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

BMC Bioinformatics
Filippo Rusconi

Abstract

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. 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) ...Continue Reading

References

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Citations

Jul 10, 2007·Nucleic Acids Research·Nadia HégaratDanièle Praseuth
Sep 25, 2012·The Journal of Physical Chemistry. B·Olivier MozziconacciChantal Houée-Levin
Jul 3, 2007·Free Radical Biology & Medicine·Yves BlouquitCécile Sicard-Roselli
Jul 3, 2007·Free Radical Biology & Medicine·Olivier MozziconacciChantal Houée-Levin
Sep 13, 2013·Analytical and Bioanalytical Chemistry·Vivien BerthelotMarie Erard
Jun 27, 2020·Mass Spectrometry Reviews·James Michael SuttonMichael G Bartlett
Jan 20, 2021·Current Protein & Peptide Science·Filippo Rusconi

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Software Mentioned

GNU
SOS
polyxcalc
libpolyxmass
mzData
polyxdef
bin
libxml2
polyxmass
massXpert

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