MSDataFileTrimmer Change Log Version 1.1.2991; March 10, 2008 - Updated version of MSDataFileReader.dll - Now supports mzXML v3.x - Removed PRISM.dll and SharedVBNetRoutines.dll Version 1.1.2713; May 3, 2007 - Added FuzzyMSDataFileNameMatching option (/Y) - Only used if using a MasterDataRow file. When enabled, the program will initially use the dataset name listed for each input line, looking for an exact matching .mzXML/.mzData and _syn.txt file. If no match is found, then the program will look for any mzXML or mzData file whose name matches the first part of the dataset name specified in the MasterDataRow file Version 1.1.2617; March 2, 2007 - Now bundling example data in the installer - Updated version of PRISM.dll and SharedVBNetRoutines.dll Version 1.1.2491; October 27, 2006 - Changed the file modes for MasterDataRow files to be 1, 2, 3, 4, or 5 columns: - If 1 column, then must be simply DatasetName - If 2 columns, they must be: DatasetName and ScanNumber - DatasetName will be used to find the mzXML/mzData file and Synopsis/First Hits file to parse - mzXML/mzData file must match the name exactly, e.g. DatasetName.mzXML - The text file is found using a search for the best matching text file starting with DatasetName - ScanNumber will be used to match values present in the second column of each line of a Synopsis/First Hits file - If 3 columns, they must be: DatasetName, ScanNumber, and DataRowNumber - DatasetName and ScanNumber are the same as described above - DataRowNumber will be matched to the first column of each line in a Synopsis/First Hits file, filtering the data to only include a single match for each scan number, as specified by the data row number - If 4 columns, they must be: DatasetName, ScanNumber, ChargeState, and Peptide - DatasetName will be used to find the mzXML/mzData and Synopsis/First Hits file to parse - ScanNumber, ChargeState, and Peptide will be matched to the appropriate columns in the Synopsis/First Hits to find matching lines - If 5 columns, they must be: DatasetName, ScanNumber, ChargeState, XCorr, and Peptide - DatasetName will be used to find the mzXML/mzData and Synopsis/First Hits file to parse - ScanNumber, ChargeState, XCorr, and Peptide will be matched to the appropriate columns in the Synopsis/First Hits to find matching lines - Added new /F switch to specify fuzzy matching of peptide sequences - Fuzzy matching means that modification symbols are ignored when looking for matching peptides - Added /X option to specify that the temporary files and temporary work directory not be deleted (as is usually the case) Version 1.1.2483; October 19, 2006 - Updated to allow the MasterDataRow text file to only contain dataset names - In this case, will use all data in each synopsis file for each dataset specified - Useful when using /G to group mzXml/mzData files and Synopsis/First Hits files together but when there is no need to filter the data Version 1.1.2481; October 18, 2006 - Added option of grouping the input data together to create a single, combined mzXml/mzData file and single, combined, Synopsis/First Hits file - To initiate this option, use /G and also provide a MasterDataRow text file using the /M:MasterDataRowFile.txt switch - When creating the combined file, the program will re-number the scans to avoid scan numbering conflicts between input files - When /G is used, the input mzXML and input synopsis files will not be replaced with the shortened forms - Instead, a temporary folder is created, the working files are created in the temporary folder, and then, after grouping, the temporary folder is deleted Version 1.0.2475; October 11, 2006 - Updated to allow reading a series of mzXML or mzData files and corresponding full-length Synopsis/First Hits files, then creating a truncated version of both the mzXML or mzData file and the Synopsis/First Hits files using a MasterDataRow file - The user specifies the rows to keep in each Synopsis/First Hits file using a MasterDataRow text file - The MasterDataRow text file can contain 2 columns, 3 columns, or 4 columns (separated by tabs) - If 2 columns, they must be: DatasetName and DataRowNumber - DatasetName will be used to find the mzXML/mzData file and Synopsis/First Hits file to parse - mzXML/mzData file must match the name exactly, e.g. DatasetName.mzXML - The text file is found using a search for the best matching text file starting with DatasetName - DataRowNumber must corresopond to the ID values present in the first column of each line of a Synopsis/First Hits file - If 3 columns, they must be: DatasetName, DataRowNumber, and ScanNumber - DatasetName and DataRowNumber are the same as described above - ScanNumber will be matched to the second column of each line in a Synopsis/First Hits file, providing a double check that the DataRowNumber is valid; an error will be raised if both DataRowNumber and ScanNumber do not match a line in the input file - If 4 columns, they must be DatasetName, ScanNumber, ChargeState, and Peptide - DatasetName will be used to find the mzXML/mzData and Synopsis/First Hits file to parse - ScanNumber, ChargeState, and Peptide will be matched to the appropriate columns in the Synopsis/First Hits to find matching lines - After a new, truncated version of each Synopsis/First Hits has been created, the old file will be renamed to have extension .bak, and then the new Synopsis/First Hits file will be used to filter the mzXML/mzData - Updated to replace the input mzXML or mzData file with the filtered version, creating a backup copy of the input file, e.g. InputFileName.mzXml.bak Version 1.0.2462; September 28, 2006 - Replaced command line parameter /A with /D since inclusion of parent MS1 spectra is now enabled by default - /D can be used to disable this option at the command line - However, parent MS1 spectra will always be included for mzXml files, since this is a requirement of the mzXml schema - Updated to more effectively find the appropriate ScanList file to use - e.g. if the input folder has files QC_06_01_17May06.raw and QC_06_01_17May06b.raw, then we want to make sure the program matches text files QC_06_01_17May06_syn.txt and QC_06_01_17May06b_syn.txt, respectively Version 1.0.2355; June 13, 2006 - Initial release