Overview

The massXpert2 software is a linear polymer chemistry modelling program that is aimed at simulating mass spectrometric data for (bio) polymeric sequences: once a polymer chemistry definition has been modelled, a polymer sequence may be entered in the editor and a large number of polymer chemistry reactions might be simulated along with theoretical mass spectrometric data.

massXpert2 comprises the following four modules

XpertDef

With this module the user defines brand new polymer chemistries. At the very least, a polymer chemistry comprises the following chemical informations:

• A table of isotopic data (isotopes needed to describe chemical elements)

• A list of monomers defined as a code (any number of letters), a name and a formula. The formula defines the residue, not the monomer.

• A list of (bio) chemical modifications defined as a name, a net chemical formula (the net atomic differential between the unmodified and modified states), a list of monomer targets that might be modified with this modification, and finally the maximum number of such modifications that can occur on a single monomer target (for methylation, that would be 3, for example, in histones; or for phosphorylation, that would be 1, for the threonine, serine, tyrosine residues).

• A list of cleaving agents (either chemical or biochemical), like proteolytic enzymes or endonucleolytic enzymes, but also like cyanogen bromide. The flexibility of the grammar used to define the modifications allows for the definition of monomer modifications occurring when using chemical reagents like cyanogen bromide, for example, where the methionyl residue is converted to a homoseryl residue.

• A list of gas phase fragmentation patterns for the detailed simulation of precursor ion fragmentation of the matching polymer definition. The grammar used for the definition of gas phase fragmentation patterns is that flexible that it allows the description of the most complex fragmentation mechanisms in the saccharidic world.

• The polymer sequence caps. In the peptide/protein world, the polymer is a chain of monomer residues that, in order to correspond to a finished polymer sequence, needs to be capped with both a proton at the N-terminal end and a hydroxyl group at the C-terminal end.

• The default ionization rule to be used when computing the elemental composition and the masses of the polymer or of the oligomer (protein or peptide, for example). An ionization rule is defined by specifying the chemical modification that the analyte is subjected to during the ionization, the charge that is brought by that ionization reaction and finally the number of times the ionization reaction is to be performed onto the analyte. For MALDI mass spectrometry of proteins, typically, that would be [+H, 1, 1] which reads like “Protonation brings one proton to the analyte, thus bringing a charge of one a single time”.

XpertCalc

With this module, you get a desktop calculator that understands your polymer chemistry definitions as defined in XpertDef. The calculator allows any kind of chemical reaction and is infinitely programmable. A chemical pad is available in which chemical reactions previously defined become available in the form of buttons, exactly like with a desktop calculator. Any calculation is recorded in a logbook that is exportable to put in the lab-book.

XpertEdit

With this module, you get a sophisticated polymer sequence editor and a chemical center where a huge amount of simulations might be performed. Anything mass-related is virtually feasible in XpertEdit. The polymer sequence editor is configurable to the extent that the graphical representation of the monomer residues in the sequence is definable using a drawing program that outputs SVG files (like Inkscape, for example).

XpertMiner

With the XpertMiner module, you have a data mining center. You can drag and drop data from the mass spectra (in the form of (m/z,z) lists) and data from the simulations performed in the XpertEdit module. Once there, all the data will be available for comparison, arbitrary calculations like, say : “all the element in this list of m/z values should be applied the following mass increase” or “this list of m/z values should be appplied this reaction: -H+Na”. The possibilities are infinite.