The disclosure features systems and methods that include: exposing a biological sample to an ion beam that is incident on the sample at a first angle to a plane of the sample by translating a position of the ion beam on the sample in a first direction relative to a projection of a direction of incidence of the ion beam on the sample; after each translation of the ion beam in the first direction, adjusting a focal length of an ion source that generates the ion beam; and measuring and analyzing secondary ions generated from the sample by the ion beam after adjustment of the focal length to determine mass spectral information for the sample, where the sample is labeled with one or more mass tags and the mass spectral information includes populations of the mass tags at locations of the sample.

A method for analyzing a multidimensional data set includes generating a multidimensional mass spectrometry data set from a sample; and generating an matrix representing the multidimensional mass spectrometry data set such that a first dimension and a second dimension of the multidimensional mass spectrometry data set correspond to a matrix cell location, and an ion intensity corresponds to a matrix cell value; and determining a class of the matrix from a plurality of matrix classes using a trained neural network matrix classifier.

A use of an anthranilic acid derivative as a matrix for a MALDI Mass spectrometry, comprising: preparing a matrix compound represented by the following formula:

##STR00001## wherein X is selected from hydrogen and a hydroxyl group, and Y is selected from hydrogen, a methyl group or an acetyl group, provided that when X is hydrogen, Y is hydrogen or an acetyl group, and when X is a hydroxyl group, Y is a methyl group; applying the matrix compound and an analyte onto a sample holder; and analyzing the analyte by the MALDI mass spectrometer.

Systems and methods for image and/or video processing of mass spectrometry data comprise a processor in communication with a storage device, and computer system code executed by the processor that causes the processor to perform an image or video analysis comparison between a second data plot image or video to a first data plot image or video, and generate a delta dataset based on the comparison. The delta dataset is representative of the differences between the first and second data plots. In additional systems and methods the computer system code can perform an image or video analysis comparison between the first and second data plots and a reference data plot, generate first and second delta datasets based on the comparisons, which are representative of the differences between the first and second data plots and the reference data plot, and perform a statistical analysis on the first and second delta datasets.

A method for the identification and localization of small molecule species in a histologic thin tissue section comprises the steps of: a) acquiring a mass/mobility image of the tissue section and generating a mass/mobility map of the small molecule species of interest for each pixel of the image; b) providing a second sample of the same tissue and extracting the small molecules of interest, separating them, and acquiring mass and ion mobility spectra from the separated small molecules; c) identifying the small molecules of interest using corresponding reference databases; and d) assigning identified small molecules to entries in the mass/mobility maps of the first tissue section by comparison of ion masses and mobilities of the identified species to those of the second thin tissue section.

In a data processing unit, alignment is performed by appropriately deforming one image among MS imaging images acquired from different samples so that positions and sizes on the MS imaging image are matched (S1 to S5). When the aligned image is displayed on a screen of a display unit and a user sets a region of interest on the image serving as a reference (S6), a micro region including a center point within a range of the set region of interest is extracted in each of an image serving as the reference and an image not serving as the reference (S7). In the image subjected to image deformation, although the shape of each micro region is distorted and micro regions are not arranged in an orderly grid manner, by assuming that the micro regions in which the center point is included within the range of the region of interest is included in the range of the region of interest, it is possible to perform a comparative analysis based on the data value within an appropriate micro region corresponding to the region of interest regardless of the image deformation.

The efficiency and accuracy of search for a compound exhibiting a distribution similar to that of a reference image such as an optical microscope image are improved in imaging mass spectrometric analysis. In an imaging mass spectrometer including a data processing device according to the present invention, a regression analysis executor (16) executes PLS using mass spectrum data and reference image data for each measurement point and calculates a regression coefficient reflecting the similarity of the distribution for each m/z value. An m/z value search section (17) selects m/z values in descending order of regression coefficients, but in each search m/z range obtained by dividing the entire measurement m/z range for each predetermined width, excludes a search m/z range including one m/z value already selected from the search target. Since the peak originating from a certain compound and its isotope peak fall within almost one search m/z range on the mass spectrum, the process described above can avoid selection of the m/z value of ions originating from a certain compound and the m/z value of ions originating from its isotope in duplicate as an m/z candidate.

After collecting mass spectrometry data for each of a large number of measurement points in the two-dimensional region on the sample with the imaging mass spectrometry unit, the user inputs the target compound whose two-dimensional distribution is desired to be observed from the input unit. The image display instruction reception unit obtains the m/z range for data integration from the precise m/z value and the allowable width of m/z for each target compound. The mass-to-charge ratio range overlap determination unit determines the presence or absence of overlap between the m/z ranges of a plurality of compounds, and if there is an overlap, the overlap determination result processing unit creates and displays on the screen of the display unit a list of compounds whose m/z ranges overlap, for example. This urges the user to review the compounds and allowable values.

The disclosure relates to a method which is suitable for the quality control and signal correction of mass spectrometry data of biological tissue samples and is based on the analysis of the chemical background signal observed in a spectrum. It exploits the fact that the chemical background signal contains components from a plurality of polymer molecules, whose chemical structure has strong regularities. These regularities mean that the observed masses are subject to certain statistical distributions, which are each characteristic of the class of molecule. By analyzing these statistical properties, it is possible to detect and correct any mass shifts which may be present.

After setting an intensity value equal to or lower than a predetermined level in mass spectrum data as invalid data, an uncompressed data array in which intensity values are arrayed in the order of m/z is divided into blocks per predetermined number of pieces of data. When significant intensity values are consecutive in order from the start of each block, this consecutive number and the respective intensity values are used as data for compression. When invalid data is consecutive, this consecutive number is used as data for compression. Then, sequence numbers of data at the start of each block after compression are collected to create an index and the index is stored together with the compressed data.