Biomarker discovery and validation: The tide is turning

Expert Review of Proteomics

Volumn 10, Issue 6, 2013, Pages 505-507

  Nice, Edouard ^a  

^a MONASH UNIVERSITY   (Australia)

Author keywords

Advances in mass spectrometry; Biomarker discovery and validation; Colorectal cancer; Proteomics; Systems biology

Indexed keywords

BIOLOGICAL MARKER; GLYCOPROTEIN; MEMBRANE PROTEIN; MONOCLONAL ANTIBODY; PEPTIDE; PHOSPHOPEPTIDE; PROTEIN; PROTEOME; TRANSCRIPTOME;

ANALYTIC METHOD; ANTIBODY AFFINITY; BIOINFORMATICS; CANCER MORTALITY; CARCINOGENESIS; COLLISIONALLY ACTIVATED DISSOCIATION; COLONOSCOPY; COLORECTAL CANCER; DRUG INDUSTRY; ENZYME LINKED IMMUNOSORBENT ASSAY; FALSE POSITIVE RESULT; FORENSIC SCIENCE; GENOMICS; HIGH PERFORMANCE LIQUID CHROMATOGRAPHY; HUMAN; ION CYCLOTRON RESONANCE MASS SPECTROMETRY; LABORATORY AUTOMATION; LUNG CARCINOMA; MASS SPECTROMETRY; NATIONAL HEALTH ORGANIZATION; OCCULT BLOOD; OCCULT BLOOD TEST; PROTEIN GLYCOSYLATION; PROTEIN PROCESSING; PROTEOMICS; REVIEW; SCREENING TEST; SENSITIVITY AND SPECIFICITY; TOXICOLOGY; VALIDATION STUDY;

COLORECTAL NEOPLASMS; HUMANS; PROTEOMICS; TUMOR MARKERS, BIOLOGICAL; VALIDATION STUDIES AS TOPIC;

EID: 84887933059     PISSN: 14789450     EISSN: 17448387     Source Type: Journal    
DOI: 10.1586/14789450.2013.858023     Document Type: Review

References (20)

1. McDermott JE, Wang J, Mitchell H et al. Challenges in biomarker discovery: combining expert insights with statistical analysis of complex omics data. Expert Opin. Med. Diagn. 7(1), 37-51 (2013)
2. Etzioni R, Urban N, Ramsey S et al. The case for early detection. Nat. Rev. Cancer 3(4), 243-252 (2003)
3. Wagner PD, Srivastava S. New paradigms in translational science research in cancer biomarkers. Transl. Res. 159(4), 343-353 (2012)
4. Legrain P, Aebersold R, Archakov A et al. The human proteome project: current state and future direction. Mol. Cell. Proteomics 10(7), M111.009993 (2011)
5. Anderson L, Hunter CL. Quantitative mass spectrometric multiple reaction monitoring assays for major plasma proteins. Mol. Cell. Proteomics 5(4), 573-588 (2006)
6. Ang CS, Rothacker J, Patsiouras H, Gibbs P, Burgess AW, Nice EC. Use of multiple reaction monitoring for multiplex analysis of colorectal cancer-associated proteins in human feces. Electrophoresis 32(15), 1926-1938 (2011)
7. Gillet LC, Navarro P, Tate S et al. Targeted data extraction of the MS/MS spectra generated by data-independent acquisition: a new concept for consistent and accurate proteome analysis. Mol. Cell. Proteomics 11(6), O111.016717 (2012)
8. 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. 3(2), 235-244 (2004)
9. Schoenherr RM, Zhao L, Whiteaker JR et al. Automated screening of monoclonal antibodies for SISCAPA assays using a magnetic bead processor and liquid chromatography-selected reaction monitoring-mass spectrometry. J. Immunol. Methods 353(1-2), 49-61 (2010)
10. Whiteaker JR, Zhao L, Anderson L, Paulovich AG. An automated and multiplexed method for high throughput peptide immunoaffinity enrichment and multiple reaction monitoring mass spectrometry-based quantification of protein biomarkers. Mol. Cell. Proteomics 9(1), 184-196 (2010)
11. Di Palma S, Zoumaro-Djayoon A, Peng M et al. Finding the same needles in the haystack? A comparison of phosphotyrosine peptides enriched by immuno-affinity precipitation and metal-based affinity chromatography. J. Proteomics 91C, 331-337 (2013)
12. Zeng Z, Hincapie M, Pitteri SJ et al. A proteomics platform combining depletion, multi-lectin affinity chromatography (MLAC), and isoelectric focusing to study the breast cancer proteome. Anal. Chem. 83(12), 4845-4854 (2011)
13. Kuzmanov U, Kosanam H, Diamandis EP. The sweet and sour of serological glycoprotein tumor biomarker quantification. BMC Med. 11, 31 (2013)
14. Catherman AD, Durbin KR, Ahlf DR et al. Large-scale top down proteomics of the human proteome: membrane proteins, mitochondria, and senescence. Mol. Cell. Proteomics doi:10.1074/mcp.M113.030114 (2013) (Epub ahead of print)
15. Harris TJ, McCormick F. The molecular pathology of cancer. Nat. Rev. Clin. Oncol. 7(5), 251-265 (2010)
16. Paik YK, Hancock WS. Uniting ENCODE with genome-wide proteomics. Nat. Biotechnol. 30(11), 1065-1067 (2012)
17. ENCODE Project Consortium. An integrated encyclopedia of DNA elements in the human genome. Nature 489(7414), 57-74 (2012)
18. Uhlen M, Oksvold P, Fagerberg L et al. Towards a knowledge-based human protein atlas. Nat. Biotechnol. 28(12), 1248-1250 (2010)
19. Hood LE, Omenn GS, Moritz RL et al. New and improved proteomics technologies for understanding complex biological systems: addressing a grand challenge in the life sciences. Proteomics 12(18), 2773-2783 (2012)
20. Poste G. Biospecimens, biomarkers, and burgeoning data: the imperative for more rigorous research standards. Trends Mol. Med. 18(12), 717-722 (2012).