What's new in massXpert 3.4.0
Jan 15, 2013
- Implemented a feature that allows one to enter a coordinates string in the sequence editor window so as to select a specific sequence, make a multi-region selection, or make a multi-selection region;
- The mzLab GUI has been refactored so as to greatly simplify its use;
- The French translation has been updated.
New in massXpert 3.3.0 (Jan 15, 2013)
- Implemented new ways to share mass data between the three main simulations contexts (polymer cleavage, oligomer fragmentation and arbitrary mass searches, of within the XpertEdit module) and the MzLab in the XpertMiner module. Also, it is now possible to first export the data from the three simulations contexts to either a file or the clipboard, to crunch the data in any way and format these data so as to reimport them in the XpertMiner module. An a posteriori connnection is now possible between the reimported data and the polymer sequence that generated these data in the first place by providing the MzLab with the identifier of the polymer sequence editor in which the proper polymer sequence has been loaded. This allows for maximum flexibility when analyzing the data, such that it is possible at any time to visualize the corresponding oligomer in the sequence editor upon clicking on any mass list item of the MzLab. All this is documented in the massXpert.pdf user manual.
New in massXpert 3.2.0 (Oct 24, 2011)
- Implemented new feature by which it is now possible to account for cross-links when simulating oligomer fragmentations. Only cross-links that involve monomers all contained in the fragmenting oligomer are taken into account.
New in massXpert 3.1.0 (Aug 30, 2011)
- Improvements in the XpertMiner module that make working with lists easier;
- Fixed calculation bug which appeared when computing the isotopic cluster of a large polymer with low resolution... the peak shape would not be centered in the average centroid value.
- Added a full spectrum simulation feature that allows one to compute a spectrum (optionally with all the isotopic clusters) on the basis of a list of oligomers obtained by cleavage of a given polymer;
- Same as above but after computing a set of m/z ratios starting from a chemical formula;
- Updated the user manual to document a number of new features since last update.
New in massXpert 3.0.0 (Jul 23, 2011)
- Thorough rewrite of the XpertMiner module with a load of new features and a great many improvements/fixes.
New in massXpert 2.9.0 (Jul 18, 2011)
- Switched to the TableView data display method the whole XpertMiner module. This allows for easier code maintaining and for clearer graphical user interface.
- Refactored code in the MzLabInputOligomerTreeView class code to improve quality and readability.
- Improved the XpertMiner window layout for more clarity.
- Added feature to call a calculator window right from the sequence editor window with either whole/selected sequence masses preseeded.
New in massXpert 2.8.0 (Jul 12, 2011)
- Changed the mass search oligomer display from a tree view to a table view which is simpler, both programmatically and functionally (for the user). That fixes a bug that would occasionally crash the software.
New in massXpert 2.7.0 (Jul 6, 2011)
- Changed the fragmentation oligomer display from a tree view to a table view which is simpler, both programmatically and functionally (for the user);
- Added the possibility to stack in the same table view fragmentation oligomers that come from different fragmentation simulations.
New in massXpert 2.6.0 (Jun 30, 2011)
- Finished improving (by a full rewrite) the isotopic cluster prediction for any chemical formula in the massXpert software. The program now runs eight times as fast as the previous version. Further, the simulations can now be performed either using the gaussian calculation or the lorentzian simulation.
New in massXpert 2.5.2 (Jun 7, 2011)
- Fix to critical regression bug introduced in version 2.5.1 which made the program crash in any kind of oligomer fragmentation.
New in massXpert 2.5.0 (May 25, 2011)
- Added feature : ability to select -H20 and -NH3 (also to set a manually-defined formula) as additional decompositions to be handled while computing fragment oligomers.
New in massXpert 2.4.0 (Jan 4, 2011)
- Fixed a problem with considering that the lightest isotope was necessarily the most abundant isotope.
- In fact this is true for the main chemical elements in biological matter, but can be not true for other chemical elements.
- This fix will only matter to people using chemical elements of which the most abundant isotope is not the lightest one.
New in massXpert 2.3.6 (May 11, 2010)
- Added an alert that triggers itself when the user tries to cleave a polymer sequence region that does not encompass all the cross-linked monomers, as this would yield non faithful oligomers;
- Fixed a small GUI bug in the sequence editor;
- Fixed a linker flag in the build of massXpert for the PPC platform (thanks to Koen van der Drift of the Fink project).
New in massXpert 2.3.5 (May 3, 2010)
- Added feature to compute the mass difference between any two monomers in the currently opened polymer chemistry definition;
- Modified the GUI of the monomer definition dialog in the XpertDef module so that masses of any monomer currently selected or upon modification of the formula are updated automatically;
- Updated the user manual to document the new feature.
New in massXpert 2.2.0 (Apr 22, 2010)
- New setup package for MS-Windows released. That new package contains a library (dll file) that was lacking in the previous setup file.
New in massXpert 2.0.9 (Nov 27, 2009)
- Bug fix release: fixes a bug that was crashing massXpert upon certain corner polymer sequence cleavage cases. Please, upgrade.
