Abstract: The invention provides methods for characterizing a target protein wherein a mass spectrum of digest peptides of the target protein is acquired and compared with measured reference mass spectra of digest peptides of reference proteins or of proteins of reference host cells. The comparison comprises determining similarity scores of the intensity patterns of the mass spectrum and the reference mass spectra. The characterization comprises assigning the target protein to a reference protein having a reference mass spectrum with a similarity score above a predetermined threshold.

Abstract: The present invention relates to a mass spectrometric method for determining isomeric amino acid residues of a peptide and comprises the steps of: generating a list of peptide candidates using the amino acid lead sequence of the peptide, said lead sequence comprising positions of determined amino acid residues and at least one position with undetermined isomeric amino acid residues; predicting the collision cross section for each peptide candidate; comparing the predicted collision cross section of each peptide candidate with an experimentally determined collision cross section of the peptide and assigning the isomeric amino acid residues of the best matching peptide candidate to the isomeric amino acid residues of the peptide.

Abstract: The invention provides methods for characterizing a target protein wherein a mass spectrum of digest peptides of the target protein is acquired and compared with measured reference mass spectra of digest peptides of reference proteins or of proteins of reference host cells. The comparison comprises determining similarity scores of the intensity patterns of the mass spectrum and the reference mass spectra. The characterization comprises assigning the target protein to a reference protein having a reference mass spectrum with a similarity score above a predetermined threshold.

Abstract: The invention relates to methods for the detailed analysis of ion mixtures from complex mixtures of organic substances in time-of-flight mass spectrometers which are equipped with a trapped ion mobility spectrometer, a quadrupole mass selector and a fragmentation cell. The invention proposes to analyze ion signals of a first mass mobility map, fragment ion spectra and the identifications of the associated substances as to whether ion mixtures not resolved according to mass and mobility, for example from isomers or isobars, are possibly present, and to subsequently measure the ion signals of interest with method parameters which allow the ion species to be measured separately by means of high mobility resolution.

Abstract: The invention relates to methods for the detailed analysis of ion mixtures from complex mixtures of organic substances in time-of-flight mass spectrometers which are equipped with a trapped ion mobility spectrometer, a quadrupole mass selector and a fragmentation cell. The invention proposes to analyze ion signals of a first mass mobility map, fragment ion spectra and the identifications of the associated substances as to whether ion mixtures not resolved according to mass and mobility, for example from isomers or isobars, are possibly present, and to subsequently measure the ion signals of interest with method parameters which allow the ion species to be measured separately by means of high mobility resolution.

Abstract: The invention relates to methods for the detailed analysis of ion mixtures from complex mixtures of organic substances in time-of-flight mass spectrometers which are equipped with a trapped ion mobility spectrometer, a quadrupole mass selector and a fragmentation cell. The invention proposes to analyze ion signals of a first mass mobility map, fragment ion spectra and the identifications of the associated substances as to whether ion mixtures not resolved according to mass and mobility, for example from isomers or isobars, are possibly present, and to subsequently measure the ion signals of interest with method parameters which allow the ion species to be measured separately by means of high mobility resolution.

Abstract: A method for the identification and localization of proteins or other biomolecules of a histologic tissue section comprises enzymatically digesting the biomolecules of two similar tissue sections while substantially preserving the biomolecule positions in the tissue sections. Next, a mass spectrometric image of the digest products in one of the tissue sections is acquired. Then, the digest products of the other tissue section are extracted and separated and the mass spectra and daughter ion spectra of all the digest products are acquired. A list of all identifiable biomolecules of the tissue section is created by comparing the mass spectra and daughter ion spectra with spectra in biomolecule structure databases or spectral libraries. Finally, the biomolecules in the list are assigned to digest products of the same mass in the mass spectra used to create the mass spectrometric image of the thin tissue section.

Abstract: The invention relates to methods for the detailed analysis of ion mixtures from complex mixtures of organic substances in time-of-flight mass spectrometers which are equipped with a trapped ion mobility spectrometer, a quadrupole mass selector and a fragmentation cell. The invention proposes to analyze ion signals of a first mass mobility map, fragment ion spectra and the identifications of the associated substances as to whether ion mixtures not resolved according to mass and mobility, for example from isomers or isobars, are possibly present, and to subsequently measure the ion signals of interest with method parameters which allow the ion species to be measured separately by means of high mobility resolution.

Abstract: A method for determining the concentration ratio in a sample of a target peptide to a reference peptide that is chemically identical with the target peptide, but labeled by isotopes, acquires mass spectra of the target and reference peptides. One of a plurality of families of superimposed bell-shaped curves which is a best fit to ion current peak groups of the target and reference peptides in the mass spectra is determined by varying parameters of the families. In each family, each bell-shaped curve has a predetermined height, the curves have fixed distances from each other and the relative curve heights and curve distances in the families are individually calculated from an elemental composition of the peptides and an isotope abundance distribution of elements composing the peptides, taking into account purity of the isotopes. The concentration ratio is then determined from the parameters of the best fit.

