL, Cazares LH, Fichlander CE, Fuller TW, Sawyer CA, Stack BC Jr, et al. Differential capture of serum proteins for expression profiling and biomarker discovery in pre- and posttreatment head and neck cancer samples. Laryngoscope 2008;118:61-8.
17. Swiss Institute of Bioinformatics. ExPASy Proteomics Server. TagIdent tool. http://www.expasy. ch/tools/tagident.html (Accessed June 2009).
18. Yildiz PB, Shyr Y, Rahman JS, Wardwell NR, Zimmerman LJ, Shakhtour B, et al. Diagnostic accuracy of MALDI mass spectrometric analysis of unfractionated serum in lung cancer. J Thorac Oncol 2007;2:893-901.
19. Salmon S, Chen H, Chen S, Herbst R, Tsao A, Tran H, et al. Classification by mass spectrometry can accurately and reliably predict outcome in patients with non-small cell lung cancer treated with erlotinib-containing regimen. J Thorac Oncol 2009;4:689-96.
20. Malle E, Sodin-Semrl S, Kovacevic A. Serum amyloid A: an acute-phase protein involved in tumour pathogenesis. Cell Mol Life Sci 2009; 66:9-26.
21. US Food and Drug Administration. FDA news release. http://www.fda.gov/ NewsEvents/Newsroom/PressAnnouncements/ucm182057.htm (Accessed September 2009).
22. McLerran D, Grizzle WE, Feng Z, Bigbee WL, Banez LL, Cazares LH, et al. SELDI-TOF MS whole serum proteomic profiling with IMAC surface does not reliably detect prostate cancer. Clin Chem 2008;54:53-60.
23. West-Norager M, Bro R, Marini F, Hogdall EV, Hogdall CK, Nedergaard L, Heegaard NHH. Feasibility of serodiagnosis of ovarian cancer by mass spectrometry. Anal Chem 2009;8:1907-13.
24. Belluco C, Petricoin EF, Mammano E, Facchiano F, Ross-Rucker S, Nitti D, et al. Serum proteomic analysis identifies a highly sensitive and specific discriminatory pattern in stage 1 breast cancer. Ann Surg Oncol 2007;14:2470-6. experiments for plasma biomarker discovery. J