Abstract
HPLC-ESI-MS is rapidly becoming an established standard method for shotgun proteomics. Currently, its major drawbacks are two-fold: quantification is mostly limited to relative quantification and the large amount of data produced by every individual experiment can make manual analysis quite difficult. Here we present a new, combined experimental and algorithmic approach to absolutely quantify proteins from samples with unprecedented precision. We apply the method to the analysis of myoglobin in human blood serum, which is an important diagnostic marker for myocardial infarction. Our approach was able to determine the absolute amount of myoglobin in a serum sample through a series of standard addition experiments with a relative error of 2.5%. Compared to a manual analysis of the same dataset we could improve the precision and conduct it in a fraction of the time needed for the manual analysis. We anticipate that our automatic quantitation method will facilitate further absolute or relative quantitation of even more complex peptide samples. The algorithm was developed using our publically available software framework OpenMS (www.openms.de).
This is a preview of subscription content, log in via an institution to check access.
Preview
Unable to display preview. Download preview PDF.
Similar content being viewed by others
References
Panteghini, M., Pagani, F., Bonetti, G.: The sensitivity of cardiac markers: an evidence-based approach. Clin. Chem. Lab. Med. 37, 1097–1106 (1999)
Wu, A.H., Laios, I., Green, S., Gornet, T.G., Wong, S.S., Parmley, L., Tonnesen, A.S., Plaisier, B., Orlando, R.: Immunoassays for serum and urine myoglobin: myoglobin clearance assessed as a risk factor for acute renal failure. Clin. Chem. 40, 796–802 (1994)
Wu, A., Apple, F., Gibler, W., Jesse, R., Warshaw, M., Valdes, J.R.: National academy of clinical biochemistry standards of laboratory practice: recommendations for use of cardiac markers in coronary artery diseases. Clinical Chemistry 45, 110–121 (1999)
Panteghini, M., Apple, F., Christenson, R., Dati, F., Mair, J., Wu, A.: Use of biochemical markers in acute coronary syndromes. Clin. Chem. Lab. Med. 37, 687–693 (1999)
Fesmire, F., Campbell, M., Decker, W., Howell, J., Kline, J.: Clinical policy: critical issues in the evaluation and management of adult patients presenting with suspected acute myocardial infarction or unstable angina. Ann. Emerg. Med. 35, 521–544 (2000)
College of American Pathologists: Cardiac markers survey, Northfield, IL (2003)
Panteghini, M.: Recent approaches to the standardization of cardiac markers. Scand. J. Clin. Lab. Invest. 61, 95–102 (2001)
Panteghini, M.: Standardization of cardiac markers. Totowa, pp. 213–229 (2003)
Dati, F., Linsinger, T., Apple, F., Christenson, R., Mair, J., Ravkilde, J., et al: IFCC project for standardization of myoglobin immunoassays. Clin. Chem. Lab. Med. 40, S311 (2002)
Dati, F., Panteghini, M., Apple, F., Christenson, R., Mair, J., Wu, A.: Proposals from the IFCC committee on standardization of markers of cardiac damage (C-SMCD): strategies and concepts on standardization of cardiac marker assays. Scand. J. Clin. Lab. Invest. 230, 113–123 (1999)
Silva, J., Denny, R., Dorschel, C., Gorenstein, M., Kass, I., Li, G., McKenna, L., Nold, M., Richardson, K., Young, P., Geromanos, S.: Quantitative rpoteomic analysis by accurate mass retention time pairs. Anal. Chem. 77, 2187–2200 (2005)
Orchard, S., Hermjakob, H., Apweiler, R.: The proteomics standards initiative. Proteomics 3, 1374–1376 (2003)
HUPO Proteomics Standards Initiative (2005), http://psidev.sourceforge.net/
de Hoffmann, E., Charette, J., Stroobant, V.: Mass Spectrometry, 2nd edn. John Wiley and Sons, Chichester (2001)
Marco, V.B.D., Bombi, G.G.: Mathematical functions for the representation of chromatographic peaks. Journal of Chromatography A 931, 1–30 (2001)
Pai, S.C.: Temporally convoluted gaussian equations for chromatographic peaks. Journal of Chromatography A 1028, 89–103 (2004)
Mayr, B.M.: Die Kopplung der Flüssigchromatographie mit der Elektrospray-Ionisations- Massenspektrometrie als Werkzeug für die Genomanalyse und die Quantitative Proteomforschung. PhD thesis, Universität des Saarlandes (2005)
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2005 Springer-Verlag Berlin Heidelberg
About this paper
Cite this paper
Gröpl, C. et al. (2005). Algorithms for the Automated Absolute Quantification of Diagnostic Markers in Complex Proteomics Samples. In: R. Berthold, M., Glen, R.C., Diederichs, K., Kohlbacher, O., Fischer, I. (eds) Computational Life Sciences. CompLife 2005. Lecture Notes in Computer Science(), vol 3695. Springer, Berlin, Heidelberg. https://doi.org/10.1007/11560500_14
Download citation
DOI: https://doi.org/10.1007/11560500_14
Publisher Name: Springer, Berlin, Heidelberg
Print ISBN: 978-3-540-29104-6
Online ISBN: 978-3-540-31726-5
eBook Packages: Computer ScienceComputer Science (R0)