For example, one field of biochemistry that has massively benefited from the mass spectrometry improvements over the last ten years is the one involving fine structural characterizations of chemically modified biopolymers, like the post-translational modification studies in protein biochemistry (see for a review). It is noteworthy that, while some experiments are almost completely automatable (like in the case of high-throughput proteomics), a majority of the experiments being performed in mass spectrometry facilities are neither automatable nor high-throughput.
#Mass spec mass finder software#
Thus, the variety of polymer chemistries analyzable by mass spectrometry is compounded by the variety of mass spectrometric experiments, producing an extremely diverse set of mass data to be either predicted or analysed with the help of appropriate software tools. The current and ever-increasing variety of mass spectrometer designs affords a rather large array of experiments that can be performed on different biopolymers. Indeed, while proteins were once the main biopolymeric analytes studied by mass spectrometry, oligo(deoxy)ribonucleotides and saccharides also are routinely analyzed today and mass spectrometry is used, for example, for the characterization of DNA-protein complexes or for the gas phase sequencing of saccharides (for reviews, see ). Mass spectrometry has proven essential in structural studies in which biopolymer molecules of a variety of polymer chemistries are involved. 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. Any aspect of the mass calculations, polymer chemistry reactions or graphical polymer sequence editing is configurable. 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. The framework is organized into three modules, all accessible from one single binary program. 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). We developed a software to address the lack of an integrated software framework able to deal with different polymer chemistries. 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.
However, all the software tools available to date are polymer chemistry-specific.
This time-consuming and painstaking data scrutiny is alleviated by using specialized software tools. 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. Nowadays, a variety of (bio-)polymers can be analyzed by mass spectrometry.
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