Free MS Data Prediction and Analysis with GNU Polyxmass

Courtesy of Filippo RusconiWhile a graduate student, Filippo Rusconi couldn't come up with the money to pay for a Microsoft developer's license to continue work on his mass spectrometry program. So instead he rewrote the whole program in GNU/Linux. It turned out to be the best thing that happened to him, he says. "It allowed me to make the program a thousand times more powerful."The program, now called GNU polyxmass http://www.polyxmass.org is a complete software suite for mass spectrometrists t

Sep 27, 2004
Sam Jaffe
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Courtesy of Filippo Rusconi

While a graduate student, Filippo Rusconi couldn't come up with the money to pay for a Microsoft developer's license to continue work on his mass spectrometry program. So instead he rewrote the whole program in GNU/Linux. It turned out to be the best thing that happened to him, he says. "It allowed me to make the program a thousand times more powerful."

The program, now called GNU polyxmass http://www.polyxmass.org is a complete software suite for mass spectrometrists to use in forecasting the kind of results they will get before even putting an analyte into the spectrometer. It also can be used to analyze existing data. Unlike software provided by mass spectrometer manufacturers, Polyxmass works for any kind of polymer, including nucleic acids, proteins, and polysaccharides.

GNU polyxmass has three modules that allow the user to define a polymer's chemistry, calculate the reaction, and then analyze the results. Its algorithms simulate gas-phase reactions and cleavage and fragmentation events. "The accuracy of the program depends entirely on the level of accuracy the user has put in to define the polymer," says Rusconi, now a staff scientist at the National Research Council in Paris.

Currently, GNU polyxmass can be used on any UNIX-based PC, as well as Mac OS X. Its graphical interface is based on X-Windows. Rusconi hopes to find someone who will volunteer to port it to Windows. "It's actually a simple programming job, but I've got better things to do with my time."

- Sam Jaffe