GNU polyxmass: A software framework for mass spectrometric simulations of linear (bio-)polymeric analytes

Abstract

Background: Nowadays, a variety of (bio-)polymers can be analyzed by mass spectrometry. The detailed interpretation of the spectra requires a huge number of "hypothesis cycles", comprising the following three actions 1) put forth a structural hypothesis, 2) test it, 3) (in)validate it. This time-consuming and painstaking data scrutiny is alleviated by using specialized software tools. However, all the software tools available to date are polymer chemistry-specific. This imposes a heavy overhead to researchers who do mass spectrometry on a variety of (bio-)polymers, as each polymer type will require a different software tool to perform data simulations and analyses. We developed a software to address the lack of an integrated software framework able to deal with different polymer chemistries. Results: The GNU polyxmass software framework performs common (bio-)chemical simulations-along with simultaneous mass spectrometric calculations-for any kind of linear bio-polymeric analyte (DNA, RNA, saccharides or proteins). The framework is organized into three modules, all accessible from one single binary program. The modules let the user to 1) define brand new polymer chemistries, 2) perform quick mass calculations using a desktop calculator paradigm, 3) graphically edit polymer sequences and perform (bio-)chemical/mass spectrometric simulations. Any aspect of the mass calculations, polymer chemistry reactions or graphical polymer sequence editing is configurable. Conclusion: The scientist who uses mass spectrometry to characterize (bio-)polymeric analytes of different chemistries is provided with a single software framework for his data prediction/ analysis needs, whatever the polymer chemistry being involved. © 2006 Rusconi; licensee BioMed Central Ltd.