Enum SoftwareTerm 

pub enum SoftwareTerm {
    Software,
    Xcalibur,
    Bioworks,
    MassLynx,
    FlexAnalysis,
    DataExplorer,
    _4700Explorer,
    MassWolf,
    VoyagerBiospectrometryWorkstationSystem,
    FlexControl,
    ReAdW,
    MzStar,
    Analyst,
    Trapper,
    MzWiff,
    Proteios,
    ProteinLynxGlobalServer,
    ProteoWizardSoftware,
    ProteomeDiscoverer,
    _4000SeriesExplorerSoftware,
    GPSExplorer,
    LightSightSoftware,
    ProteinPilotSoftware,
    TissueViewSoftware,
    MarkerViewSoftware,
    MRMPilotSoftware,
    BioAnalyst,
    ProID,
    ProICAT,
    ProQuant,
    ProBLAST,
    Cliquid,
    MIDASWorkflowDesigner,
    MultiQuant,
    MassHunterDataAcquisition,
    MassHunterEasyAccess,
    MassHunterQualitativeAnalysis,
    MassHunterQuantitativeAnalysis,
    MassHunterMetaboliteID,
    MassHunterBioConfirm,
    GenespringMS,
    MassHunterMassProfiler,
    METLIN,
    SpectrumMillForMassHunterWorkstation,
    _6300SeriesIonTrapDataAnalysisSoftware,
    AgilentSoftware,
    SCIEXSoftware,
    AppliedBiosystemsSoftware,
    BrukerSoftware,
    ThermoFinniganSoftware,
    WatersSoftware,
    ApexControl,
    BioTools,
    CLINPROT,
    CLINPROTMicro,
    CLINPROTRobot,
    ClinProTools,
    Compass,
    CompassForHCTEsquire,
    CompassForMicrOTOF,
    CompassOpenAccess,
    CompassSecurityPack,
    CompassXport,
    CompassXtract,
    DataAnalysis,
    DpControl,
    EsquireControl,
    FlexImaging,
    GENOLINK,
    GenoTools,
    HCTcontrol,
    MicrOTOFcontrol,
    PolyTools,
    ProfileAnalysis,
    PROTEINEER,
    PROTEINEERDp,
    PROTEINEERFc,
    PROTEINEERSpII,
    PROTEINEERLC,
    ProteinScape,
    PureDisk,
    QuantAnalysis,
    SpControl,
    TargetAnalysis,
    WARPLC,
    TOPPSoftware,
    BaselineFilter,
    DBExporter,
    DBImporter,
    FileConverter,
    FileFilter,
    FileMerger,
    InternalCalibration,
    MapAligner,
    MapNormalizer,
    NoiseFilter,
    PeakPicker,
    Resampler,
    SpectraFilter,
    TOFCalibration,
    CustomUnreleasedSoftwareTool,
    HyStar,
    SRMSoftware,
    MaRiMba,
    PeptideAttributeCalculationSoftware,
    SSRCalc,
    Skyline,
    TIQAM,
    ATAQS,
    QuantitationSoftwareName,
    Mascot,
    SEQUEST,
    Phenyx,
    Spectronaut,
    AcquisitionSoftware,
    AnalysisSoftware,
    DataProcessingSoftware,
    Greylag,
    OMSSA,
    XTandem,
    SpectraST,
    MascotParser,
    SCIEXTOFTOFSeriesExplorerSoftware,
    ProteinExtractor,
    MascotDistiller,
    MascotIntegra,
    Percolator,
    ShimadzuCorporationSoftware,
    MALDISolutions,
    Scaffold,
    XCMS,
    MaxQuant,
    MyriMatch,
    DirecTag,
    TagRecon,
    Pepitome,
    Empower,
    UNIFY,
    LECOSoftware,
    ChromaTOFSoftware,
    ProgenesisLCMS,
    SILACAnalyzer,
    ChromaTOFHRTSoftware,
    MALDISolutionsMicrobialIdentification,
    SQID,
    PinPoint,
    PymzML,
    PEAKSStudio,
    PEAKSOnline,
    PEAKSNode,
    BSISoftware,
    DeBunker,
    MSQuant,
    AscoreSoftware,
    ProteinProspector,
    MSGF,
    MSGFplus,
    MicrosoftExcel,
    FindPairs,
    PAnalyzer,
    XTracker,
    ProteoSuite,
    ITRAQAnalyzer,
    TOPPNoiseFilter,
    TOPPNoiseFilterGaussian,
    TOPPNoiseFilterSGolay,
    TOPPPeakPicker,
    TOPPPeakPickerHiRes,
    TOPPPeakPickerWavelet,
    TOPPSpectraFilter,
    TOPPSpectraFilterBernNorm,
    TOPPSpectraFilterMarkerMower,
    TOPPSpectraFilterNLargest,
    TOPPSpectraFilterNormalizer,
    TOPPSpectraFilterParentPeakMower,
    TOPPSpectraFilterScaler,
    TOPPSpectraFilterSqrtMower,
    TOPPSpectraFilterThresholdMower,
    TOPPSpectraFilterWindowMower,
    TOPPMapAligner,
    TOPPMapAlignerIdentification,
    TOPPMapAlignerPoseClustering,
    TOPPMapAlignerSpectrum,
    TOPPDTAExtractor,
    TOPPIDMerger,
    TOPPIDFileConverter,
