EDit: a computer program to assist in the presentation of energy-dependent mass spectraEnergy-dependent mass spectrometry 1 (ED-MS) uses collision-induced dissociation 2 (CID) to fragment ions, generating a 2D projection (collision energy vs. m/z) of a 3D surface (the 3rd dimension, ion intensity, is on the axis perpendicular to the plane). The approach has most frequently been applied to electrospray ionization (EDESI To date, we have produced EDESI spectra using the Map function of the MassLynx software. This generates a plot with scan number (or time) on the x axis and m/z on the y axis in bitmap (.bmp) format. The appearance of the bitmap can be altered using various colour schemes, including one which may be user-defined by selection of appropriate colours (a greyscale being most suitable for publication purposes). Selecting a Map Intensity Range start value of >0 (e.g. 2%) minimizes the contribution of noise to the spectrum, and an end value of <100 similarly assists in the enhancement of minor peaks in the spectrum. Play- Table 1). The MassLynx software compresses the data by eliminating sequential zero intensity values, as is clear upon inspection of the list of data in Table 1.Each scan in the continuum spectrum is listed sequentially, and, even with the compression mentioned, the files are large (typically tens of MB). Graphing programs require data in a matrix format to plot 3D graphs, be this in the form of a color map, a contour map, or a 3D surface. We have written a program called 'EDit', which converts the ASCII file into a matrix (in comma , run in negative ion mode with methanol as the mobile phase, drawn using Origin 1 . The top spectrum is a summation of the 151 spectra used to generate the map.Copyrightseparated value format, .csv, which is readable by all graphing programs) whose dimensions can be specified. Using typical parameters (e.g. a resolution of 1 m/z  1 scan), the reduction in file size is approximately a factor of 50 when taking raw data from a Micromass Q-Tof micro instrument. Detailed instructions for the use of EDit, including screenshots, may be found in the supporting information ('Step-by-step instructions for creating a 3D Origin plot from a MassLynx continuum file'). The program itself may be freely downloaded, 9 along with source code, and is released as free software under the terms of the GNU General Public License (GNU GPL). however, the important sections of code (contained in the file 'MassSpecDataDlg.cpp') can be easily ported to any other operating system. The output produced by the EDit program can be manipulated using graphing software to generate image maps, contour maps, or 3D surfaces. An image map is shown in Fig. 1. To aid in the assessment of the relative peak intensities, we generally include a conventional mass spectrum at the top of the map in which all the spectra used in the map are summed together (using the 'Combine' function in MassLynx).The relative heights of crosspeaks in the EDESI spectrum may be depicted in the form of a 3D surface (Fig. 2...
