- Original Article
- Open Access
Technical evaluation of MALDI-TOF mass spectrometry for quantitative proteomic profiling matrix formulation and application
Clinical Proteomics volume 1, pages259–270(2004)
Matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry (MS) has been recently used to identify disease markers by directly profiling and quantifying the peptide/proteins in biological samples under different physiological or experimental conditions. The information of reproducibility of such quantitative profiling method has not been available. It is important to evaluate and reduce error from technical variation. In this study, an unbiased signal acquisition strategy was used to evaluate the effects of three sample-matrix spotting methods and two matrix chemicals, α-cyano-4-hydroxycinnamic acid (CHCA) and sinapinic acid, on the reproducibility of the peptide/protein signal intensities. The sandwich spotting method using 0.1% nitrocellulose coating film and CHCA gave the best quantitative results for the standard peptides and proteins with mass<66.5 kDa. The normalized signal intensities of the standard peptides and proteins were directly proportional to their concentrations with intra-assay (within-day) coefficient of variations (CVs) ranging from 6.5% to 17%. When analyzing serum peptides <6000 m/z, the interassay (between-days) CVs of all the evaluated peptide peaks were <15%. These data indicate that with the right MS analysis conditions, MALDI-TOF MS appears to be a feasible tool for directly profiling and quantifying the peptide/ proteins in biological samples.
Poon, T.C.W. and Johnson, P.J. (2001). Proteome analysis and its impact on the discovery of serological tumor markers. Clin. Chim. Acta 313:231–239.
Petricoin, E.F., Ardekani, A.M., Hitt, B.A., Levine P.J., Fusaro V.A., Steinberg S.M., et al. (2002). Use of proteomic patterns in serum to identify ovarian cancer. Lancet 359:572–577.
Poon, T.C.W., Yip, T.T., Chan, A.T.C., Yip, C., Yip, V., Mok, T.S., et al. (2003) Comprehensive proteomic profiling identifies serum proteomic signatures for detection of hepatocellular carcinoma and its subtypes. Clin. Chem. 49:752–760.
Poon, T.C.W., Chan, K.C.A., Ng, P.C., Chiu, R.W., Ang, I.L., Tong, Y.K., et al. (2004) Serial analysis of plasma proteomic signatures in pediatric patients with severe acute respiratory syndrome and correlation with viral load. Clin. Chem. 50:1452–1455.
Stoeckli, M., Chaurand P., Hallahan, D.E., and Caprioli, R.M. (2001). Imaging mass spectrometry: a new technology for the analysis of protein expression in mammalian tissues. Nat. Med. 7:493–496.
Chaurand, P. and Caprioli, R.M. (2002). Direct profiling and imaging of peptides and proteins from mammalian cells and tissue sections by mass spectrometry. Electrophoresis 23:3125–3135.
Wang, M.Z., Howard, B., Campa, M.J., Patz, E.F., Jr., and Fitzgerald, M.C. (2003). Analysis of human serum proteins by liquid phase isoelectric focusing and matrix-assisted laser desorption/ionization-mass spectrometry. Proteomics 3:1661–1666.
Howard, B.A., Wang, M.Z., Campa, M.J., Corro, C., Fitzgerald, M.C., and Patz, E.F. Jr. (2003). Identification and validation of a potential lung cancer serum biomarker detected by matrix-assisted laser desorption/ionization-time of flight spectra analysis. Proteomics 3:1720–1724.
Beavis, R.C. and Chait, B.T. (1996). Matrix-assisted laser desorption ionization mass-spectrometry of proteins. Methods Enzymol. 270:519–551.
Lachin, J. (1981). Introduction to sample size determination and power analysis for clinical trials. Control Clin. Trials 2:93–113.
Molloy, M.P., Brzezinski, E.E., Hang, J., McDowell, M.T., and VanBogelen, R.A. (2003). Overcoming technical variation and biological variation in quantitative proteomics. Proteomics 3:1912–1919.
Paweletz, C.P., Gillispie, J.W., Ornstein, D.K., Simone, N.L., Brown, M.R., Cole, K.A., et al. (2000). Rapid protein display profiling of cancer progression directly from human tissue using a protein biochip. Drug Develop Res. 49:34–42.
Preston, L.M., Murray, K.K., and Russell, D.H. (1993). Reproducibility and quantitation of matrix-assisted laser desorption ionization mass spectrometry: Effects of nitrocellulose on peptide ion yields. Biol. Mass Spectrom. 22:544–550.
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Pang, R.T.K., Johnson, P.J., Chan, C.M.L. et al. Technical evaluation of MALDI-TOF mass spectrometry for quantitative proteomic profiling matrix formulation and application . Clin Proteom 1, 259–270 (2004) doi:10.1385/CP:1:3-4:259
- Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry
- quantitative proteomics