    TOPPSpectraMerger,
    TOPPMzTabExporter,
    TOPPMassTraceExtractor,
    TOPPPrecursorMassCorrector,
    TOPPHighResPrecursorMassCorrector,
    TOPPAdditiveSeries,
    TOPPDecharger,
    TOPPEICExtractor,
    TOPPFeatureFinder,
    TOPPFeatureFinderCentroided,
    TOPPFeatureFinderRaw,
    TOPPFeatureFinderIsotopeWavelet,
    TOPPFeatureFinderMetabo,
    TOPPFeatureFinderMRM,
    TOPPProteinQuantifier,
    TOPPConsensusMapNormalizer,
    TOPPMapRTTransformer,
    TOPPFeatureLinker,
    TOPPFeatureLinkerLabeled,
    TOPPFeatureLinkerUnlabeled,
    TOPPFeatureLinkerUnlabeledQT,
    TOPPCompNovo,
    TOPPCompNovoCID,
    TOPPSoftwareAdaptor,
    TOPPInspectAdapter,
    TOPPMascotAdapter,
    TOPPMascotAdapterOnline,
    TOPPOMSSAAdapter,
    TOPPPepNovoAdapter,
    TOPPXTandemAdapter,
    TOPPSpecLibSearcher,
    TOPPConsensusID,
    TOPPIDConflictResolver,
    TOPPIDFilter,
    TOPPIDMapper,
    TOPPIDPosteriorErrorProbability,
    TOPPIDRTCalibration,
    TOPPPeptideIndexer,
    TOPPPrecursorIonSelector,
    TOPPMRMMapper,
    TOPPOpenSwathComponent,
    TOPPOpenSwathAnalyzer,
    TOPPOpenSwathChromatogramExtractor,
    TOPPOpenSwathDecoyGenerator,
    TOPPOpenSwathFeatureXMLToTSV,
    TOPPOpenSwathRTNormalizer,
    TOPPProteinInference,
    TOPPFalseDiscoveryRate,
    ProteoWizardMsconvert,
    ProteoWizardIdconvert,
    ProteoWizardChainsaw,
    ProteoWizardMsaccess,
    ProteoWizardSeeMS,
    IsobariQ,
    MRMaid,
    MzidLib,
    MzidLibOmssa2Mzid,
    MzidLibTandem2Mzid,
    MzidLibCsv2Mzid,
    MzidLibProteoGrouper,
    MzidLibThresholder,
    MzidLibPerformEmPAIOnMzid,
    MzidLibFalseDiscoveryRate,
    MzidLibMzidentml2Csv,
    MzidLibCombineSearchEngines,
    MzidLibInsertMetaDataFromFasta,
    Comet,
    Byonic,
    TransProteomicPipeline,
    TransProteomicPipelineSoftware,
    PeptideProphet,
    IProphet,
    ProteinProphet,
    XPRESS,
    Libra,
    PTMProphet,
    ConversionSoftware,
    ProCon,
    PRIDEConverter2,
    Amanda,
    Andromeda,
    Mzmine,
    Maltcms,
    MALDISolutionsLCMALDI,
    SCiLSSoftware,
    SCiLSLab,
    PreprocessingSoftware,
    PIA,
    Anubis,
    PostprocessingSoftware,
    Maui,
    PeptideShaker,
    PepFinder,
    XiFDR,
    Xi,
    SkylineMzQuantMLConverter,
    ASAPRatio,
    Tide,
    ProLuCID,
    DTASelect,
    MSDK,
    Morpheus,
    OpenXQuest,
    FLASHDeconv,
    WatersDATAConvert,
    MSPathFinder,
    NISTMSPepSearch,
    MetaMorpheus,
    MzR,
    MSnbase,
    CAMERA,
    SmallMoleculeAnalysisSoftware,
    ProgenesisQI,
    CompoundDiscoverer,
    MyCompoundID,
    TopPIC,
    TopFD,
    TopMG,
    LipidomicsAnalysisSoftware,
    LipidDataAnalyzer,
    LipidHunter,
    LipidXplorer,
    LipidMatch,
    Greazy,
    LipidBlast,
    LipidPro,
    LipidFinder,
    LipiDex,
    LIQUID,
    ALEX,
    ALEX123,
    LIMSA,
    LOBSTAHS,
    LipidQA,
    Proline,
    PepNovo,
    PNovo,
    Novor,
    IdentiPy,
    MsDeisotope,
    PythonPsims,
    LPPtiger,
    PFind,
    I3tms,
    MSFragger,
    Philosopher,
    OpenPepXL,
    MSDIAL,
    PatternLab,
    SIMXL,
    QUINXL,
    EPIFANY,
    ProSight,
    TDPortal,
    ThermoRawFileParser,
    Pyteomics,
    PTXQC,
    QuaMeterIDFree,
    IMonDB,
    BiblioSpec,
    LibraryCreationSoftware,
    PeakForest,
    DIANN,
    Casanovo,
    Goslin,
    ANNSoLo,
    ChemClipse,
    OpenChrom,
    WatersConnect,
    Spectra,
    MetaboAnnotation,
    CompoundDb,
    QualityControlSoftware,
    Rmzqc,
    Jmzqc,
    Pymzqc,
    MzRecal,
    SpectrumClusteringSoftware,
    Scout,
    Kojak,
    Quantms,
    XQuestXProphet,
    PeakView,
    Perseus,
    FragPipe,
    OpenMS,
    PLink,
    PLink2,
    SCIEXOS,
    SCIEXMSDataConverter,
    TimsControl,
    MetaboScape,
    TASQ,
    InstaNovo,
    InstaNovoplus,
    MsQuality,
    DIAMetric,
}

