EDit: a computer program to assist in the presentation of energy‐dependent mass spectra

Energy-dependent mass spectrometry (ED-MS) uses collision-induced dissociation (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), but we have also shown that varying other parameters capable of fragmenting ions (temperature, laser power) can generate related maps. Current mass spectrometry software does not allow facile production of ED spectra, as the ‘Map’ function produces an image that is difficult to manipulate and ill-suited for publication purposes. We present a program (‘EDit’) for conversion of MassLynx (Waters Corporation) continuum spectra into a matrix format suitable for direct introduction into scientific graphing packages such as Origin or SigmaPlot, or even Excel. 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. Playing these two values off against one another makes for a clear, uncluttered map. Any graphics program, even one as simple as Microsoft Paint, allows transformation (rotation and reflection) of the data into a conventional format (m/z increasing left to right on the x axis). The spectrum summing all the data used to produce the map is added to the top of the spectrum, and the scale moved to the bottom of the map. The y axis is relabelled with cone (or collision) voltage replacing scan number. These procedures are timeconsuming and the attainable resolution is limited by the bitmap format. A more convenient, flexible method is highly desirable. The MassLynx proprietary file format (.raw) may be converted into ASCII format by use of the DataBridge program (part of the MassLynx suite). The resulting (.txt) file is not in a format suitable for scientific graphing programs, as it consists of sequential spectra listed as m/z vs. intensity (see 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