MSMS Spectra Preprocessor Change Log Version 1.7.3507; August 8, 2009 - New version of MsMsSpectrumFilter.dll that has 3 modes for matching collision mode (Exact, Contains, or RegEx) - The GUI will always set MSCollisionModeMatchType to "Contains" Version 1.7.3492; July 24, 2009 - New version of MsMsSpectrumFilter.dll that has support for filtering by collision mode (e.g. etd or cid) - Updated GUI to include MS Collision Mode Filter textbox Version 1.6.2991; March 10, 2008 - New version of MsMsSpectrumFilter.dll that has interface ISpectraFilter defined in AnalysisManagerProg.exe rather than in AnalysisManagerBase.dll Version 1.6.2959; February 7, 2008 - Updated to always compute and report the score values for Filter Mode 1 and Filter Mode2 if either filter mode is selected - The value in column Quality_Score will depend on the filter mode chosen - If Evaluate Spectrum Quality Only is unchecked, then the score value used to filter spectra will also depend on the filter mode chosen - Added option to use Log(Intensity) values when computing the Filter Mode 1 score values - The default mode when using the program with the GUI is now "Evaluate Spectrum Quality Only" Version 1.5.2958; February 6, 2008 - Expanded the functionality of the Intensity Threshold Filter (Filter Mode 2) Version 1.5.2957; February 5, 2008 - Updated the Amino Acid Spacing Filter (Mode 1) to choose the top data points to examine using S/N rather than raw abundance - By default, the top 50 data points with S/N values >= 5 are used - Improved the scoring scheme used by the Amino Acid Spacing Filter to consider all possible ion pairing options for a given data point, but only keep the match with the highest product of LightMember_S/N * HeavyMember_S/N - Updated to report the highest scoring SequenceTag found - A SequenceTag is a peptide fragment that matches a continuous set of peaks in a fragmentation spectrum - SequenceTag Scores are computed using the sum of the product of the S/N values for each pairwise set of peaks that defines the residues in a sequence tag - Updated the _SpectraQuality.txt file created by the Amino Acid Spacing Filter to include several new columns - See the RevisionHistory for the MSMS Spectrum Filter (MsMsSpectrumFilter.dll) for more information Version 1.5.2953; February 1, 2008 - Extended the Amino Acid Spacing Filter to look for sequence tags and to compute additional scoring metrics - Updated the application to Visual Studio 2008, compiling for .NET Framework 2.0 Version 1.5.2952; January 31, 2008 - Updated the Amino Acid Spacing filter (filter mode 1) to return a quality score between 0 and 1 - Score values are dependent on the number of standard mass spacing values found - Seprate minimum and maximum mass spacing values can be defined for charges 1+, 2+, 3+, and 4+ (charges of 5+ or higher use the 4+ settings) - Data can now be filtered by signal to noise (S/N) ratios Version 1.4.2795; August 27, 2007 - Now quoting the path to the .Raw file when calling Extract_MSN.exe if the path contains spaces - Updated version of MsMsSpectrumFilter.dll Version 1.4.2579; January 23, 2007 - Using updated version of MsMsSpectrumFilter.dll Version 1.4.2578; January 22, 2007 - Switched to using Finnigan_Datafile_Info_Scanner.exe for reading the MS Level from Finnigan .Raw files Version 1.4.2572; January 16, 2007 - Added support for filtering by MS Level (i.e. only keep MS2 spectra or only keep MS3 spectra) Version 1.4.2566; January 10, 2007 - Fixed bug that prevented messages from being displayed when running the program from the command line Version 1.4.2565; January 9, 2007 - Updated the quality score value saved for spectra analyzed with Filter Mode 3 to be 0 or 1 (or -1 or 1), depending on MinimumQualityScore Version 1.4.2564; January 8, 2007 - Now checking for loss of (98+18) = 116 (if "Consider Water Loss" is enabled) - Rearranged the order of the NL intensity columns in the _SpectraQuality.txt file - Also, now rounding the neutral loss intensity values to 0 decimal places - Created an installer for the application Version 1.4.2560; January 4, 2007 - Added option "Include BPI and Neutral Loss Stats" - When enabled, then the _SpectraQuality.txt file (created if "Generate Filter Report" is enabled) contains the columns: - PrecursorMZ, the m/z of the parent (aka precursor) ion - BPI, aka Base Peak Intensity. This is the intensity of the most intense ion in the fragmentation spectrum - NL98, NL49, NL58, NL107, NL33, NL65, NL39, & NL71, which correspond to the normalized intensities of the m/z values matching the neutral losses listed below for Build 2543 - The value shown for each of these columns is a percentage between 0% and 100%, computed using (100 * (NL_Intensity / BPI)) Version 1.4.2543; December 18, 2006 - Updated the GUI to provide descriptions of the three filter modes - Reworked Mode 3 (Phosphorylation Neutral Loss Filter) - Removed submodes for this filter and instead now have options "Limit to Charge Specific Ions" and "Consider Water Loss" - Expanded the phosphorylation masses searched for (considers charge only if "Limit to Charge Specific Ions" is enabled) - 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 (if Consider Water Loss is enabled) - 2+ spectra: loss of (98*2+18)/2 = 107 (if Consider Water Loss is enabled) - 3+ spectra: loss of 98/3 = 32.66 - 3+ spectra: loss of (98*2)/3 = 65.32 - 3+ spectra: loss of (98+18)/3 = 38.66 (if Consider Water Loss is enabled) - 3+ spectra: loss of (98*2+18)/3 = 71.32 (if Consider Water Loss is enabled) - Changed from allowing user to enter a specific m/z value to search for to allowing the user to provide a specific list of m/z values to consider for neutral loss from the parent ion Version 1.3.2144; November 14, 2005 - Updated to new version of MsMsSpectrumFilter.dll using AnalysisManagerBase.dll instead of AnalysisManagerIFC.dll Version 1.3.2095.31751; September 26, 2005 - Renamed setting in XML parameter file to EvaluateSpectrumQualityOnly (was EvalulateSpectrumQualityOnly) Version 1.3.2081.30030; September 12, 2005 - Changed the parameter names for FilterMode3 - Old Name New Name BasePeakIntensityMinimum MarginOfError MassToleranceHalfWidthMZ Tolerance AbundanceFactor AbundanceFactor PeakMZ PeakMZForMode4 - Renamed the GenerateMissingChargeStates parameters from MinValue and MaxValue to MinimumCharge and MaximumCharge - Fixed bugs in the GUI related to textbox validation - Fixed bugs that kept the Spectra Quality text file open after analysis of _dta.txt files finished - Added ability for program to create a blank .Xml parameter file if the default file is missing - Changed ResetToDefaults method to be more robust - Changed maximum allowable charge value to 6 in the GUI (was 5) Version 1.2.2069.22160; August 31, 2005 - Updated the status statements displayed in the Console window to fix some minor bugs - Updated the logic used to determine whether headers should be written to the spectrum quality report file Version 1.2.2068.31564; August 30, 2005 - Updated the property functions in class clsMsMsSpectrumFilter to consolidate and group related settings for each filter into SetFilterMode() and GetFilterMode() functions August 17, 2005 - Fixed bug that incorrectly called SortSpectrumQualityTextFile when FilterSpectra was False August 15, 2005 - Renamed some of the FilterMode3 parameters in the XML Settings file August 3, 2005 - Updated to use SharedVBNetRoutines.dll June 15, 2005 - Updated to include the filter mode 3 (neutral loss filter) and to use the IDtaGenerator interface Mar 22, 2005 - Initial release