Variants

Software

software - Software related to the recording or transformation of spectra.

Xcalibur

Xcalibur - Thermo Finnigan software for data acquisition and analysis.

Bioworks

Bioworks - Thermo Finnigan software for data analysis of peptides and proteins.

MassLynx

MassLynx - Micromass software for data acquisition and analysis.

FlexAnalysis

FlexAnalysis - Bruker software for data analysis.

DataExplorer

Data Explorer - Applied Biosystems software for data acquisition and analysis.

_4700Explorer

4700 Explorer - Applied Biosystems software for data acquisition and analysis.

MassWolf

massWolf - A software for converting Waters raw directory format to mzXML or mzML. MassWolf was originally developed at the Institute for Systems Biology.

VoyagerBiospectrometryWorkstationSystem

Voyager Biospectrometry Workstation System - Applied Biosystems MALDI-TOF data acquisition and analysis system.

FlexControl

FlexControl - Bruker software for data acquisition.

ReAdW

ReAdW - A software program for converting Thermo Finnigan RAW file format to mzXML or mzML. ReAdW was originally developed at the Institute for Systems Biology. Its whimsical interleaved spelling and capitalization is pronounced ‘readraw’.

MzStar

MzStar - A software program for converting Applied Biosystems wiff file format to mzXML format. MzStar was originally developed at the Institute for Systems Biology. It is now obsoleted by the MzWiff program.

Analyst

Analyst - SCIEX or Applied Biosystems|MDS SCIEX software for data acquisition.

Trapper

Trapper - A software program for converting Agilent MassHunter format to mzXML or mzML. Trapper was originally developed at the Institute for Systems Biology.

MzWiff

MzWiff - A software program for converting Applied Biosystems wiff file format to the mzXML or mzML format. MzWiff is currently maintained at the Institute for Systems Biology. It replaces the slower mzStar program.

Proteios

Proteios - Database application and analysis platform for proteomics.

ProteinLynxGlobalServer

ProteinLynx Global Server - Waters software for data analysis.

ProteoWizardSoftware

ProteoWizard software - ProteoWizard software for data processing and analysis. Primarily developed by the labs of P. Malick and D. Tabb.

