Evaluation of LC-MS data for the absolute quantitative analysis of marker proteins.pdf

Evaluation of LC-MS data for the absolute quantitative analysis of marker proteins Nathana?l Delmotte1, Bettina Mayr1, Andreas Leinenbach1, Knut Reinert2, Oliver Kohlbacher3, Christoph Klein4, and Christian Huber1 1 Instrumentelle Analytik und Bioanalytik, Universit?t des Saarlandes, Postfach 15 11 50, 66041 Saarbruecken, Germany n.delmotte@mx.uni-saarland.de 2 FB Mathematik und Informatik, AG Algorithmische Bioinformatik, Freie Universit?t Berlin, Takustrasse 9, 14195 Berlin, Germany 3 Wilhelm-Schickard-Institut für Informatik, Universit?t Tübingen, 72076 Tübingen, Germany 4 IRMM / IHCP-ECVAM, European Commission-Joint Research Centre, Ispra, Italy Abstract. The potential of mass spectrometric peptide identification in complex mixtures by means of peptide mass fingerprinting (PMF) and peptide fragment fingerprinting (PFF) was evaluated and compared utilizing synthetic mixtures of commercially available proteins and electrospray-ion trap- or electrospray time-of-flight mass spectrometers. While identification of peptides by PFF is fully supported by automated spectrum interpretation and database search routines, reliable identification by PMF still requires substantial efforts of manual calibration and careful data evaluation in order to avoid false positives. Quantitation of the identified peptides, however, is preferentially performed utilizing full-scan mass spectral data typical of PMF. For the absolute quantitation of serum proteins, we have developed an analytical scheme based on first-dimension separation of the intact proteins by anion-exchange high- performance liquid chromatography (HPLC), followed by proteolytic digestion and second-dimension separation of the tryptic peptides by reversed-phase HPLC in combination with electrospray ionization mass spectrometry (ESI- MS). 1 Mass spectrometric peptide identification 1.1 Peptide Mass Fingerprinting In the Peptide Mass Fingerprinting (PMF) approach, the complex protein mixture on