Abstract: The invention relates to the determination of the relative concentrations of proteins or protein derivatives in liquids. The invention provides a method which uses nanoparticles coated with specific affinity collectors in order to fish the desired proteins or protein derivatives out of the liquids and to separate them, in order to introduce them to the mass spectrometric frequency analysis after elution from the affinity collectors. This makes it possible to determine the concentrations of several proteins or several forms of protein modification or mutation relative to each other with relatively high measuring dynamics.

Abstract: The invention relates to the acquisition of spectra of biopolymers, especially of proteins, in tandem mass spectrometers with ionization using matrix-assisted laser desorption (MALDI) for the examination or determination of sequence patterns. The invention consists of a method of measuring granddaughter spectra of terminal fragment ions of the bipolymers in tandem mass spectrometers, wherein a so-called in-source fragmentation to generate a first generation of fragment or daughter ions of a biopolymer is coupled with a subsequent measurement of granddaughter ions, which have been obtained by a further fragmentation of a selected type of daughter ions. The method according to the invention enables the determination of the terminal sequences which are otherwise very difficult to measure.

Abstract: The invention relates to the analysis of complex protein mixtures such as entire proteomes, and in particular the rapid detection of previously unknown or unusually expressed proteins by common enzymatic digestion, subsequent chromatographic separation and analysis of the digestion peptides by mass spectrometry. The invention consists in subjecting fractions of the digestion peptides separated by liquid chromatography to analysis by mass spectrometry, at a time other than that of the chromatography, in a tandem time-of-flight mass spectrometer with ionization by matrix assisted laser desorption (MALDI). This method finds many times more proteins than are found through the procedures predominantly used until now of two-dimensional gel electrophoresis with subsequent time-of-flight mass spectrometry. It also removes the time pressure that dominates the real-time analysis of coupled LC-MS processes, and it allows measurements to be reduced to the interesting proteins by intermediate analysis.