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== Overview == GlyQ-IQ is a program that performs a targeted, chromatographic centric search of mass spectral data for glycans. It is designed for high resolution LC-MS datasets. The software uses a list of glycan targets to search for expected features in MS1 spectra. Features are characterized by monoisotopic mass, elution time, and isotopic fit score. Features are annotated by glycan family relationships and optionally by in-source fragmentation patterns. At present, GlyQ-IQ only supports data acquired on Thermo instruments (.raw files). IQGlyQ_Console.exe is the main application. Source code for the 64-bit version is located at GetPeaks3\IQGlyQ_Console though the master solution file is GetPeaks3\GetPeaks3.sln When compiling and debugging, use the MixedPlatforms configuration of GetPeaks3.sln There is also a 32-bit version, but the code-base may be a bit out of date. That solution file is at GetPeaks2\GetPeaks2.sln === Manuscript === GlyQ-IQ: glycomics quintavariate-informed quantification with high-performance computing and GlycoGrid 4D visualization. Anal Chem. 2014 Jul 1;86(13):6268-76. doi: 10.1021/ac501492f. https://www.ncbi.nlm.nih.gov/pubmed/24881670 === Support === Important Note: GlyQ-IQ is provided on an as-is basis and is no longer supported. == Usage == The IQGlyQ_Console.exe program requires several input files, including: - Thermo .Raw file - Targets file - Several parameter files === Peak Detection === The first step is to create the Peaks.txt file using HammerOrDeconSimplePeakDetector.exe which you can find at bin\DeconPeakDetector To retrieve the required DLLs, run batch file _GetDLLs.bat in that directory This file contains peak lists for each mass spectrum, i.e. the mass and intensity values for each isotopic species above a computed noise threshold. The program syntax is: HammerOrDeconSimplePeakDetector.exe Dataset.raw /P:ParameterFile.txt /O:OutputFolderPath The default parameter file is HPC_SpinExactive_PeakDetector_Parameters.txt which you can find at bin\ParameterFiles\PeakDetection === Parameter File Configuration === The next step is to customize the parameter files in the Working Directory and the WorkingParameters folder. There are quite a few folders and files to customize; for a model layout, see bin\WorkDir\WorkingParametersCore1 For the example files to work-as is, copy the WorkDir folder to C:\Temp\WorkDir Place the following files in folder WorkingParametersCore1 - FragmentedParameters_Velos_7ppm_H.txt or FragmentedParameters_Velos_7ppm_DH.txt - Use the DH file if the sample includes a spike-in of deuterium labeled peptides, which provides a better chance of identifying the glycans. These labeled peptides should be similar to your sample of interest, but labeled with deuterium - If the sample does not contain labeled peptides, use the _H.txt file - Both of these parameter files have a MS1 ion tolerance of +/-7 ppm. Optionally adjust this tolerance wider if necessary - Factors_L10.txt - AlignmentParameters.xml - Targets file (glycans to search for) - Use L_13_HighMannose_TargetsFirstAll.txt for testing - Use L_13_Alditol_No_PSA.txt for production - Runtime parameters file - Suggested name GlyQIQ_Params_DatasetName.txt - Example contents: ResultsFolderPath,C:\Temp\WorkDir\Results LoggingFolderPath,C:\Temp\WorkDir\Results FactorsFile,Factors_L10.txt ExecutorParameterFile,ExecutorParametersSK.xml XYDataFolder,XYDataWriter WorkflowParametersFile,FragmentedParameters_Velos_7ppm_DH.txt Alignment,C:\Temp\WorkDir\WorkingParametersCore1\AlignmentParameters.xml BasicTargetedParameters,C:\Temp\WorkDir\WorkingParametersCore1\BasicTargetedWorkflowParameters.xml - ExecutorParameters file - The file paths in this file don't matter - Thus, just use the default Executor file, ExecutorParametersSK.xml === Start IQGlyQ_Console.exe === Program syntax / paths (these will all be on one line when you actually run it): IQGlyQ_Console.exe "%WorkDirPath%" "%DatasetName%" "raw" "L_13_HighMannose_TargetsFirstAll_Part1.txt" "GlyQIQ_Params_DatasetName.txt" "%WorkDirPath%\WorkingParametersCore1" "Lock_1" "%WorkDirPath%\Results" "1" It is probably best to include all of the double quotes on these parameters, even if they don't have spaces. For an example command line with full paths, see file bin\WorkDir\StartProgram_Core1.bat For a second example, see