FUGE bioinformatics platform FUGE
 
Platform partners:
UiB
UiO
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Research:
Recent publications
Online tools:
BOMP
ELM
Ka/Ks calculation
LIPO
Pratt
RegExpMaker
Spratt
WEBnm@
TMM@
XHM
ParAlign
Stitchprofiles
Genetools
siRNA
TargetBoost
BLAST
preAssemble

bioportal.uio.no
Databases:
CHRABCHRAB
TAEDTAED
PubGenePubgene
repairGenesrepairGenes
Software:
J-Express
Phyrex
SciCraft
Softparsmap
MassSorter
RBR and xsact
Widget Toolbox:
Alignment Conversion
Sequence Conversion
Tree Conversion
Alignment to coding
Site map
===============
RELEASE NOTES
===============

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Changes from v3.00 to v3.1
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  • Increased the accuracy for the modification masses and for the mass of a proton.

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Changes from v2.00.02 to v3.00
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  • The user interface has been updated with a more modern platform idependent look.
  • Some minor (mainly) graphical user interface bugs have been fixed.
  • The help files have been updated.

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Changes from v1.05.04 to v2.00.02
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  • The concept of a Project is added to make the creation of an data sheet table easier. A wizard to create a Project is also added.
  • Importing experimental data is now easier and more data formats are supported (XML, delimited text files, cut and paste).
  • It is now possible to add, remove or alter experimental data from/in the current DST.
  • It is also possible to alter the theoretical data in the current DST.
  • The accuracy used for a the comparison in given DST can be altered without having to recreate the DST.
  • Filters can now be added and removed from the current DST without having to recreate the DST.
  • The graphics in the plot windows are improved and a lot of smaller graphical bugs are fixed.
  • The graphical user interface is updated and the text is improved and unified.
  • A Welcome-window is added.
  • The order of the experimental data in the DST can now be altered via the new Add Experimental data window.
  • A residual plot is added to the Report.
  • Hydropathy can now be colored coded in the fractional mass and accuracy plot.
  • Regression lines are added to the fractional mass plot which can be switched on or off.
  • Filternames with spaces are now allowed.
  • Hits inserted from SequenceSuggester and UniMod are now included in the coverage calculations.
  • The correct edt's are now shown when selecting a data point in the plots.
  • Help files and tutorial are updated.
  • Tooltips are updated or added.
  • The "Ribbon"-model in the ProteinViewer is no longer available, due to the page providing the data no longer exists.
  • The ChangeModifications tool had become absolete and has therfore been removed.
  • Adding or removing data in the ConsideredModifications lists can now be done be double clicking on the given item(s).
  • The problems with some plotting colors changing after selection are now fixed.
  • The regression lines are now not drawn if the data only contains one data point.
  • The files names shown at the top of the frames are now shortened to only include Project name and file name.
  • Made it easier to import more then one experimental data file.
  • Creating new Modifications is moved from the main window to the windows where modifications are used (ProteinDigester etc.).
  • Theoretical and experimental data can now be accessed by rightclicking on the column header in the DST.
  • EDT filenames can now included spaces.
  • The last visited folder is now remembered.
  • Fixed a bug in Report where a cutting site was disregarded if it was the last aminoacid in the sequence.
  • A list of the recently opened files are added to the file menu in the main window.
  • Right clicking in the modifcations column in the DST now brings up data on the modifications (if any) at the given row.
  • MassSorter can now also be run from a folder starting with "//" (in addtion to "C:", "D:" etc.).

