├── LICENSE ├── MANIFEST.in ├── README.md ├── multiplierz ├── __init__.py ├── _msparser.pyd ├── fasta.py ├── internalAlgorithms.py ├── mass_biochem.py ├── mgf │ ├── __init__.py │ └── extraction.py ├── msparser.py ├── mzAPI │ ├── D.py │ ├── __init__.py │ ├── agilentdlls │ │ ├── AgtFileSelectionDialog.dll │ │ ├── AgtFileSelectionDialog.pdb │ │ ├── BaseCommon.XML │ │ ├── BaseCommon.dll │ │ ├── BaseCommon.pdb │ │ ├── BaseCommon.tlb │ │ ├── BaseDataAccess.XML │ │ ├── BaseDataAccess.dll │ │ ├── BaseDataAccess.dll.config │ │ ├── BaseDataAccess.pdb │ │ ├── BaseDataAccess.tlb │ │ ├── BaseError.XML │ │ ├── BaseError.dll │ │ ├── BaseError.pdb │ │ ├── BaseTof.dll │ │ ├── BaseTof.pdb │ │ ├── Interop.shell32.dll │ │ ├── MIDAC.XML │ │ ├── MIDAC.dll │ │ ├── MIDAC.pdb │ │ ├── MassSpecDataReader.dll │ │ ├── MassSpecDataReader.pdb │ │ ├── MassSpecDataReader.tlb │ │ ├── RegisterMassHunterDataAccess64.bat │ │ ├── UnregisterMassHunterDataAccess64.bat │ │ ├── agtsampleinforw.dll │ │ ├── msvcp120.dll │ │ └── msvcr120.dll │ ├── bruker.py │ ├── brukerlib │ │ ├── timsdata.dll │ │ └── timsdata.lib │ ├── management.py │ ├── mzML.py │ ├── mzMemo.py │ ├── mzT2D.py │ ├── mzURL.py │ ├── mzWiff.py │ ├── raw.py │ ├── rawdlls │ │ ├── RawReader.dll │ │ ├── RawReader.dll.config │ │ ├── RawReader.pdb │ │ ├── RawReader.tlb │ │ ├── ThermoFisher.CommonCore.BackgroundSubtraction.dll │ │ ├── ThermoFisher.CommonCore.Data.dll │ │ ├── ThermoFisher.CommonCore.MassPrecisionEstimator.dll │ │ └── ThermoFisher.CommonCore.RawFileReader.dll │ ├── t2ddlls │ │ ├── BlaisT2D.dll │ │ ├── BlaisT2D.pdb │ │ ├── BlaisT2D.tlb │ │ ├── Clearcore2.Data.CommonInterfaces.dll │ │ ├── Clearcore2.Data.dll │ │ ├── Clearcore2.InternalRawXYProcessing.dll │ │ ├── Clearcore2.Muni.dll │ │ ├── Clearcore2.RawXYProcessing.dll │ │ ├── Clearcore2.Utility.dll │ │ ├── Sciex.ClearCore.FMan.dll │ │ ├── Sciex.Data.Processing.dll │ │ ├── Sciex.Data.SimpleTypes.dll │ │ ├── Sciex.Data.XYData.dll │ │ ├── Sciex.FMan.UI.dll │ │ ├── Sciex.FMan.dll │ │ ├── Sciex.TofTof.T2DFMan.dll │ │ └── zlib.net.dll │ └── wiffdlls │ │ ├── BlaisWiff.dll │ │ ├── BlaisWiff.pdb │ │ ├── BlaisWiff.tlb │ │ ├── Clearcore2.Compression.dll │ │ ├── Clearcore2.Data.AnalystDataProvider.dll │ │ ├── Clearcore2.Data.CommonInterfaces.dll │ │ ├── Clearcore2.Data.WiffReader.dll │ │ ├── Clearcore2.Data.dll │ │ ├── Clearcore2.InternalRawXYProcessing.dll │ │ ├── Clearcore2.Muni.dll │ │ ├── Clearcore2.ProjectUtilities.dll │ │ ├── Clearcore2.RawXYProcessing.dll │ │ ├── Clearcore2.StructuredStorage.dll │ │ ├── Clearcore2.Utility.dll │ │ ├── Sciex.TofTof.T2DFMan.dll │ │ ├── WiffReaderCOM.dll │ │ ├── WiffReaderCOM.pdb │ │ ├── WiffReaderCOM.tlb │ │ ├── fmanerrata │ │ ├── Sciex.ClearCore.FMan.dll │ │ ├── Sciex.ClearCore.FMan.xml │ │ ├── Sciex.Data.Processing.dll │ │ ├── Sciex.Data.Processing.xml │ │ ├── Sciex.Data.SimpleTypes.dll │ │ ├── Sciex.Data.SimpleTypes.xml │ │ ├── Sciex.Data.XYData.dll │ │ ├── Sciex.Data.XYData.xml │ │ ├── Sciex.FMan.UI.dll │ │ ├── Sciex.FMan.UI.xml │ │ ├── Sciex.FMan.dll │ │ ├── Sciex.FMan.xml │ │ ├── Sciex.TofTof.T2DFMan.dll │ │ ├── Sciex.TofTof.T2DFMan.xml │ │ └── zlib.net.dll │ │ └── regWiff.bat ├── mzGUI_standalone.py ├── mzReport │ ├── __init__.py │ ├── formats │ │ ├── __init__.py │ │ ├── mzIdentML.py │ │ ├── omssa.py │ │ ├── protein_pilot.py │ │ └── xtandem.py │ ├── mzCSV.py │ ├── mzDB.py │ ├── mzIdentML.py │ ├── mzSpreadsheet.py │ └── mzSpreadsheetClassic.py ├── mzSearch │ ├── __init__.py │ ├── comet_search.py │ ├── mascot │ │ ├── __init__.py │ │ ├── interface.py │ │ └── report.py │ ├── mascot_search.py │ ├── msgf_search.py │ └── tandem_search.py ├── mzTools │ ├── __init__.py │ ├── chargeTransform.py │ ├── featureDetector.py │ ├── featureUtilities.py │ ├── isoDist.py │ ├── labelEvaluation.py │ ├── multifile.py │ ├── mzIdentMLAPI.py │ ├── mz_image.py │ ├── pep2gene.py │ └── silacAnalysis.py ├── mzml.py ├── post_process.py ├── settings.py ├── spectral_process.py ├── unimod.py └── unimod.sqlite └── setup.py /LICENSE: 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