The relative composition of a material can be assessed using the technique of Atom Probe Tomography (APT), and is done so through a quantitative analysis of an APT-generated mass spectrum. Compositions are determined from an integration (summation) of counts over a determined range defining the mass peaks of interest. Currently in the field of APT, mass spectral analysis is performed by either using: 1) IVAS (Integrated Visualization and Analysis Software from Cameca Instruments, the maker of the Local Electrode Atom Probe). IVAS is a software package used to analyze the raw APT data, including mass spectra compositional analysis); 2) custom methods developed/used by individuals or groups of individuals within different research groups. The PeakWorks software is designed to assist in the quantitative analysis of atom probe tomography (APT) generated mass spectra. Specifically, through an interactive user interface, mass peaks can be identified automatically (defined by a threshold) and/or identified manually. The software then provides a means to assign specific elemental isotopes (including more than one) to each peak. The software also provides a means for the user to choose background subtraction of each peak based on background fitting functions, the choice of which is left to the users discretion. Peak ranging (the mass range over which peaks are integrated) is also automated allowing the user to chose a quantitative range (e.g. full-width-half-maximum). The software then integrates all identified peaks, providing a background-subtracted composition, which also includes the deconvolution of peaks (i.e. those peaks that happen to have overlapping isotopic masses). The software is also able to output a 'range file' that can be used in other software packages, such as within IVAS. A range file lists the peak identities, the mass range of each identified peak, and a color code for the peak. The software is also able to generate 'dummy' peak ranges within an outputted range file that can be used within IVAS to provide a means for background subtracted proximity histogram analysis. The software was written in the MatLab language code, and if the user has a version of Matlab installed on their computer, is designed to be used by launching the application file. Otherwise, if the user doesn't have a version of Matlab on their computer, an independent application can be installed via and 'executable' file which automatically downloads and installs the appropriate free files from the Matlab website. This later version requires the user to have their computer connected to the internet.