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<revhistory xmlns="http://docbook.org/ns/docbook" version="5.0">

	<revision>
		<revnumber>5.7.0</revnumber>
		<date>20190115</date>
		<authorinitials>fr</authorinitials>

		<revremark>

			Finished porting of the historical LaTeX-based documentation to the
			DocBook/DAPS/FOP publishing system. Please, see Colophon for details;

		</revremark>
	</revision>

	<revision>
		<revnumber>not_set</revnumber>
		<date>20150918</date>
		<authorinitials>fr</authorinitials>

		<revremark>

			Update the manual to reflect the changes in the way ion product masses are
			computed in massXpert and update the various examples. Now, the
			fragmentation specification must produce fragments that are
			uncharged. The software will then ionize the/gc
			fragments using the ionization rule currently in use in the XpertEdit module;

		</revremark>
	</revision>

	<revision>
		<revnumber>not_set</revnumber>
		<date>20121205</date>
		<authorinitials>fr</authorinitials>

		<revremark>

			Update the manual to document the various new ways to import data in the
			m/z list in the XpertMiner module;

		</revremark>
	</revision>

	<revision>
		<revnumber>not_set</revnumber>
		<date>20111022</date>
		<authorinitials>fr</authorinitials>

		<revremark>

			Update the manual to describe the new fragmentation of oligomer containing
			cross-linked monomers feature;

		</revremark>
	</revision>

	<revision>
		<revnumber>not_set</revnumber>
		<date>20110829</date>
		<authorinitials>fr</authorinitials>

		<revremark>

			Update the manual to describe a number of new features;

		</revremark>
	</revision>

	<revision>
		<revnumber>not_set</revnumber>
		<date>20100429</date>
		<authorinitials>fr</authorinitials>

		<revremark>

			Updated the section about the definition of monomers to document the new
			feature about computing the mass difference between any two monomers in
			the definition;

		</revremark>
	</revision>

	<revision>
		<revnumber>not_set</revnumber>
		<date>20100427</date>
		<authorinitials>fr</authorinitials>

		<revremark>

			Updated the section about the cleavages of polymer sequences (XpertEdit
			chapter) to document the new feature that allows to only perform a
			cleavage in the currently selected region of a polymer sequence;

		</revremark>
	</revision>

	<revision>
		<revnumber>not_set</revnumber>
		<date>20090619</date>
		<authorinitials>fr</authorinitials>

		<revremark>

			Updated the section about the chemical pad (XpertCalc chapter) to reflect
			improvements in the use of the chemical pad buttons (either immediate
			evaluation of the formula or mere insertion of the formula in the formula
			line edit widget);

		</revremark>
	</revision>

	<revision>
		<revnumber>not_set</revnumber>
		<date>20090617</date>
		<authorinitials>fr</authorinitials>

		<revremark>

			Updated the section about the chemical pad (XpertCalc chapter) to reflect
			improvements in the graphical display of the chemical pad buttons as
			programmed in the chem_pad.conf configuration files;

		</revremark>
	</revision>

	<revision>
		<revnumber>not_set</revnumber>
		<date>20090401</date>
		<authorinitials>fr</authorinitials>

		<revremark>

			Although not visible in the documentation, I wanted to publically extend
			my warm thanks to Lionel Élie Mamane, who helped me along these last
			months with the Debian packaging of massXpert. Note that this work also
			proved useful for other areas in the project.

		</revremark>
	</revision>

	<revision>
		<revnumber>not_set</revnumber>
		<date>20090220</date>
		<authorinitials>fr</authorinitials>

		<revremark>

			Updated the XpertEdit chapter to show how to configure the options about the
			number of decimals to be used for display of numerals in the program;

		</revremark>
	</revision>

	<revision>
		<revnumber>not_set</revnumber>
		<date>20090205</date>
		<authorinitials>fr</authorinitials>

		<revremark>

			Updated the XpertEdit chapter to show the simplified polymer sequence editing
			feature whereby editing of the sequence might be performed by clicking on
			monomer items in the list of all the monomers defined in the polymer
			chemistry definition. Fixed small bug in the documentation of about
			multi-region selection behaving as oligomers or residual chains.