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Changes from v1.05.03 to v1.05.04
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  • The possibility of creating a plot of the fractional masses (also called HDPR-plot) has been added.
  • The Report is now extended with the display of the combined sequence coverage of all experiments. This can also be visualized on the 3D model.
  • The TBT window is improved. The parameters used when doing the digestion is now displayed along with the protein sequence.
  • The user is now asked if he/she wants to save before closing an unsaved or altered EDT, TBT, modifications or DST window.
  • When importing a sequence into ProteinDigester, SequenceSuggester and MassFinder lines beginning with ">" are now ignored. Sequences in the Fasta format can therefore easily be imported.
  • Numbers between the residues are also ignored when processing a sequence in ProteinDigester, SequenceSuggester or MassFinder.
  • It is now possible to create an empty EDT. This makes it easier to import data from external formats.
  • ProteinDigester has now completely replaced the importing of theoretical data from MS-Digest.
  • An error message is now given if a user tries to run MassSorter on Linux on a path containing spaces.
  • It is now possible to position the Help-window behind the other windows.
  • Average (and not mono) amino acid mass is now used for the calculation of molecular mass for the proteins digested by ProteinDigester.
  • The proteins molecular mass is now displayed in the TBT window.
  • An error message is now shown if the user tries to start MassSorter from within the zip file without unzipping it first.
  • Right clicking on a modification cell (ex. "2gk, 1om") in the DST now brings up the details about the modification(s).
  • The Help menus are extended and language corrections have been performed.
  • Pasting into the tables is now supported in the EDT and TBT windows.
  • The use of "Delete" to delete only the contents of the selected cells is also added to the EDT and TBT tables.
  • Made some smaller improvements/corrections in the EDT/TBT windows.

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Changes from v1.05.02 to v1.05.03
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  • The default available memory size is now increased. This will hopefully remove the "out of memory error" that earlier could occur when using the ProteinViewer.
  • All the model types in the ProteinViewer is now available.
  • The model type "Ribbons" retrieves the secondary structure elements from http://www.rcsb.org, and uses them on the 3D model.
  • Fixed a bug that occured in the accuracy plot when the first match was a match with a filter.
  • Made it possible for the user to decide if matches with filters appears in the accuracy plot.
  • Added the possibility of drawing lines between the data points in the accuracy plot.
  • Enhanced the appearence of the "Peak details" presented when clicking on a data point in the accuracy plot.
  • Fixed two minor bugs in the EDT and TBT tables that caused an exception to be thrown when the selection type was not set.
  • Fixed a similar bug in the SequenceSuggester.

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Changes from v1.05.01 to v1.05.02
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  • The displaying of hits with filter masses in the accuracy plot can now be turned on and off. (The regression line is then updated.)
  • The "selection type" is now reused when opening an EDT/TBT from an EDT/TBT window.
  • Fixed a bug that made part of the text in the Options window not visible.
  • Fixed a bug with non-integer numbers in ChangeModification.
  • "Atom nr." is altered to "Element nr." in the Atom details window.
  • The correct residue name is now used in the Atom details window.
  • The accuracy type is now saved with a DST file.
  • Some minor visual updates on the "question-windows".
  • Fixed a bug that made it impossible to open old DST files.

-------------------------------------------
Changes from v1.04 to v1.05.01
-------------------------------------------
  • Added graphics for the accuracy statistics. A plot of the m/z values against the accuracy values.
  • It is possible to click on a point in the plot and get details on the given experimental value.
  • The plots can be exported to png-files.
  • Fixed a bug in the DST that sometimes removed the greyscaling of selected rows.
  • Added "Ctrl+D" as a shortcut for removing rows in the EDT and TBT tables.
  • Intensity is now set to zero for masses added to an EDT if no intensity is given.
  • Made it possible to create DSTs based on EDTs from different folders.
  • Simplified the check for "MassSorterHome".
  • The unimod search and results windows are combined into one window and the results is now presented as an html table.
  • A filter is added when searching the unimod database.
  • Made it possible to highlight rows with user-selected colors.
  • Removed a bug that created an error when the Report or the Protein- Viewer contained a unimod modification.
  • Fixed a problem with the scrollbar and the size of the main window.
  • Removed System.out.exit(1)'s from the ProteinViewer package.
  • Linux-problem: modification data now appears in the middle of the screen and not in the upper left corner.
  • Made it possible to use Da in the accuracy plots.
  • Fixed a bug in the accuracy statistics that showed vales like 0.0600000001 Da. Now changed to 0.06 Da.
  • Da accuracy values is now rounded of to four decimals.
  • Added the possibility of altering the plot colors.
  • Fixed a bug with "Hide description" in the EDT which showed parts of the window which should be hidden.
  • Made it possible to display more then one unimodsearch at the time.
  • The cursor changes to a cross when over a data point in the accuracy plot.
  • Altered the unimod boundries. Uses "-" for the negative boundries. Also added some larger upper boundries.
  • Fixed a problem with the plot having the same color as the axis.
  • Added the possibility of displaying linear regression lines for the accuracy plots.
  • Fixed a bug that caused the apply button not to work when altering the intensity ranges.
  • Updated the tutorial
  • Updated the help files.