ProteomeDiscoverer

Proteome Discoverer - Thermo Scientific software for data analysis of peptides and proteins.

_4000SeriesExplorerSoftware

4000 Series Explorer Software - SCIEX or Applied Biosystems software for data acquisition and analysis.

GPSExplorer

GPS Explorer - SCIEX or Applied Biosystems software for data acquisition and analysis.

LightSightSoftware

LightSight Software - SCIEX or Applied Biosystems|MDS SCIEX software metabolite identification.

ProteinPilotSoftware

ProteinPilot Software - SCIEX or Applied Biosystems|MDS SCIEX software for protein ID and quant.

TissueViewSoftware

TissueView Software - Applied Biosystems|MDS SCIEX software for tissue imaging.

MarkerViewSoftware

MarkerView Software - Applied Biosystems|MDS SCIEX software for metabolomics and biomarker profiling.

MRMPilotSoftware

MRMPilot Software - Applied Biosystems|MDS SCIEX software for MRM assay development.

BioAnalyst

BioAnalyst - Applied Biosystems|MDS SCIEX software for bio-related data exploration.

ProID

Pro ID - Applied Biosystems|MDS SCIEX software for protein identification.

ProICAT

Pro ICAT - Applied Biosystems|MDS SCIEX software for protein ID and quant by ICAT.

ProQuant

Pro Quant - Applied Biosystems|MDS SCIEX software for protein ID and quant by iTRAQ.

ProBLAST

Pro BLAST - Applied Biosystems|MDS SCIEX software for MS-BLAST identification.

Cliquid

Cliquid - SCIEX Cliquid software for data analysis and quantitation.

MIDASWorkflowDesigner

MIDAS Workflow Designer - Applied Biosystems|MDS SCIEX software for MRM assay development.

MultiQuant

MultiQuant - Applied Biosystems|MDS SCIEX software for MRM-based quantitation.

MassHunterDataAcquisition

MassHunter Data Acquisition - Software for data acquisition of 6000 series instruments.

MassHunterEasyAccess

MassHunter Easy Access - Software for open access data acquisition.

MassHunterQualitativeAnalysis

MassHunter Qualitative Analysis - Software for data analysis of data from 6000 series instruments.

MassHunterQuantitativeAnalysis

MassHunter Quantitative Analysis - Software for quantitation of Triple Quadrupole and Quadrupole Time-of-Flight data.

MassHunterMetaboliteID

MassHunter Metabolite ID - Software for identification of metabolites.

MassHunterBioConfirm

MassHunter BioConfirm - Software for protein characterization.

GenespringMS

Genespring MS - Software for quantitation and statistical analysis of TOF and Q-TOF LC/MS data.

MassHunterMassProfiler

MassHunter Mass Profiler - Software for quantitation and statistical analysis of TOF and Q-TOF LC/MS data.

METLIN

METLIN - Personal Metabolite Database for MassHunter Workstation. Software for identification of human metabolites.

SpectrumMillForMassHunterWorkstation

Spectrum Mill for MassHunter Workstation - Software for protein identification and characterization of complex protein digest mixtures.

_6300SeriesIonTrapDataAnalysisSoftware

6300 Series Ion Trap Data Analysis Software - Software for data analysis of 6300 series ion trap mass spectrometers.

AgilentSoftware

Agilent software - Agilent software for data acquisition and analysis.

SCIEXSoftware

SCIEX software - SCIEX or Applied Biosystems software for data acquisition and analysis.

AppliedBiosystemsSoftware

Applied Biosystems software - Applied Biosystems|MDS SCIEX software for data acquisition and analysis.

BrukerSoftware

Bruker software - Bruker software for data acquisition and analysis.

ThermoFinniganSoftware

Thermo Finnigan software - Thermo Finnigan software for data acquisition and analysis.

WatersSoftware

Waters software - Waters software for data acquisition and analysis.

ApexControl

apexControl - Bruker software for data acquisition.

BioTools

BioTools - Bruker software for data analysis.

CLINPROT

CLINPROT - Bruker CLINPROT software.

CLINPROTMicro

CLINPROT micro - Bruker CLINPROT micro software.

CLINPROTRobot

CLINPROT robot - Bruker CLINPROT robot software.

ClinProTools

ClinProTools - Bruker ClinProTools software.

Compass

Compass - Bruker Compass software.

CompassForHCTEsquire

Compass for HCT/esquire - Bruker Compass for HCT/esquire software.