bin\ExampleData\StartProgram_Core1.bat and the releated files in that directory. == Results File == The results file has 85 columns with numerous details on putatively identified glycans. The first thing to do with the result file is open with Microsof Excel (or similar) and sort the data on the FinalDecision column (in Excel this is column AM). Results with "Future Target" are low quality results and can likely be ignored. The important results say "CorrectGlycan". == Multithreading == When searching for a large number of targets, you can split the targets file into multiple parts then launch multiple copies of IQGlyQ_Console.exe When doing this, make duplicate copies of the WorkingParametersCore1 folder, for example: WorkingParametersCore1 WorkingParametersCore2 WorkingParametersCore3 The parameter files in each one will be nearly identical, but each one will contain a different section of the targets file. In addition, update the paths for these two entries in the Runtime parameters file: Alignment,C:\Temp\WorkDir\WorkingParametersCore2\AlignmentParameters.xml BasicTargetedParameters,C:\Temp\WorkDir\WorkingParametersCore2\BasicTargetedWorkflowParameters.xml You then make a series of batch files, with each one pointing to a different WorkingParametersCore folder. In addition, update the LockFile name and the Core ID. For example: C:\GlyQ-IQ\IQGlyQ_Console.exe "C:\Temp\WorkDir" "Gly09_Velos3_Jaguar_230nL30_C14_DB10" "raw" "L_13_Alditol_No_PSA_Part1.txt" "GlyQIQ_Params_Gly09_Velos3_Jaguar_230nL30_C14_DB10.txt" "C:\Temp\WorkDir\WorkingParametersCore1" "Lock_1" "C:\Temp\WorkDir\Results" "1" C:\GlyQ-IQ\IQGlyQ_Console.exe "C:\Temp\WorkDir" "Gly09_Velos3_Jaguar_230nL30_C14_DB10" "raw" "L_13_Alditol_No_PSA_Part2.txt" "GlyQIQ_Params_Gly09_Velos3_Jaguar_230nL30_C14_DB10.txt" "C:\Temp\WorkDir\WorkingParametersCore2" "Lock_2" "C:\Temp\WorkDir\Results" "2" C:\GlyQ-IQ\IQGlyQ_Console.exe "C:\Temp\WorkDir" "Gly09_Velos3_Jaguar_230nL30_C14_DB10" "raw" "L_13_Alditol_No_PSA_Part3.txt" "GlyQIQ_Params_Gly09_Velos3_Jaguar_230nL30_C14_DB10.txt" "C:\Temp\WorkDir\WorkingParametersCore3" "Lock_3" "C:\Temp\WorkDir\Results" "3" C:\GlyQ-IQ\IQGlyQ_Console.exe "C:\Temp\WorkDir" "Gly09_Velos3_Jaguar_230nL30_C14_DB10" "raw" "L_13_Alditol_No_PSA_Part4.txt" "GlyQIQ_Params_Gly09_Velos3_Jaguar_230nL30_C14_DB10.txt" "C:\Temp\WorkDir\WorkingParametersCore4" "Lock_4" "C:\Temp\WorkDir\Results" "4" ------------------------------------------------------------------------------- Written by Scott Kronewitter for the Department of Energy (PNNL, Richland, WA) Copyright 2014, Battelle Memorial Institute. All Rights Reserved. E-mail: email@example.com or firstname.lastname@example.org Website: http://omics.pnl.gov/ or http://panomics.pnnl.gov/ ------------------------------------------------------------------------------- Licensed under the Apache License, Version 2.0; you may not use this file except in compliance with the License. You may obtain a copy of the License at http://www.apache.org/licenses/LICENSE-2.0 All publications that utilize this software should provide appropriate acknowledgement to PNNL website. However, if the software is extended or modified, then any subsequent publications should include a more extensive statement, using this text or a similar variant: Portions of this research were supported by the NIH National Center for Research Resources (Grant RR018522), the W.R. Wiley Environmental Molecular Science Laboratory (a national scientific user facility sponsored by the U.S. Department of Energy's Office of Biological and Environmental Research and located at PNNL), and the National Institute of Allergy and Infectious Diseases (NIH/DHHS through interagency agreement Y1-AI-4894-01). PNNL is operated by Battelle Memorial Institute for the U.S. Department of Energy under contract DE-AC05-76RL0 1830. Notice: This computer software was prepared by Battelle Memorial Institute, hereinafter the Contractor, under Contract No. DE-AC05-76RL0 1830 with the Department of Energy (DOE). All rights in the computer software are reserved by DOE on behalf of the United States Government and the Contractor as provided in the Contract. NEITHER THE GOVERNMENT NOR THE CONTRACTOR MAKES ANY WARRANTY, EXPRESS OR IMPLIED, OR ASSUMES ANY LIABILITY FOR THE USE OF THIS SOFTWARE. This notice including this sentence must appear on any copies of this computer software.