		</revremark>
	</revision>

	<revision>
		<revnumber>not_set</revnumber>
		<date>20081211</date>
		<authorinitials>fr</authorinitials>

		<revremark>

			Updated the XpertEdit chapter to show the feature by which it is now
			possible to force the calculation engine to take into account the
			left/right end modification(s) when calculating the masses of a sequence
			region that does not encompass the left/right end of the polymer sequence.
			This new feature was essential in trying to perform full simulations of
			the molecular heterogeneity of the telokin protein (Rusconi et al.  1997
			Biochemistry). Added a paragraph about max count of chemical modifications
			of a given monomer at once in the XpertDef chapter and another one in the
			XpertEdit chapter to explain its working;

		</revremark>
	</revision>

	<revision>
		<revnumber>not_set</revnumber>
		<date>20080911</date>
		<authorinitials>fr</authorinitials>

		<revremark>

			Finally indexed the whole document. Performed some minor modifications so
			that the documentation system does not produce HTML files anymore (the
			HTML production was not really worth it anyways);

		</revremark>
	</revision>

	<revision>
		<revnumber>not_set</revnumber>
		<date>20080805</date>
		<authorinitials>fr</authorinitials>

		<revremark>

			Updated the user manual with a bunch of updated screen shots;

		</revremark>
	</revision>

	<revision>
		<revnumber>not_set</revnumber>
		<date>20080730</date>
		<authorinitials>fr</authorinitials>

		<revremark>

			Updated the XpertMiner chapter to illustrate the m/z--z mass list matching
			feature;

		</revremark>
	</revision>

	<revision>
		<revnumber>not_set</revnumber>
		<date>20080708</date>
		<authorinitials>fr</authorinitials>

		<revremark>

			Updated the XpertEdit chapter to illustrate the new multi-cleavage feature;

		</revremark>
	</revision>

	<revision>
		<revnumber>not_set</revnumber>
		<date>20080701</date>
		<authorinitials>fr</authorinitials>

		<revremark>

			Updated the XpertEdit chapter to illustrate the new multi-region and
			multi-selection features;

		</revremark>
	</revision>

	<revision>
		<revnumber>not_set</revnumber>
		<date>20080529</date>
		<authorinitials>fr</authorinitials>

		<revremark>

			Changed the install instructions for the Mac OS X system;

		</revremark>
	</revision>

	<revision>
		<revnumber>not_set</revnumber>
		<date>20080527</date>
		<authorinitials>fr</authorinitials>

		<revremark>

			Added a chapter about XpertMiner to document the new features in that module.
			Some fixes here and there.

		</revremark>
	</revision>

	<revision>
		<revnumber>not_set</revnumber>
		<date>20080526</date>
		<authorinitials>fr</authorinitials>

		<revremark>

			Modified the documentation to reflect switch to version 3 of the GNU
			General Public License;

		</revremark>
	</revision>

	<revision>
		<revnumber>not_set</revnumber>
		<date>20080425</date>
		<authorinitials>fr</authorinitials>

		<revremark>

			The installation chapter was updated to illustrate the installation of the
			software in the Mac OS X system;

		</revremark>
	</revision>

	<revision>
		<revnumber>not_set</revnumber>
		<date>20080424</date>
		<authorinitials>fr</authorinitials>

		<revremark>

			The installation chapter was updated to reflect the changes in the way the
			package might be installed (the package is now relocatable, provided the
			user indicates where the directories are located);

		</revremark>
	</revision>

	<revision>
		<revnumber>not_set</revnumber>
		<date>20080402</date>
		<authorinitials>fr</authorinitials>

		<revremark>

			The XpertDef chapter was updated to detail the new way of defining
			fragmentation specifications where the side chain is decomposed in the
			gas-phase. The section about fragmentations is now much better documented;

		</revremark>
	</revision>

	<revision>
		<revnumber>not_set</revnumber>
		<date>20080330</date>
		<authorinitials>fr</authorinitials>

		<revremark>

			The XpertEdit chapter was updated to include a description of the new
			fragmentation/mass searching data in-place filtering. A section is now
			devoted to data filtering;

		</revremark>
	</revision>

	<revision>
		<revnumber>not_set</revnumber>
		<date>20080325</date>
		<authorinitials>fr</authorinitials>

		<revremark>

			The XpertEdit chapter was updated to include a description of the new sequence
			cleavage data in-place filtering;