CompassForMicrOTOF

Compass for micrOTOF - Bruker Compass for micrOTOF software.

CompassOpenAccess

Compass OpenAccess - Bruker compass OpenAccess software.

CompassSecurityPack

Compass Security Pack - Bruker compass Security Pack software.

CompassXport

CompassXport - Bruker stand-alone software for data conversion.

CompassXtract

CompassXtract - Bruker software library for data access.

DataAnalysis

DataAnalysis - Bruker software for data analysis.

DpControl

dpControl - Bruker software for data acquisition.

EsquireControl

esquireControl - Bruker software for data acquisition.

FlexImaging

flexImaging - Bruker software for data analysis.

GENOLINK

GENOLINK - Bruker GENOLINK software.

GenoTools

GenoTools - Bruker GenoTools software.

HCTcontrol

HCTcontrol - Bruker software for data acquisition.

MicrOTOFcontrol

micrOTOFcontrol - Bruker software for data acquisition.

PolyTools

PolyTools - Bruker PolyTools software.

ProfileAnalysis

ProfileAnalysis - Bruker software for data analysis.

PROTEINEER

PROTEINEER - Bruker PROTEINEER software.

PROTEINEERDp

PROTEINEER dp - Bruker PROTEINEER dp software.

PROTEINEERFc

PROTEINEER fc - Bruker PROTEINEER fc software.

PROTEINEERSpII

PROTEINEER spII - Bruker PROTEINEER spII software.

PROTEINEERLC

PROTEINEER-LC - Bruker PROTEINEER-LC software.

ProteinScape

ProteinScape - Bruker ProteinScape software.

PureDisk

PureDisk - BrukerPureDisk software.

QuantAnalysis

QuantAnalysis - Bruker software for data analysis.

SpControl

spControl - Bruker software for data acquisition.

TargetAnalysis

TargetAnalysis - Bruker TargetAnalysis software.

WARPLC

WARP-LC - Bruker WARP-LC software.

TOPPSoftware

TOPP software - TOPP (The OpenMS proteomics pipeline) software.

BaselineFilter

BaselineFilter - Removes the baseline from profile spectra using a top-hat filter.

DBExporter

DBExporter - Exports data from an OpenMS database to a file.

DBImporter

DBImporter - Imports data to an OpenMS database.

FileConverter

FileConverter - Converts between different MS file formats.

FileFilter

FileFilter - Extracts or manipulates portions of data from peak, feature or consensus feature files.

FileMerger

FileMerger - Merges several MS files into one file.

InternalCalibration

InternalCalibration - Applies an internal calibration.

MapAligner

MapAligner - OBSOLETE Corrects retention time distortions between maps.

MapNormalizer

MapNormalizer - Normalizes peak intensities in an MS run.

NoiseFilter

NoiseFilter - OBSOLETE Removes noise from profile spectra by using different smoothing techniques.

PeakPicker

PeakPicker - OBSOLETE Finds mass spectrometric peaks in profile mass spectra.

Resampler

Resampler - Transforms an LC/MS map into a resampled map or a png image.

SpectraFilter

SpectraFilter - OBSOLETE Applies a filter to peak spectra.

TOFCalibration

TOFCalibration - Applies time of flight calibration.

CustomUnreleasedSoftwareTool

custom unreleased software tool - A software tool that has not yet been released. The value should describe the software. Please do not use this term for publicly available software - contact the PSI-MS working group in order to have another CV term added.

HyStar

HyStar - Bruker software for hyphenated experiments.

SRMSoftware

SRM software - Software used to predict, select, or optimize transitions or analyze the results of selected reaction monitoring runs.

MaRiMba

MaRiMba - Software used to predict transitions for selected reaction monitoring experiments based on observed spectrum libraries developed and distributed by the Institute for Systems Biology.

PeptideAttributeCalculationSoftware

peptide attribute calculation software - Software used to predict or calculate numerical attributes of peptides.

SSRCalc

SSRCalc - Sequence Specific Retention Calculator estimates the retention time of peptides based on their sequence.

Skyline

Skyline - Software used to predict, select, and optimize transitions as well as analyze the results of selected reaction monitoring runs developed and distributed by the MacCoss lab at the University of Washington.

TIQAM

TIQAM - Software used to predict, select, and optimize transitions for selected reaction monitoring experiments developed and distributed by the Institute for Systems Biology.