Abstract: A method for determining the concentration ratio in a sample of a target peptide to a reference peptide that is chemically identical with the target peptide, but labeled by isotopes, acquires mass spectra of the target and reference peptides. One of a plurality of families of superimposed bell-shaped curves which is a best fit to ion current peak groups of the target and reference peptides in the mass spectra is determined by varying parameters of the families. In each family, each bell-shaped curve has a predetermined height, the curves have fixed distances from each other and the relative curve heights and curve distances in the families are individually calculated from an elemental composition of the peptides and an isotope abundance distribution of elements composing the peptides, taking into account purity of the isotopes. The concentration ratio is then determined from the parameters of the best fit.

Abstract: The invention relates to the characterization of samples which are located in their many hundreds up to tens or hundreds of thousands on a sample support plate in a regular pattern, a so-called array, by ionization with matrix-assisted laser desorption and mass spectrometric measurement, for example. The invention proposes that the position of the sample pattern, and thus the position of each sample in the measuring instrument, for example a mass spectrometer, should be determined by measuring at least two finely structured internal position recognition patterns, such as fine crosses. The position recognition patterns are preferably applied as the samples are generated, with the same apparatus which also generates the sample pattern. A mass spectrometer in which laser spots with diameters of only four to five micrometers can be generated, which can preferably be positioned with an accuracy of one micrometer or better, is particularly suitable for the characterization.

Abstract: A method for determining an expression of human epidermal growth factor receptor 2 (HER2) of a subject. The method includes providing a sample from the subject; measuring one of (i) amounts of two or more proteins in the sample, each protein having a molecular weight substantially equal to 4740, 8404, 8419, 8435, 8450, 8455, 8465, 8570, 8607 or 8626 atomic mass units, and (ii) amounts of at least one of human cystein-rich intestinal protein 1 (CRIP1), one or more variants of the human cystein-rich intestinal protein 1 (CRIP1 variants), and proteolytic digestion products thereof in the sample; and comparing the amounts of the proteins to control amounts, which control amounts are determinative of the expression of the human epidermal growth factor receptor 2.

Abstract: The invention relates to the characterization of samples which are located in their many hundreds up to tens or hundreds of thousands on a sample support plate in a regular pattern, a so-called array, by ionization with matrix-assisted laser desorption and mass spectrometric measurement, for example. The invention proposes that the position of the sample pattern, and thus the position of each sample in the measuring instrument, for example a mass spectrometer, should be determined by measuring at least two finely structured internal position recognition patterns, such as fine crosses. The position recognition patterns are preferably applied as the samples are generated, with the same apparatus which also generates the sample pattern. A mass spectrometer in which laser spots with diameters of only four to five micrometers can be generated, which can preferably be positioned with an accuracy of one micrometer or better, is particularly suitable for the characterization.

Abstract: A method for determining the concentration ratio in a sample of a target peptide to a reference peptide that is chemically identical with the target peptide, but labeled by isotopes, acquires mass spectra of the target and reference peptides. One of a plurality of families of superimposed bell-shaped curves which is a best fit to ion current peak groups of the target and reference peptides in the mass spectra is determined by varying parameters of the families. In each family, each bell-shaped curve has a predetermined height, the curves have fixed distances from each other and the relative curve heights and curve distances in the families are individually calculated from an elemental composition of the peptides and an isotope abundance distribution of elements composing the peptides, taking into account purity of the isotopes. The concentration ratio is then determined from the parameters of the best fit.

Abstract: A method for the identification and localization of proteins or other biomolecules of a histologic tissue section comprises enzymatically digesting the biomolecules of two similar tissue sections while substantially preserving the biomolecule positions in the tissue sections. Next, a mass spectrometric image of the digest products in one of the tissue sections is acquired. Then, the digest products of the other tissue section are extracted and separated and the mass spectra and daughter ion spectra of all the digest products are acquired. A list of all identifiable biomolecules of the tissue section is created by comparing the mass spectra and daughter ion spectra with spectra in biomolecule structure databases or spectral libraries. Finally, the biomolecules in the list are assigned to digest products of the same mass in the mass spectra used to create the mass spectrometric image of the thin tissue section.

Abstract: A method for determining an expression of human epidermal growth factor receptor 2 (HER2) of a subject. The method includes providing a sample from the subject; measuring one of (i) amounts of two or more proteins in the sample, each protein having a molecular weight substantially equal to 4740, 8404, 8419, 8435, 8450, 8455, 8465, 8570, 8607 or 8626 atomic mass units, and (ii) amounts of at least one of human cystein-rich intestinal protein 1 (CRIP1), one or more variants of the human cystein-rich intestinal protein 1 (CRIP1 variants), and proteolytic digestion products thereof in the sample; and comparing the amounts of the proteins to control amounts, which control amounts are determinative of the expression of the human epidermal growth factor receptor 2.

Abstract: The invention relates to the determination and visualization of the spatial distribution of tissue states in histologic tissue sections on the basis of mass spectrometric signals acquired so as to be spatially resolved. The invention provides a method which determines the tissue state for the tissue spots as a state characteristic, which is calculated as a mathematical or logical expression from at least two mass signals of this tissue spot, and which indicates the tissue state as a gray-level or false-color image in one or two dimensions.

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.

Abstract: The invention relates to the determination and visualization of the spatial distribution of tissue states in histologic tissue sections on the basis of mass spectrometric signals acquired so as to be spatially resolved. The invention provides a method which determines the tissue state for the tissue spots as a state characteristic, which is calculated as a mathematical or logical expression from at least two mass signals of this tissue spot, and which indicates the tissue state as a gray-level or false-color image in one or two dimensions.