- Original Article
- Open Access
Comparison between surface and bead-based MALDI profiling technologies using a single bioinformatics algorithm
Clinical Proteomicsvolume 2, pages145–152 (2006)
In this manuscript, we compared serum profiles obtained with two related technologies, SELDI-TOF and Clinprot, using a single bioinformatic algorithm. These two approaches rely on mass spectrometry to detect proteins and peptides initially selected by binding to various chromatographic matrices. They are proposed by two different companies, and they are competing for being the reference in high throughput serum profiling for clinical proteomics. This independent evaluation of these two technologies put the light on some of their differences, suggests that they address different proteome fractions and, thus, could be complementary. Taken together, our data could contribute to the parameters relevant for the choice of one technology or the other.
Anderson, N. L. and Anderson, N. G. (2002) The human plasma proteome: history, character, and diagnostic prospects.Mol. Cell. Proteomics 1, 845–867.
Pieper, R., Gatlin, C. L., Makusky, A. J., et al. (2003) The human serum proteome: display of nearly 3700 chromatographically separated protein spots on two-dimensional electrophoresis gels and identification of 325 distinct proteins.Proteomics 3, 1345–1364.
Yang, Z., Hancock, W. S., Chew, T. R., and Bonilla, L. (2005) A study of glycoproteins in human serum and plasma reference standards (HUPO) using multilectin affinity chromatography coupled with RPLC-MS/MS.Proteomics 5, 3353–3366.
Hortin, G. L. (2006) The MALDI-TOF mass spectrometric view of the plasma proteome and peptidome.Clin. Chem. 52, 1223–1237.
Petricoin, E. F., Ardekani, A. M., Hitt, B. A., et al. (2002) Use of proteomic patterns in serum to identify ovarian cancer.Lancet 359, 572–577.
Coombes, K. R., Morris, J. S., Hu, J., Edmonson, S. R., and Baggerly, K. A. (2005) Serum proteomics profiling: a young technology begins to mature.Nat. Biotechnol. 23, 291–292.
Zhang, Z., Bast, R. C., Jr. Yu, Y., et al. (2004) Three biomarkers identified from serum proteomic analysis for the detection of early stage ovarian cancer.Cancer Res.64, 5882–5890.
Issaq, H. J., Conrads, T. P., Janini, G. M., and Veenstra, T. D. (2002) Methods for fractionation, separation and profiling of proteins and peptides.Electrophoresis 23, 3048–3061.
Pieper, R., Su, Q., Gatlin, C. L., Huang, S. T. Anderson, N. L., and Steiner, S. (2003) Multicomponent immunoaffinity subtraction chromatography: an innovative step towards a comprehensive survey of the human plasma proteome.Proteomics 3, 422–432.
Guerrier, L., Thulasiraman, V., Castagna, A., et al. (2006) Reducing protein concentration range of biological samples using solid-phase ligand libraries.J. Chromatogr. B Analyt. Technol. Biomed. Life Sci. 833, 33–40.
Tuszynski, J. (2006) caMassClass: processing and classification of protein mass spectra (SELDI) data. http://cranr-projectorg/src/contrib/Descriptions/caMassClasshtml (The caMassClass Software License, Version 1.0).
Friedman, J. (1984) A variable span scatterplot smoother: Laboratory for Computational Statistics, Stanford University, report no.: Technical Report No. 5.
Fung, E. T., Wright, G. L., Jr., and Dalmasso, E. A. (2000) Proteomic strategies for biomarker identification: progress and challenges.Curr. Opin. Mol. Ther. 2, 643–650.
Cottrell, J. S. (1994) Protein identification by peptide mass fingerprinting.Pept. Res. 7, 115–124.
The first two authors contributed equally to this work.