- The user manual is no more shipped within the MS-Windows and MacOSX and source packages. This almost divides by two the size of the packages. Please, download the user manual from the UserManual page.
New in massXpert 2.0.8 (Nov 23, 2009)
- Add the nucac polymer chemistry definition to include monomers from DNA and RNA, as sometimes polymer sequences inlcude both deoxy-ribo-nucleotides;
- Fixed bug with failed parsing of cleavage specifications which have multicharacter codes involved in their definition if the number of characters was less than the max authorized code length;
- Formulas now accept a double-quoted title and any number of spaces, like : "acetylation" -H + COCH3;
- Improve fragmentation definitions for the dna polymer chemistry definition;
- Each polymer chemistry definition-specific calculator window now has its own geometry settings;
- Fix two potentially massive memory leaks, thanks to the cppcheck utility;
- Fix monomer def for uracile;
- Added feature to regularly recall to the user to cite massXpert in the About dialog window.
New in massXpert 2.0.7 (Oct 7, 2009)
- XpertCalc: added possibility to insert formulas in the formula line edit by Ctrl-clicking buttons in the chemical keypad;
- XpertCalc: added possibility to surround formulas with spaces for much better readability in case of complex structures. This is performed by Shit-Ctrl-cliking on the chemical pad buttons;
- XpertCalc: automatically seed m/z calculation dialog window with masses from the XpertCalc main window;
- XpertEdit: bug fix in the sequence editor's feedback to the user upon entering a bad monomer code character. When a new valid character is entered this old error message is removed;
- XpertCalc: added lots of useful buttons to the dna chemical pad configuration file;
- Added bibliographical reference to the massXpert paper in _Bioinformatics_ to the man pages;
- XpertCalc: added possibility to store formula in a drop-down list so as to be able to recall them in ulterior calculations;
- XpertCalc: implemented new feature by which it is possible to set a title to a formula like the following : "initial-dimer" C5H6O9P3, which will be interpreted as formula "C5H6O9P3".
- Sequence editing plugins: added possibility to perform more sophisticated translation, like from codon to 1-letter code or from codon to 3-letters code (protein chemistry);
- XpertEdit: the tool box (available monomers/mass calculation engine configuration) now saves its position;
- Improved the CMake-based build system to automatically build the binary and the data if nothing is specified on the configuration command line (usermanual is not built by default; thanks to Pere Constans for reporting);
- Bunch of code tidying and memory leaks fixing (thanks to cppcheck, as suggested by Pere Constans);
- XpertEdit: fixed wrong behaviour in the whole/selected sequence logic in the mass search dialog window;
- XpertEdit: fixed the multi-character code disambiguation mechanism in the sequence editor's available codes tool box widget: it's triggered by hitting Ctrl-Enter;
- Xpertedit/XpertDef: improved feedback to the user on file save operation errors;
- XpertEdit/XpertDef: added possibility to show non-*.mxp/non-*.xml files in the openfile dialogs;
- XpertEdit: improved fragmentation with multiply-charged fragments: When there are multiply-charged fragments, the mass now takes into account the ionization rule that sits in the sequence editor windows's calculation engine configuration.
- XpertEdit: fix bug in elementalComposition() that would fail when count is negative. Added simplify() function that calls elementalComposition() in turn. Also fixed the way atomCount objects are added to the list of such objects : when an atomCount object reaches a 0-count, it gets removed from the list.
- XpertCalc: added possibility to simplify a complex set of formulas into a single factorized formula.
New in massXpert 2.0.5 (Sep 21, 2009)
- Bug fix release: fixed a bug that would crash the program upon re-cleavage of a polymer sequence in the same cleavage dialog window.
New in massXpert 2.0.4 (Sep 10, 2009)
- Fix a bug due to not clearing effectively seed/result masses when using the chemical pad;
- Rework the chemical pad configuration process by adding the ability to both group pad buttons according to user's desires and color the buttons' test and background to ease readability when lots of buttons are stuffed in the chemical pad (which is the case for me when I deal with saccharides);
- Add possibility to send the chemical pad button's formula to the formula line edit widget in the calculator's main window (very useful when dealing with long successions of computations like when constructing a ramified oligosaccharide);
- Completed the French translation, which also happened to trigger better naming of features in English;
- Update the User Manual with a description of the new features.
New in massXpert 2.0.1 (Apr 16, 2009)
- Fixed bug due to not taking into account the locale while exporting oligomer results as text;
- Fixed small glitches with locale-specific input/output in the graphical user interface;
- Bettered the faithfullness of the textual representation of results exported as text: sorting/filtering in the result treeviews now reflects fully in the exported text;
- Switched to UseLATEX.cmake for building the user manual.
New in massXpert 1.9.9 (Apr 2, 2009)
- Fixed bug with the file writing process (polymer chemistry definitions and polymer sequences) which would lead to unusable files.
- Fixed XpertDef crash due to not checking if a modification is used by a cross-linker prior to removing it from the definition.
New in massXpert 1.9.8 (Mar 26, 2009)
- Fixed sorting of fragmentation oligomers based on their name.