----------------------------------------
Changes from v1.03 to v1.04
----------------------------------------
  • Made it possible to alter the color and style of how detected peptides and modifications are shown in the Report.
  • Saves the default ppm/Da-values.
  • Both ppm and Da can be used as accuracy measurements.
  • The appearance of MassInfo and ColumnInfo has been updated.
  • Fixed a bug that set the number of secondary matches and the number of matches with filters to zero in the Report if "Hide secondary matches" or "Hide filtered matches" were selected.
  • Created a connection between the ProteinViewer and the DST. This makes it possible to click on an atom in the ProteinViewer and get the details about all the peptides passing through the given residue.
  • The cursor now changes to a "text cursor" when held over text areas.
  • All tables are updated such that a "resize cursor" appears when the cursor is positioned in the column headers between two columns.
  • An update of the consistent use of left, right or centering of text in text fields.
  • Links are added in the Peptide statistics window.
  • Average peptide mass is added to the Peptide statistics.
  • Select primary is removed from the "Edit" menu. Is now only available by right clicking on the given cell.
  • Altered how the users access the enzyme information. The users no longer has to interact directly with the *.enz files.
  • The enzyme lists in the ProteinDigester and the SequenceSuggester is now sorted alphabetically.
  • Added the possibility of choosing the starting residue and the protein chain in the ProteinDigester and the SequenceSuggester.
  • Linux-problem: the wait-cursor is now turned of when the CreateDST window is opened.
  • Linux-problem: the problems with �hide description� are fixed.
  • System.out.println's are removed from the ProteinViewer package.
  • Color coding in the ProteinViewer (residues, modifications, amino acids and detected vs. undetected peptides).
  • ProteinViewer can now be opened directly from the main window.
  • Created a window displaying both atom and peptide details at the same time. Along with a 2D model of the protein sequence. (Used in ProteinViewer.)
  • Updated the appearance of the SequenceSuggesterResults.
  • Linux-problem: fixed a bug that made the modification window appearing in the upper left corner.
  • Added color grading to the DST table.
  • Consistent use of "OK" instead of "Ok" on buttons.
  • Updated the help files.

-----------------------------------------
Changes from v1.02 to v1.03
-----------------------------------------
  • Standard deviation added to the peptide length statistics.
  • Removed an error in the Report and SequenceSuggesterResults that marked too many cleavage sites (i.e. R|P for trypsin).
  • The mouse pointer morphs into <--> when between two column headers in the DST and CreateDST tables.
  • Added tool-tips to all enzyme combo boxes, displaying the complete enzyme name.
  • Some smaller changes to the graphical user interface.
Home

Download MassSorter v3.1

How to Install MassSorter

Tutorial

Example Scenario: MMP2

Licence and Copyrights

Release Notes

Screenshots

Documentation (pdf)



Papers About MassSorter:

BMC Bioinformatics:


Methods in Molecular Biology:



Papers Using MassSorter:

JournalOfBacteriology: