The DMS Analysis Tool Manager is a part of PRISM, the Proteomics Research Information and Management System. The analysis manager performs automated processing of available job steps, tracked by the in the DMS_Pipeline database. Plugin DLLs implement the processing details for each analysis tool.
| DMS Pipeline Step Tool | Description | Plugin Folder | Plugin DLL |
|---|---|---|---|
| APE | Runs workflows to filter and aggregate data | AM_Ape_PlugIn | AnalysisManager_Ape_PlugIn.dll |
| AScore | Calculates phosphoproteomics FDR for datasets and aggregates the results | AM_AScore_PlugIn | AnalysisManager_AScore_PlugIn.dll |
| Bruker_DA_Export | Creates XML files from Bruker .D folders | AM_Bruker_DA_Export | AnalysisManagerBrukerDAExportPlugin.dll |
| Cyclops | Performs various statistical analysis | AM_Cyclops_PlugIn | AnalysisManager_Cyclops_PlugIn.dll |
| DataExtractor | Creates loadable peptide ID file and first hits file | AM_Extraction_PlugIn | AnalysisManagerExtractionPlugin.dll |
| DataImport | Copies data files from an external source into an analysis job folder | AM_DataImport_Plugin | AnalysisManagerDataImportPlugIn.dll |
| Decon2LS | Uses Decon2LS to deisotope spectra | AM_Decon2ls_PlugIn | (obsolete) |
| Decon2LS_V2 | Uses Decon2LS AutoProcessor to deisotope spectra (supports IMS data and RAPID) | AM_Decon2ls_PlugIn_Decon2LSV2 | AnalysisManagerDecon2lsV2PlugIn.dll |
| DeconPeakDetector | Detects peaks in mass spectra using the DeconTools peak finder or the Hammer peak finder | AM_DeconPeakDetector_PlugIn | AnalysisManagerDeconPeakDetectorPlugIn.dll |
| DTA_Gen | Creates DTA files according to values in settings file | AM_DTASpectraFileGen_PlugIn | DTASpectraFileGen.dll |
| DTA_Import | Imports manually generated DTA files | AM_DTA_Import_PlugIn | AnalysisManagerDtaImportPlugIn.dll |
| DTA_Refinery | Reads DTA files (typically created by DeconMSn), then refines the parent mass for each spectrum using and X!Tandem search | AM_DtaRefinery_PlugIn | AnalysisManagerDtaRefineryPlugIn.dll |
| DTA_Split | Splits DTA files created by DTAGen | AM_DTA_Split_PlugIn | AnalysisManagerDtaSplitPlugIn.dll |
| Formularity | |||
| GlyQ_IQ | Searches a dataset for signatures of glycans using GlyQ-IQ | AM_GlyQIQ_Plugin | AnalysisManagerGlyQIQPlugin.dll |
| ICR2LS | Uses ICR-2LS to deisotope spectra for Bruker datasets | AM_ICR2LS_PlugIn | AnalysisManagerICR2LSPlugIn.dll (obsolete) |
| IDM | Tool for calculating interference within isolation window | AM_IDM_Plugin | AnalysisManager_IDM_Plugin.dll |
| IDPicker | Runs IDPicker | AM_IDPicker_PlugIn | AnalysisManagerIDPickerPlugIn.dll |
| Inspect | Identify peptides by searching protein collection | AM_InSpecT_PlugIn | AnalysisManagerInSpecTPlugIn.dll |
| InspectResultsAssembly | Combines peptide search result files generated by running Inspect in parallel | AM_InspectResultsAssembly_PlugIn | AnalysisManagerInspResultsAssemblyPlugIn.dll |
| LCMSFeatureFinder | Groups deisotoped data from Decon2LS to form LC-MS Features | AM_LCMSFeatureFinder_Plugin | AnalysisManagerLCMSFeatureFinderPlugIn.dll |
| LipidMapSearch | Searches a single dataset or a pair of datasets (positive mode and negative mode) against the Lipid Maps database | AM_LipidMapSearch_Plugin | AnalysisManagerLipidMapSearchPlugIn.dll |
| Mage | Performs various types of data extraction | AM_Mage_PlugIn | AnalysisManager_Mage_PlugIn.dll |
| MASIC_Finnigan | Run MASIC on Thermo .Raw files | AM_Masic_Plugin | AnalysisManagerMasicPlugin.dll |
| MODa | Runs MODa | AM_MODa_PlugIn | AnalysisManagerMODaPlugIn.dll |
| MODPlus | Runs MODPlus | AM_MODPlus_Plugin | AnalysisManagerMODPlusPlugin.dll |
| MSAlign | Searches MSAlign result files for peptides | AM_MSAlign_Plugin | AnalysisManagerMSAlignPlugIn.dll |
| MSAlign_Histone | Searches MSAlign result files for histone peptides | AM_MSAlign_Histone_Plugin | AnalysisManagerMSAlignHistonePlugIn.dll |
| MSAlign_Quant | Quantifies MSAlign results | AM_MSAlign_Quant_Plugin | AnalysisManagerMSAlignQuantPlugIn.dll |
| MSClusterDTAtoDAT | Produce an MSCluster-compatible DAT file from an existing DTA | AM_MSClusterDTAtoDAT_PlugIn | (obsolete) |
| MSDeconv | Deisotopes peptides with charge 4+ or higher; intended for top-down or middle-down datasets | AM_MSDeconv_Plugin | AnalysisManagerMSDeconvPlugIn.dll |
| MSGF | Runs MSGF, aka the MS-GeneratingFunction | AM_MSGF_PlugIn | AnalysisManagerMSGFPlugin.dll |
| MSGFPlus | Runs MSGF+ | AM_MSGFDB_PlugIn | AnalysisManagerMSGFDBPlugIn.dll |
| MSGFPlus_IMS | Processes IMS MSn data with MSGFDB_IMS; requires a DeconTools job as import | AM_MSGFDB_IMS_Plugin | (obsolete) |
| MSMSSpectraPreprocessor | Produce modified DTA by filtering existing DTA | AM_MSMSSpectrumFilter_PlugIn | MSMSSpectrumFilterAM.dll |
| MSPathFinder | Searches top down datasets for proteins | AM_MSPathFinder_Plugin | AnalysisManagerMSPathFinderPlugIn.dll |
| MSXML_Bruker | Creates mzXML or mzML files from Bruker .D folders using CompassXtract | AM_MSXML_Bruker_PlugIn | AnalysisManagerMsXmlBrukerPlugIn.dll |
| MSXML_Gen | Creates mzXML or mzML files from .Raw files | AM_MSXML_Gen_PlugIn | AnalysisManagerMsXmlGenPlugIn.dll |
| MultiAlign | Matches LCMSFeatureFinder results across datasets and/or to an AMT tag database | AM_MultiAlign_Plugin | AnalysisManagerMultiAlignPlugIn.dll (obsolete) |
| MultiAlign_Aggregator | Matches LCMSFeatureFinder results across datasets and/or to an AMT tag database | AM_MultiAlign_Aggregator_PlugIn | AnalysisManagerMultiAlign_AggregatorPlugIn.dll (obsolete) |
| Mz_Refinery | Updates the m/z values in a .mzML file based on the results from a MSGF+ search | AM_Mz_Refinery_Plugin | AnalysisManagerMzRefineryPlugIn.dll |
| mzXML_Aggregator | Extracts mzXML results from multiple mzXML jobs and aggregates the result | AM_PRIDE_MzXML_PlugIn | AnalysisManagerPRIDEMzXMLPlugIn.dll (obsolete) |
| NOMSI | Process XML files created by Bruker_DA_Export | AM_NOMSI | AnalysisManagerNOMSIPlugin.dll |
| OMSSA | Runs OMSSA | AM_OMSSA_PlugIn | AnalysisManagerOMSSAPlugIn.dll |
| PBF_Gen | Creates PBF (PNNL Binary Format) files; if a new .Exe results in a different file format, increment PbfFormatVersion in MSPF_TopDown_Standard.xml | AM_PBFSpectraFileGen_PlugIn | AnalysisManagerPBFGenerator.dll |
| Phospho_FDR_Aggregator | Calculates phosphoproteomics FDR for datasets and aggregates the results | AM_Phospho_FDR_Aggregator_PlugIn | AnalysisManagerPhospho_FDR_AggregatorPlugIn.dll |
| PRIDE_Converter | Converts Peptide_Hit results (Sequest, X!Tandem, or MSGFDB) to the msgf-pride.xml format | AM_PRIDE_Converter_PlugIn | AnalysisManagerPRIDEConverterPlugIn.dll |
| ProMex | Deisotopes high resolution spectra in PBF files | AM_ProMex_Plugin | AnalysisManagerProMexPlugIn.dll |
| ProSight_Quant | Quantifies ProSightPC results | AM_ProSightPC_Quant_Plugin | AnalysisManagerProSightQuantPlugIn.dll |
| QC-ART | Runs QC-ART; requires R 3.x. | AM_QC-ART_PlugIn | AnalysisManagerQCARTPlugIn.dll |
| RepoPkgr | Aggregates data and results files from DMS into package that can be uploaded to a public proteomics repository | AM_RepoPkgr_PlugIn | AnalysisManager_RepoPkgr_PlugIn.dll |
| Results_Cleanup | Looks for Results.db3 files in MAC jobs; deletes all except the one in the final job step | AM_ResultsCleanup_PlugIn | AnalysisManagerResultsCleanupPlugin.dll |
| Results_Transfer | Moves results folder from Xfer to storage | AM_ResultsXfer_PlugIn | AnalysisManagerResultsXferPlugin.dll |
| Sequest | Identify peptides by searching protein collection | AM_Sequest_PlugIn | AnalysisManagerSequestPlugin.dll |
| SMAQC | Runs SMAQC | AM_SMAQC_PlugIn | AnalysisManagerSMAQCPlugIn.dll |
| TopFD | Runs TopFD | AM_TopFD_Plugin | AnalysisManagerTopFDPlugIn.dll |
| TopPIC | Runs TopPIC | AM_TopPIC_Plugin | AnalysisManagerTopPICPlugIn.dll |
| UIMFtoMassHunter | Run UIMFtoMassHunter | AM_UIMFtoMassHunter_Plugin | AnalysisManagerUIMFtoMassHunterPlugin.dll (unused) |
| XTandem | Identify peptides by searching protein collection | AM_XTandem_PlugIn | AnalysisManagerXTandemPlugIn.dll |
| XTandem_HPC | Runs XTandem on Chinook high-performance computer | AM_XTandemHPC_PlugIn | (obsolete) |
Written by Matthew Monroe and Dave Clark for the Department of Energy (PNNL, Richland, WA)
E-mail: [email protected] or [email protected]
Website: https://github.com/PNNL-Comp-Mass-Spec/ or https://www.pnnl.gov/integrative-omics
The DMS Analysis Manager is licensed under the 2-Clause BSD License; you may not use this program except in compliance with the License. You may obtain a copy of the License at https://opensource.org/licenses/BSD-2-Clause
Copyright 2018 Battelle Memorial Institute