A method of mass spectrometry comprising: determining a first physico-chemical property and a second physico-chemical property of components, molecules or analytes in a first sample, wherein said first physico-chemical property comprises the mass or mass to charge ratio and said second physico-chemical property comprises the elution time, hydrophobicity, hydrophilicity, migration time, or chromatographic retention time; determining said first physico-chemical property and said second physico-chemical property of components, molecules or analytes in a second sample; characterised by probabilistically clustering data relating to components, molecules or analytes in said first sample with data relating to components, molecules or analytes in said second sample; said step of probabilistically clustering comprising: comparing data points related to components, molecules or analytes in said first sample with data points related to components, molecules or analytes in said second sample, clustering said data into one or more first clusters of data points, probabilistically clustering the initially clustered data points into one or more second clusters of data points, wherein a probabilistic measure is used to assess the closeness of data points on a pair-wise basis, interrogating said one or more second clusters of data points to determine one or more third clusters of data points which include only one data point representing a molecule, analyte or ion from each of said first sample and said second sample, wherein the data relating to said second physico-chemical property of molecules, analytes or ions in each of said one or more third clusters of data points is averaged to form an average value for said second physico-chemical property; the method further comprising: determining a calibration function to correlate data relating to the observed second physico-chemical property with said average value for said second physico-chemical property; and adjusting data points from each sample to align the second physico-chemical property for all data sets. determining a first physico-chemical property and a second physico-chemical property of components, molecules or analytes in a first sample, wherein said first physico-chemical property comprises the mass or mass to charge ratio and said second physico-chemical property comprises the elution time, hydrophobicity, hydrophilicity, migration time, or chromatographic retention time; determining said first physico-chemical property and said second physico-chemical property of components, molecules or analytes in a second sample; characterised by probabilistically clustering data relating to components, molecules or analytes in said first sample with data relating to components, molecules or analytes in said second sample; said step of probabilistically clustering comprising: comparing data points related to components, molecules or analytes in said first sample with data points related to components, molecules or analytes in said second sample, clustering said data into one or more first clusters of data points, probabilistically clustering the initially clustered data points into one or more second clusters of data points, wherein a probabilistic measure is used to assess the closeness of data points on a pair-wise basis, interrogating said one or more second clusters of data points to determine one or more third clusters of data points which include only one data point representing a molecule, analyte or ion from each of said first sample and said second sample, wherein the data relating to said second physico-chemical property of molecules, analytes or ions in each of said one or more third clusters of data points is averaged to form an average value for said second physico-chemical property; comparing data points related to components, molecules or analytes in said first sample with data points related to components, molecules or analytes in said second sample, clustering said data into one or more first clusters of data points, probabilistically clustering the initially clustered data points into one or more second clusters of data points, wherein a probabilistic measure is used to assess the closeness of data points on a pair-wise basis, interrogating said one or more second clusters of data points to determine one or more third clusters of data points which include only one data point representing a molecule, analyte or ion from each of said first sample and said second sample, wherein the data relating to said second physico-chemical property of molecules, analytes or ions in each of said one or more third clusters of data points is averaged to form an average value for said second physico-chemical property; determining a calibration function to correlate data relating to the observed second physico-chemical property with said average value for said second physico-chemical property; and adjusting data points from each sample to align the second physico-chemical property for all data sets.