ATAQS

ATAQS - Software suite used to predict, select, and optimize transitions as well as analyze the results of selected reaction monitoring runs developed and distributed by the Institute for Systems Biology.

QuantitationSoftwareName

quantitation software name - Quantitation software name.

Mascot

Mascot - The name of the Mascot search engine.

SEQUEST

SEQUEST - The name of the SEQUEST search engine.

Phenyx

Phenyx - The name of the Phenyx search engine.

Spectronaut

Spectronaut - Commercial cross-vendor software for library (peptide centric), and library-free (spectrum centric) analysis and quantification of DIA data.

AcquisitionSoftware

acquisition software - Acquisition software.

AnalysisSoftware

analysis software - Analysis software.

DataProcessingSoftware

data processing software - Data processing software.

Greylag

greylag - Greylag identification software.

OMSSA

OMSSA - Open Mass Spectrometry Search Algorithm was used to analyze the spectra.

XTandem

X!Tandem - X!Tandem was used to analyze the spectra.

SpectraST

SpectraST - Open-source software for mass spectral library creation and searching, developed at the Institute for Systems Biology and the Hong Kong University of Science and Technology. Part of the Trans-Proteomic Pipeline.

MascotParser

Mascot Parser - Mascot Parser was used to analyze the spectra.

SCIEXTOFTOFSeriesExplorerSoftware

SCIEX TOF/TOF Series Explorer Software - SCIEX or Applied Biosystems software for TOF/TOF data acquisition and analysis.

ProteinExtractor

ProteinExtractor - An algorithm for protein determination/assembly integrated into Bruker’s ProteinScape.

MascotDistiller

Mascot Distiller - Mascot Distiller.

MascotIntegra

Mascot Integra - Mascot Integra.

Percolator

Percolator - Percolator.

ShimadzuCorporationSoftware

Shimadzu Corporation software - Shimadzu Corporation software.

MALDISolutions

MALDI Solutions - Shimadzu Biotech software for data acquisition, processing, and analysis.

Scaffold

Scaffold - Scaffold analysis software.

XCMS

XCMS - Bioconductor package XCMS for preprocessing high-throughput, untargeted analyte profiling data.

MaxQuant

MaxQuant - MaxQuant is a quantitative proteomics software package designed for analyzing large mass spectrometric data sets. It is specifically aimed at high resolution MS data.

MyriMatch

MyriMatch - Tabb Lab software for directly comparing peptides in a database to tandem mass spectra.

DirecTag

DirecTag - Tabb Lab software for generating sequence tags from tandem mass spectra.

TagRecon

TagRecon - Tabb Lab software for reconciling sequence tags to a protein database.

Pepitome

Pepitome - Tabb Lab software for spectral library searches on tandem mass spectra.

Empower

Empower - Waters Empower software for liquid chromatography and mass spectrometry acquisition.

UNIFY

UNIFY - Waters UNIFY software for liquid chromatography and mass spectrometry acquisition.

LECOSoftware

LECO software - LECO software for data acquisition and analysis.

ChromaTOFSoftware

ChromaTOF software - Software for acquisition, processing and analysis of data for LECO instruments.

ProgenesisLCMS

Progenesis LC-MS - Software from Nonlinear Dynamics for LC-MS label-free workflow.

SILACAnalyzer

SILACAnalyzer - Software for SILAC workflow.

ChromaTOFHRTSoftware

ChromaTOF HRT software - Software for acquisition, processing and analysis of data for LECO instruments.

MALDISolutionsMicrobialIdentification

MALDI Solutions Microbial Identification - Shimadzu Biotech software for data acquisition, processing, and analysis.

SQID

SQID - Software for data analysis of peptides and proteins.

PinPoint

PinPoint - Thermo Scientific PinPoint SRM analysis software.

PymzML

pymzML - Python module to interface mzML Data.

PEAKSStudio

PEAKS Studio - PEAKS Studio software for data analysis.

PEAKSOnline

PEAKS Online - PEAKS Online software for high throughput data analysis.

PEAKSNode

PEAKS Node - PEAKS Node software for high throughput data analysis.

BSISoftware

BSI software - Bioinformatics Solutions Inc. Software for data processing and analysis.

DeBunker

DeBunker - DeBunker software.

MSQuant

MSQuant - MSQuant software.

AscoreSoftware

Ascore software - Ascore software.

ProteinProspector

ProteinProspector - ProteinProspector software for data acquisition and analysis.