		</revremark>
	</revision>

	<revision>
		<revnumber>not_set</revnumber>
		<date>20080318</date>
		<authorinitials>fr</authorinitials>

		<revremark>

			The XpertEdit chapter was updated to include a description of the find
			sequence motif feature;

		</revremark>
	</revision>

	<revision>
		<revnumber>not_set</revnumber>
		<date>20080313</date>
		<authorinitials>fr</authorinitials>

		<revremark>

			The XpertEdit chapter was
			updated to include a new paragraph about monomer cross-linking as
			this is now implemented in the software;

		</revremark>
	</revision>

	<revision>
		<revnumber>not_set</revnumber>
		<date>20080221</date>
		<authorinitials>fr</authorinitials>

		<revremark>

			The XpertEdit chapter was
			updated to include a new figure of the polymer modification
			procedure and to describe the enhanced modification procedure;

		</revremark>
	</revision>

	<revision>
		<revnumber>not_set</revnumber>
		<date>20080215</date>
		<authorinitials>fr</authorinitials>

		<revremark>

			The XpertEdit chapter was
			updated to include a new figure of the monomer modification
			procedure and to describe the enhanced modification procedure;

		</revremark>
	</revision>

	<revision>
		<revnumber>not_set</revnumber>
		<date>20071217</date>
		<authorinitials>fr</authorinitials>

		<revremark>

			The chapter about installation of massXpert has been rewritten to reflect
			changes in the building of massXpert and in the installation of Debian
			GNU/Linux and Fedora core GNU/Linux packages;

		</revremark>
	</revision>

	<revision>
		<revnumber>not_set</revnumber>
		<date>20071216</date>
		<authorinitials>fr</authorinitials>

		<revremark>

			The chapter about polymer
			chemistry definitions has been refactored to reflect the rewriting
			of the corresponding code. Added a small section about m/z ratio
			calculation, that was missing, although the feature was added a long
			time ago;

		</revremark>
	</revision>

	<revision>
		<revnumber>not_set</revnumber>
		<date>20070922</date>
		<authorinitials>fr</authorinitials>

		<revremark>

			The new multi-charged cleavage and fragmentation oligomers have been
			documented;

		</revremark>
	</revision>

	<revision>
		<revnumber>not_set</revnumber>
		<date>20070819</date>
		<authorinitials>fr</authorinitials>

		<revremark>

			Switched back to version 2 of the GPL in the Appendices chapters, as
			massXpert cannot be licensed otherwise: the Qt libraries are licensed using
			version 2 of the GPL without the ``or any later version, at your option''
			wording;

		</revremark>
	</revision>

	<revision>
		<revnumber>not_set</revnumber>
		<date>20070728</date>
		<authorinitials>fr</authorinitials>

		<revremark>

			Updated the XpertDef chapter (modifications) to show the new ``targets''
			feature. Updated the XpertEdit chapter to show the new monomer modification
			dialog.

		</revremark>
	</revision>

	<revision>
		<revnumber>not_set</revnumber>
		<date>20070719</date>
		<authorinitials>fr</authorinitials>

		<revremark>

			Added explanation on the arbitrary formula-based polymer sequence ends
			modification.

		</revremark>
	</revision>

	<revision>
		<revnumber>not_set</revnumber>
		<date>20070713</date>
		<authorinitials>fr</authorinitials>

		<revremark>

			Revision of the whole document for a better printed output;

		</revremark>
	</revision>

	<revision>
		<revnumber>not_set</revnumber>
		<date>20070710</date>
		<authorinitials>fr</authorinitials>

		<revremark>

			Added a section to the XpertEdit chapter about the data mining mass list lab
			feature added recently.  Mentioned the installation of
			Debian packages;

		</revremark>
	</revision>

	<revision>
		<revnumber>not_set</revnumber>
		<date>20070630</date>
		<authorinitials>fr</authorinitials>

		<revremark>

			Switched the project and all accompanying documentation and other data
			files to GPL version 3; 

		</revremark>
	</revision>

	<revision>
		<revnumber>not_set</revnumber>
		<date>2007 mid-june</date>
		<authorinitials>fr</authorinitials>

		<revremark>

			Start of the writing by taking inspiration of the GNU polyxmass manual.

		</revremark>
	</revision>

</revhistory>


