Mass spectrometry-based clinical proteomics profiling: current status and future directions

References

• Pusch W, Flocco M, Leung SM, Thiele H, Kostrzewa M. Mass spectrometry-based clinical proteomics. Pharmacogenomics4(4), 463–476 (2003).
   PubMed Web of Science ®Google Scholar
• Diamandis E. Serum proteomic profiling by matrix-assisted laser desorption-ionization time-of-flight mass spectrometry for cancer diagnosis: next steps. Cancer Res.66(11), 5540–5541 (2006).
   PubMed Web of Science ®Google Scholar
• Cazares L, Diaz J, Drake R, Semmes O. MALDI/SELDI protein profiling of serum for the identification of cancer biomarkers. In: Clinical Proteomics: Methods in Molecular Biology. Antonia V (Ed.). Springer, UK, 125–140 (2008).
   Google Scholar
• Qian WJ, Jacobs JM, Liu T, Camp DG, Smith RD. Advances and challenges in liquid chromatography-mass spectrometry-based proteomics profiling for clinical applications. Mol. Cell. Proteomics5(10), 1727–1744 (2006).
   PubMed Web of Science ®Google Scholar
• Weissinger E, Wittke S, Kaiser T et al. Proteomic patterns established with capillary electrophoresis and mass spectrometry for diagnostic purposes. Kidney Int.65(6), 2426–2434 (2004).
   PubMed Web of Science ®Google Scholar
• Decramer S, Gonzalez de Peredo A, Breuil B et al. Urine in clinical proteomics. Mol. Cell. Proteomics7(10), 1850–1862 (2008).
   PubMed Web of Science ®Google Scholar
• Callesen AK, Vach W, Jorgensen PE et al. Reproducibility of mass spectrometry based protein profiles for diagnosis of breast cancer across clinical studies: a systematic review. J. Proteome Res.7(4), 1395–1402 (2008).
   PubMed Web of Science ®Google Scholar
• Findeisen P, Neumaier M. Mass spectrometry based proteomics profiling as diagnostic tool in oncology: current status and future perspective. Clin. Chem. Lab. Med.47(6), 666–684 (2009).
   PubMed Web of Science ®Google Scholar
• Findeisen P, Sismanidis D, Riedl M, Costina V, Neumaier M. Preanalytical impact of sample handling on proteome profiling experiments with matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. Clin. Chem.51(12), 2409–2411 (2005).
   PubMed Web of Science ®Google Scholar
• McLerran D, Grizzle WE, Feng Z et al. Analytical validation of serum proteomic profiling for diagnosis of prostate cancer: sources of sample bias. Clin. Chem.54(1), 44–52 (2008).
   PubMed Web of Science ®Google Scholar
• McLerran D, Grizzle WE, Feng Z et al. SELDI-TOF MS whole serum proteomic profiling with imac surface does not reliably detect prostate cancer. Clin. Chem.54(1), 53–60 (2008).
   PubMed Web of Science ®Google Scholar
• Liebler DC. Summary of United States Human Proteome Organisation (HUPO) symposium entitled ‘Standardized clinical proteomics platforms’. Mol. Cell. Proteomics8(5), 1165–1166 (2009).
   PubMedGoogle Scholar
• Koomen J, Shih L, Coombes K et al. Plasma protein profiling for diagnosis of pancreatic cancer reveals the presence of host response proteins. Clin. Cancer Res.11(3), 1110–1118 (2005).
   PubMed Web of Science ®Google Scholar
• Mischak H, Apweiler R, Banks R et al. Clinical proteomics: a need to define the field and to begin to set adequate standards. Proteomics Clin. Appl.1(2), 148–156 (2007).
   PubMed Web of Science ®Google Scholar
• Slany A, Haudek VJ, Gundacker NC et al. Introducing a new parameter for quality control of proteome profiles: consideration of commonly expressed proteins. Electrophoresis30(8), 1306–1328 (2009).
   PubMedGoogle Scholar
• Taylor C, Paton N, Lilley K et al. The minimum information about a proteomics experiment (MIAPE). Nat. Biotechnol.25(8), 887–893 (2007).
   PubMed Web of Science ®Google Scholar
• Hanash S. It takes a village to develop biomarkers. J. Proteome Res.6(9), 3362 (2007).
   PubMed Web of Science ®Google Scholar
• Hoffman S, Won AJ, Echan L, Speicher D. Higher dimensional (Hi-D) separation strategies dramatically improve the potential for cancer biomarker detection in serum and plasma. J. Chromatogr. B849(1–2), 43–52 (2007).
   PubMed Web of Science ®Google Scholar
• Schiess R, Wollscheid B, Aebersold R. Targeted proteomic strategy for clinical biomarker discovery. Mol. Oncol.3(1), 33–44 (2009).
   PubMed Web of Science ®Google Scholar
• Lopez M, Mikulskis A, Kuzdzal S et al. A novel, high-throughput workflow for discovery and identification of serum carrier protein-bound peptide biomarker candidates in ovarian cancer samples. Clin. Chem.53(6), 1067–1074 (2007).
   PubMed Web of Science ®Google Scholar
• Sparbier K, Wenzel T, Dihazi H et al. Immuno-MALDI-TOF MS: new perspectives for clinical applications of mass spectrometry. Proteomics9(6), 1442–1450 (2009).
   PubMed Web of Science ®Google Scholar
• Boschetti E, Righetti PG. The art of observing rare protein species in proteomes with peptide ligand libraries. Proteomics9(6), 1492–1510 (2009).
   PubMed Web of Science ®Google Scholar
• Cornett D, Reyzer M, Chaurand P, Caprioli R. MALDI imaging mass spectrometry: molecular snapshots of biochemical systems. Nat. Methods4(10), 828–833 (2007).
   PubMed Web of Science ®Google Scholar
• Borro M, Gentile G, Stigliano A, Misiti S, Toscano V, Simmaco M. Proteomic analysis of peripheral T lymphocytes, suitable circulating biosensors of strictly related diseases. Clin. Exp. Immunol.150(3), 494–501 (2007).
   PubMed Web of Science ®Google Scholar
• Findeisen P, Post S, Wenz F, Neumaier M. Addition of exogenous reporter peptides to serum samples before mass spectrometry-based protease profiling provides advantages over profiling of endogenous peptides. Clin. Chem.53(10), 1864–1866 (2007).
   PubMedGoogle Scholar
• 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. Proteomics7(3), 509–518 (2008).
   PubMed Web of Science ®Google Scholar
• Findeisen P, Peccerella T, Post S, Wenz F, Neumaier M. Spiking of serum specimens with exogenous reporter peptides for mass spectrometry based protease profiling as diagnostic tool. Rapid Commun. Mass Spectrom.22(8), 1223–1229 (2008).
   PubMedGoogle Scholar
• Witt I. Test systems with synthetic peptide substrates in haemostaseology. Eur. J. Clin. Chem. Clin. Biochem.29(6), 355–374 (1991).
   PubMedGoogle Scholar
• Petricoin E, Ardekani A, Hitt B et al. Use of proteomic patterns in serum to identify ovarian cancer. Lancet359(9306), 572–577 (2002).
   PubMed Web of Science ®Google Scholar
• Diamandis E. Peptidomics for cancer diagnosis: present and future. J. Proteome Res.5(9), 2079–2082 (2006).
   PubMed Web of Science ®Google Scholar