MSGF

MS-GF - MS-GF software used to re-score the peptide-spectrum matches.

MSGFplus

MS-GF+ - MS-GF+ software used to analyze the spectra.

MicrosoftExcel

Microsoft Excel - Microsoft Excel (can be used for spectral counting).

FindPairs

FindPairs - Software e.g. for SILAC and 14N/15N workflow, part of the PeakQuant suite.

PAnalyzer

PAnalyzer - PAnalyzer software for getting protein evidence categories.

XTracker

x-Tracker - X-Tracker generic tool for quantitative proteomics.

ProteoSuite

ProteoSuite - ProteoSuite software for the analysis of quantitative proteomics data.

ITRAQAnalyzer

ITRAQAnalyzer - Software for iTRAQ workflow. Extracts and normalizes iTRAQ information from an MS experiment.

TOPPNoiseFilter

TOPP noise filter - Noise filter component of the TOPP software.

TOPPNoiseFilterGaussian

TOPP NoiseFilterGaussian - Removes noise from profile spectra by using a gaussian smoothing.

TOPPNoiseFilterSGolay

TOPP NoiseFilterSGolay - Removes noise from profile spectra by using a Savitzky-Golay smoothing.

TOPPPeakPicker

TOPP peak picker - Peak picker component of the TOPP software.

TOPPPeakPickerHiRes

TOPP PeakPickerHiRes - Finds mass spectrometric peaks in high-resoluted profile mass spectra.

TOPPPeakPickerWavelet

TOPP PeakPickerWavelet - Finds mass spectrometric peaks with a wavelet algorithm in low-resoluted profile mass spectra.

TOPPSpectraFilter

TOPP spectra filter - Spectra filter component of the TOPP software.

TOPPSpectraFilterBernNorm

TOPP SpectraFilterBernNorm - Applies a Bern et al normalization to peak spectra.

TOPPSpectraFilterMarkerMower

TOPP SpectraFilterMarkerMower - Applies a filter to peak spectra for marked peaks.

TOPPSpectraFilterNLargest

TOPP SpectraFilterNLargest - Retains the n largest peaks of a peak spectra.

TOPPSpectraFilterNormalizer

TOPP SpectraFilterNormalizer - Applies a TIC/maximal intensity normalization to peak spectra.

TOPPSpectraFilterParentPeakMower

TOPP SpectraFilterParentPeakMower - Filters putative unfragmented precursor ions from tandem spectra.

TOPPSpectraFilterScaler

TOPP SpectraFilterScaler - Applies a filter to peak spectra after intensity scaling according to rank.

TOPPSpectraFilterSqrtMower

TOPP SpectraFilterSqrtMower - Applies a filter to peak spectra after intensity scaling to the square root.

TOPPSpectraFilterThresholdMower

TOPP SpectraFilterThresholdMower - Applies a filter of peaks below a given threshold to peak spectra.

TOPPSpectraFilterWindowMower

TOPP SpectraFilterWindowMower - Applies a filter of the largest peaks in a sliding window over a peak spectrum.

TOPPMapAligner

TOPP map aligner - Map aligner component of the TOPP software.

TOPPMapAlignerIdentification

TOPP MapAlignerIdentification - Corrects retention time distortions between maps based on common peptide identifications.

TOPPMapAlignerPoseClustering

TOPP MapAlignerPoseClustering - Corrects retention time distortions between maps using a pose clustering approach.

TOPPMapAlignerSpectrum

TOPP MapAlignerSpectrum - Corrects retention time distortions between maps by spectrum alignment.

TOPPDTAExtractor

TOPP DTAExtractor - Extracts spectra of an MS run file to several files in DTA format.

TOPPIDMerger

TOPP IDMerger - Merges several protein/peptide identification files into one file.

TOPPIDFileConverter

TOPP IDFileConverter - Converts identification engine file formats.

TOPPSpectraMerger

TOPP SpectraMerger - Merges spectra from an LC/MS map, either by precursor or by RT blocks.

TOPPMzTabExporter

TOPP MzTabExporter - Exports various XML formats to an mzTab file.

TOPPMassTraceExtractor

TOPP MassTraceExtractor - Annotates mass traces in centroided LC/MS maps.

TOPPPrecursorMassCorrector

TOPP PrecursorMassCorrector - Correct the precursor entries of tandem MS scans.

TOPPHighResPrecursorMassCorrector

TOPP HighResPrecursorMassCorrector - Performs precursor mz correction on centroided high resolution data.