New in massXpert 1.9.5 (Mar 14, 2009)
- Bug fix: when computing partial cleavage of a sequence holding KD motifs, and asking the cleavage to cut according to "/D;K/", for example, the partial cleavage algorithm failed. Indeed, missing the cut at KD might be due to missing the cut at /D but also missing the cut at K/ !!
- Feature improvement: added the ability to edit a polymer sequence by simply clicking onto items in a list of available monomers. Useful feature when one has lots of monomers in a polymer chemistry definition... and remembering them all is difficult.
- Note that the 1.9.0 bump is because we consider massXpert to be nearing the featureful state we designed it for in the first place.
New in massXpert 1.8.1 (Dec 18, 2008)
- Bug fix release and feature improvement about cleaving a polymer sequence asking that masses be computed with no charge at all (that is the molecular weight of the oligomer and not of the ion is provided).
- There was a bug that would crash the program if, after a cleavage that would provide no oligomers (the treeview is empty), another cleavage was performed. This has been fixed.
New in massXpert 1.8.0-1 (Dec 16, 2008)
- Fixing a problem with mangled symbols crashing the program in some circumstances.
New in massXpert 1.8.0 (Dec 13, 2008)
- A crash would occur upon pasting, in the sequence editor, of text containing invalid monomer codes, thus triggering the "sequence purification feature". This is a pure regression. It has been fixed now. Sorry for any inconvenience. Only source/MS-Windows packages are ready at the present time.
New in massXpert 1.7.9 (Dec 11, 2008)
- Potent improvements to the list matching feature in the mzLab;
- Added ability to define the maximum number by which a single monomer might be modified with one given modification. This is typically useful with making multiple methylation modifications to lysyl or arginyl residues;
- Many fixes and improvements in the mzLab XpertMiner module (masses of fragments are now treated problem with respect to their charge);
- Implemented a work-flow by which masses dropped from a cleavage/fragmentation/mass search results window into the mzLab retain their connection with the sequence that generated them in the first place, so that it is possible to display the corresponding sequence when double-clicking onto them;
- Implemented a connection between the cross-links listed in the list of current cross-links and their corresponding cross-linked oligomers, such that it is possible to display them automatically in the sequence editor upon double-clicking of a cross-link item in the list;
- Improved the saccharide polymer chemistry definition;
- Indexed the user manual;
- Fixed bug which would crash the program upon selection of a sequence starting after its last monomer;
- Fixed bug which would crash the program upon trying to select an empty sequence;
- Fix of a recently-introduced bug about calculation of the right end boundary of fragments;
- Fix of a regression in the mechanics of uncross-linking monomers;
- Does not connect anymore to massxpert.org to probe for usage (never worked, in fact);
- Internally, implemented Oligomer as a class derived from Sequence so that it is possible to store the sequence of the oligomer inside it
- Internally, very much improved the cleavage oligomer/fragment oligomer charge handling (fragmentation-generated oligomers' charge is handled very differently than the cleavage oligomers' charge);
- GUI improvements;
- Bug fixes here and there;
- Updated the documentation.
New in massXpert 1.7.8 (Jul 9, 2008)
- Implemented the possibility to add oligomers obtained via cleavage with different cleaving agents in the same window;
- Updated the User Manual;
- Usual bug fixes.
New in massXpert 1.7.7 (Jul 7, 2008)
- Implemented a new powerful feature: multi-region selection and multi-selection regions. Multi-region selections make it possible to select any number of polymer sequence regions which are all distinct. Multi-selection regions make it possible to select overlapping sequences in the polymer sequence. These selections make it possible to simulate cross-linked oligomers (typically disulfide bond-linked pepties, for example) directly from the sequence editor.
- Updated the User Manual;
- Usual bug fixes.
New in massXpert 1.7.5 (Apr 26, 2008)
- Finally one Mac OS X package;
- The whole software program is now relocatable;
- The french translation is now 100 % complete;
- Huge code cleanup work, along with implementation of namespaces in the whole project;
- Some classes added along with some existing classes redesigned;
- Bug fixes here and there;
- Updated the documentation.
New in massXpert 1.7.4 (Apr 3, 2008)
- Implemented a new fragmentation specification method for fragmentation patterns where the monomer undergoing fragmentation has its lateral chain decomposed. This is particularly useful in nucleic acids chemistry where the nucleic base might be eliminated at the monomer undergoing fragmentation according to the pattern `a';
- Updated the french translation;
- Fixed memory leak and bugs;
- Updated the user manual.
New in massXpert 1.7.1 (Mar 20, 2008)
- Implemented intra-molecular cross-links. For protein chemists, this means that sulfide bonds are now handled in the sequence and that simulation of the fluorescent proteins also (their chromophore is created by internal cross-links involving three monomers). Because this new feature required extensive rewrite of the internals of massXpert, I suspect that bugs might have crept in. So, please, be sure to double-check your results prior to publication;
- Implemented find sequence motif in polymer sequence. This is a rather simple implementation but a very handy one when long polymer sequences are dealt with;
- Fixed a serious bug with how composite formulas are handled in certain cases. You should really be upgrading to version 1.7.1 for this reason;
- Various bug fixes and other small improvements.