I forgot to give two more reasons to keep you working on MSGRAPH:
- the .MS file format compresses a lot better than mzXML or the RAW files.
- the eagle eye works a lot better than the Xcalibur software.
(Daniel Macedo Lorenzini)
MSGraph is a program designed for the interactive, fast, qualitative analysis of mass spectrometric (MS) data. It is a tool to provide fast and simple access to all the information contained in an LC/MS analysis run.
MSGraph was developed from 1992 onwards, and it was first published 1993 as a paper in Spectrochimica Acta . Throughout the years, I continued to use the program for my daily work, and during that time I added some features that I found useful. Probably the most important addition was the implementation of the component detection algorithm (CODA) described by W. Windig in 1996 . The version given here is a thoroughly revised, almost completely re-written and in many details improved version of the initial program.
Using LC/MS, particularly using electrospray or thermospray as ionization technique, often results in chromatograms with a high level of noise. Using conventional background subtraction techniques or "differential chromatograms" is of limited success. A dynamic selection procedure was developed by Windig and coworkers  that selects mass chromatograms with both low noise and low background; these selected chromatograms are then combined to form a "reduced TIC" trace. This is achieved by calculating a "similarity index" between each raw mass chromatogram and its smoothed and mean-subtracted version. The "similarity index" is called Mass Chromatogram Quality index (MCQ); a value of 1 indicates a perfect match, values around 0.7...0.8 are usually still reasonable chromatograms, and data with an MCQ index below 0.6 are usually not worth being considered. Details are outlined in the reference cited above.
The approach is named COmponent Detection Algorithm (CODA). In LC/MS, it allows to reduce the number of "useful" mass chromatograms by more than an order of magnitude without losing significant information, and it results in a large reduction in data analysis times.
MSGraph does CODA processing somewhat different from some commercial packages (that I am aware of): Once the MCQ values are determined, there is no need to re-run CODA processing if you want to modify the threshold. MSGraph does not perform a "data reduction" of the original data file; all data are always there, are never modified, and the MCQ threshold value be adjusted anytime.
The following figures show a few examples of "raw data vs. CODA-processed data". By clicking on the preview images you can download a PostScript file of the original graphics. By the way, these files are as exported by MSGraph and were not altered in any way later on.
For historical reasons, the program is designed to read data files in a proprietary, yet simple format; a detailed description of the file format is included. Other data must be converted to this format. Ready-to-use converters are available for the following formats:
The program runs under using MS-DOS and can be used in a "DOS box" of at least Microsoft Windows 3.11, 95b, 98, NT4, and 2000. However, the program has to be opened full screen, and the "DOS Window" apparently causes severe load on the operating system, which means that e.g. playing MP3 files simultaneously is no longer a pleasure for your ears. It runs nicely, even in the high-resolution graphic modes, under Linux DOSEMU. This implies that you can visualize your data with MSGraph even if you are actually sitting on a Unix machine, as the window running MSGraph can be redirected to any other X display!
A standard graphic driver for standard VGA is implemented, which should work on all systems. A VESA compliant SVGA driver for higher screen resolutions (up to 1280x1024) is provided, but its proper function depends on the operating system.
Detailed instructions for installation, operational qualification testing, and maintenance are provided.
For several years now, MSGraph is in a stable state. The software is fully operational and has quite a lot of features, so there are no plans for further development (except, perhaps, the port to Linux ... but this will require a major rewrite of the code, so do not ask me about this these days ;-).
MSGraph and all related software are Free Software and are published under Version 2 of the GNU General Public License (GPL). You can redistribute it and/or modify it under the same terms, which ensures that its source code is free and that any derivatization, or implementation of it in other software, will also remain free.
The difference between "free software" and "freeware" is of legal importance. If you do not understand any portion of this license, please seek appropriate professional legal advice. If you do not or if - for any reason - you can not accept all of the conditions of the GPL, then you must not use nor distribute this software.
Since early 2009, the Analyses Database is hosted at sourceforge.net. To download, you have several possibilities:
The principal author is Jörg Hau.
Contributions - be it with suggestions, testing, discussions or code - came from many people, namely Michael Linscheid who supported to develop this program "seriously", and Walter Nigge who gave many little hints and performed much testing especially in the early years of the development. Thanks go also to Daniel Lorenzini for the development of the mzXML converter, and to many others that have sent constructive feedback over the years. Thank you!
 J. Hau and M. Linscheid. MSGraph: A Program for the Display of LC/MS Data. Spectrochimica Acta 48B (1993), E1047-E1051.
 W. Windig, J. M. Phalp, A. W. Payne. A Noise and Background Reduction Method for Component Detection in Liquid Chromatography/Mass Spectrometry. Analytical Chemistry 68 (1996), 3602-3606.