Abstract: A method of processing mass spectral data is provided. The mass spectral data includes a plurality of MS1 mass spectra and a plurality of MSN mass spectra each having a respective associated retention time. A group of features is detected in the plurality of MS1 mass spectra, each feature of the group having a respective mass, and the features of the group having corresponding retention times. The method includes, for each of one or more features of the group: submitting a corresponding MSN mass spectrum to a mass spectral search engine in order to obtain an identification result for that feature, and determining a candidate ion type for the feature based on a mass difference between the mass associated with the feature and an expected mass from the identification result. The method also includes identifying one or more compounds based on the group of features and the candidate ion type(s).

Abstract: In one aspect, a method for detecting the labelling state of unknown species of molecules M contained in a sample exposed to a non-changing isotope labelling process using mass spectrometry is described.

Abstract: Methods of identification of at least one most likely elemental composition of at least one species of molecules contained in a sample and/or originated from a sample by at least one ionisation process are provided. The method includes measuring a mass spectrum of the sample and may include reducing the measured mass spectrum to a neutral mass spectrum. The method further includes determining for a peak of interest a set of candidate species of molecules which have an expected peak with a peak position within a peak position tolerance range in the corresponding measured mass spectrum or neutral mass spectrum. An identification mass spectrum is identified for each candidate species and a range of peak positions is determined of all peaks of the identification mass spectrum. Two subscores of candidate species are determined by comparing the identification spectra with the measured or neutral mass spectrum and final scores are calculated from the subscores.

Abstract: In one aspect, a method for detecting the labelling state of unknown species of molecules M contained in a sample exposed to a non-changing isotope labelling process using mass spectrometry is described.

Abstract: Methods of identification of at least one most likely elemental composition of at least one species of molecules contained in a sample and/or originated from a sample by at least one ionisation process are provided. The method includes measuring a mass spectrum of the sample and may include reducing the measured mass spectrum to a neutral mass spectrum. The method further includes determining for a peak of interest a set of candidate species of molecules which have an expected peak with a peak position within a peak position tolerance range in the corresponding measured mass spectrum or neutral mass spectrum. An identification mass spectrum is identified for each candidate species and a range of peak positions is determined of all peaks of the identification mass spectrum. Two subscores of candidate species are determined by comparing the identification spectra with the measured or neutral mass spectrum and final scores are calculated from the subscores.