SpectrumLook Change Log

Version 1.5, Build 37, October 16, 2009
	- Recompiled version of CWSpectrumDll.dll

Version 1.5, Build 36, August 10, 2009
	- Now showing the parent ion m/z in the plot title
	- Added option to display the m/z values of the identified peaks in the fragmentation spectrum

Version 1.5, Build 35; August 3, 2009
	- Added ampersand mod symbol (&)
	- Now calling .AutoScaleY after adding annotations to the fragmentation spectrum
		- Necessary to allow user to read the annotation names for the most intense peaks in a spectrum
	- New versions of MZXmlFileReaderDLL.dll and MZDataFileReaderDLL.dll that fix an overflow bug when reading large .mzXML files

Version 1.5, Build 34; May 21, 2009
	- Added option for static mods to the N-terminus and K
		- Default mass for these static mods is iTRAQ (144.1021)

Version 1.5, Build 32; February 26, 2009
	- Added option to switch between CID mode (b/y ions) and ETD mode (c/z ions)
		- Used Edit->Match Settings->Fragmentation Mode

Version 1.4, Build 31; March 10, 2008
	- Updated version of MZXmlFileReaderDLL.dll
		- Now supports mzXML v3.x

Version 1.4, Build 30; March 5, 2008
	- Updated the GUI to allow the user to enter negative modification masses in the Settings window (Edit->Program and Mass Settings)

Version 1.4, Build 29; February 4, 2008
	- Fixed indexing bug that skipped the first mass value in each mass spectrum when looking for b or y ions matching theoretical masses

Version 1.4, Build 28; December 20, 2007
	- Added option for multiple losses from the b/y ions and from the parent peak
		- For example, water + water, water + ammonia

Version 1.4, Build 27; December 13, 2007
	- Now checking for loss of two water molecules from the parent peak
		-36.02 if 1+, -18.01 if 2+, and -12 if 3+
	- Recompiled with latest version of Xcalibur that supports ETD datasets

Version 1.4, Build 26; September 26, 2007
	- Now checking for and removing double or single quotes if the protein name or peptide sequence is surrounded with quotes

Version 1.4, Build 25; September 21, 2007
	- Now displays Sp for Sequest data and Log_EValue for X!Tandem data

Version 1.4, Build 24; September 20, 2007
	- Fixed bug that mis-numbered the b and y ion labels when displaying modified peptides

Version 1.4, Build 23; September 15, 2007
	- Added support for X!Tandem _xt.txt files, which are created by the Peptide Hit Results Processor
		- Already have support for Sequest _syn.txt files

Version 1.4, Build 22; June 28, 2007
	- New version of CWSpectrumDll.dll

Version 1.4, Build 21; May 8, 2007
	- Added a phosphate neutral loss mass value for 1+ spectra: loss of (98+18) = 116

Version 1.4, Build 20; December 18, 2006
	- Added one more phosphate neutral loss mass for 3+ spectra: loss of (98*2)/3 = 65.32

Version 1.4, Build 19; December 14, 2006
	- Fixed bug that used the wrong mass for phosphate neutral loss from 2+ b/y ions
	- Added a minimum mass on the m/z values shown for 2+ b/y ions; the user can edit the mass using Edit->Program and Mass Settings
	- Fragment ladder improvements
		- Updated the scrollbar on the Fragment Ladder window to scroll in the standard Windows direction
		- Changed the fonts to use a darker green and to not print in italics
		- Now displaying the ion types at the left of the fragment ladder
		- Removed the "View" button since it was unused
	- Now searching for additional phosphate neutral loss mass values from the parent ion mass
		- All spectra: loss of 98 from the parent m/z
		- 2+ spectra: loss of 98/2 = 49
		- 2+ spectra: loss of (98+18)/2 = 58
		- 2+ spectra: loss of (98*2+18)/2 = 107
		- 3+ spectra: loss of 98/3 = 32.66
		- 3+ spectra: loss of (98*2)/3 = 65.32		(actually added in Build 20)
		- 3+ spectra: loss of (98+18)/3 = 38.66
		- 3+ spectra: loss of (98*2+18)/3 = 71.32
	- Rearranged the match settings and program settings
		- Reworded many of the descriptions to more clearly explain them
	- Added ability to show/hide various annotation types, e.g. a ions, water loss, ammonia loss, etc.
	- Created a separate window for searching "all spectra for Neutral Loss"

Version 1.3, Build 18; November 16, 2006
	- Decreased maximum number of data points displayed in the grid down to 40000
		- The reason this maximum is there is that the DataGrid can only allocate a certain amount of memory, which appears to be enough for a little over 40000 rows

Version 1.3, Build 17; November 15, 2006
	- Increased maximum number of data points displayed in the grid to 60000
	- Fixed bug that incorrectly labelled some of the black peaks in the mass spectrum

Version 1.3, Build 16; October 24, 2006
	- Now looking for a .ini file with the same base name as the .raw, .mzXML, or .mzData file when opening a datafile
		- If found, the settings from the .ini file are loaded, updating the settings in memory
		- If no .Ini file is found, then the user is informed that they may wish to customize the settings in the "Match Settings" or "Other Settings" dialog boxes

Version 1.3, Build 15; October 24, 2006
	- Now hiding the controls when reading the input files
		- Updated to warn the user that loading may take a few minutes if reading an .mzXML or .mzData file larger than 15 MB
	- Updated to print column headers to the text files created using the NeutralLoss menu item commands

Version 1.3, Build 14; October 19, 2006
	- Added support for two more modification symbols
		- Now supports *, #, @, and $
	- Added option to save an annotated picture of every peptide ID in memory
		- Can save WMF files or .PNG files (similar to .GIF files)
	- Added Reset to Defaults buttons on the settings forms

Version 1.3, Build 13; September 29, 2006
	- Updated to the SP2 version of MSXML4.DLL

Version 1.3, Build 12; September 28, 2006
	- Added additional error handling messages when loading input data files
		- Useful for debugging instances where a given DLL is not registered
	- Updated the installer to include additional dependent DLLs
	- Updated to display a status message if the user selects a scan number in the peptide grid that does not have corresponding MS data in memory

Version 1.3, Build 11; September 15, 2006
	- Updated water loss from parent ions to be -18.01 if 1+, -9.005 if 2+, and -6 if 3+ since water loss is a neutral loss

Version 1.3, Build 10; September 14, 2006
	- Updated water loss from parent ion to be -18 if 1+, -9.5 if 2+, and -6.675 if 3+
	- Updated labelling of peaks to display b3-NL or b3-H2O instead of b#3 or b*3
	- Now labelling peaks that correspond to loss of ammonia (-17)
	- Change the mass of a proton from 1.01 to 1.00727649

Version 1.3, Build 9; September 14, 2006
	- Updated program to consider the assumed charge state when determining which neutral loss ions to check for
		- Tests for loss of 98 from the parent m/z ion for all charge states
		- Tests for loss of 49 from the parent m/z ion for 2+ spectra 
		- Tests for loss of 32.67 from the parent m/z ion for 3+ spectra 

Version 1.2, Build 8; August 18, 2006
	- Recompiled source due to new development computer

Version 1.2, Build 6; May 19, 2006
	- Added support for reading mzXML and mzData files
	- Created an installer for the program

Version 1.2, Build 4; May 17, 2006
	- Initial release version
	- Can read Finnigan .Raw files and Synopsis files
	- User can navigate through the spectra or browse the search results
		- The program displays the spectra and labels the peaks based on the sequence listed in the synopsis file