TOPPAdditiveSeries

TOPP AdditiveSeries - Computes an additive series to quantify a peptide in a set of samples.

TOPPDecharger

TOPP Decharger - Decharges and merges different feature charge variants of the same chemical entity.

TOPPEICExtractor

TOPP EICExtractor - Quantifies signals at given positions in (raw or picked) LC/MS maps.

TOPPFeatureFinder

TOPP feature finder - Feature finder component of the TOPP software.

TOPPFeatureFinderCentroided

TOPP FeatureFinderCentroided - Detects two-dimensional features in centroided LC-MS data.

TOPPFeatureFinderRaw

TOPP FeatureFinderRaw - Detects two-dimensional features in uncentroided LC-MS data.

TOPPFeatureFinderIsotopeWavelet

TOPP FeatureFinderIsotopeWavelet - Detects two-dimensional features in uncentroided LC-MS data with a wavelet algorithm.

TOPPFeatureFinderMetabo

TOPP FeatureFinderMetabo - Detects two-dimensional features in centroided LC-MS data of metabolites.

TOPPFeatureFinderMRM

TOPP FeatureFinderMRM - Quantifies features LC-MS/MS MRM data.

TOPPProteinQuantifier

TOPP ProteinQuantifier - Computes protein abundances from annotated feature/consensus maps.

TOPPConsensusMapNormalizer

TOPP ConsensusMapNormalizer - Normalizes maps of one consensus XML file (after linking).

TOPPMapRTTransformer

TOPP MapRTTransformer - Applies retention time transformations to maps.

TOPPFeatureLinker

TOPP feature linker - Feature linker component of the TOPP software.

TOPPFeatureLinkerLabeled

TOPP FeatureLinkerLabeled - Groups corresponding isotope-labeled features in a feature map.

TOPPFeatureLinkerUnlabeled

TOPP FeatureLinkerUnlabeled - Groups corresponding features from multiple maps.

TOPPFeatureLinkerUnlabeledQT

TOPP FeatureLinkerUnlabeledQT - Groups corresponding features from multiple maps using a quality threshold clustering approach.

TOPPCompNovo

TOPP CompNovo - Performs a peptide/protein identification with the CompNovo engine.

TOPPCompNovoCID

TOPP CompNovoCID - Performs a peptide/protein identification with the CompNovo engine in collision-induced dissociation (CID) mode.

TOPPSoftwareAdaptor

TOPP software adaptor - Software adaptor to an external program in the TOPP software.

TOPPInspectAdapter

TOPP InspectAdapter - Identifies MS2 spectra using the external program Inspect.

TOPPMascotAdapter

TOPP MascotAdapter - Identifies MS2 spectra using the external program Mascot.

TOPPMascotAdapterOnline

TOPP MascotAdapterOnline - Identifies MS2 spectra using the online version of the external program Mascot.

TOPPOMSSAAdapter

TOPP OMSSAAdapter - Identifies MS2 spectra using the external program OMSSA.

TOPPPepNovoAdapter

TOPP PepNovoAdapter - Identifies MS2 spectra using the external program PepNovo.

TOPPXTandemAdapter

TOPP XTandemAdapter - Identifies MS2 spectra using the external program XTandem.

TOPPSpecLibSearcher

TOPP SpecLibSearcher - Identifies peptide MS2 spectra by spectral matching with a searchable spectral library.

TOPPConsensusID

TOPP ConsensusID - Computes a consensus identification from peptide identifications of several identification engines.

TOPPIDConflictResolver

TOPP IDConflictResolver - Resolves ambiguous annotations of features with peptide identifications.

TOPPIDFilter

TOPP IDFilter - Filters results from protein or peptide identification engines based on different criteria.

TOPPIDMapper

TOPP IDMapper - Assigns protein/peptide identifications to feature or consensus features.

TOPPIDPosteriorErrorProbability

TOPP IDPosteriorErrorProbability - Estimates posterior error probabilities using a mixture model.

TOPPIDRTCalibration

TOPP IDRTCalibration - Calibrate Retention times of peptide hits to standards.

TOPPPeptideIndexer

TOPP PeptideIndexer - Refreshes the protein references for all peptide hits.

TOPPPrecursorIonSelector

TOPP PrecursorIonSelector - A tool for precursor ion selection based on identification results.

TOPPMRMMapper

TOPP MRMMapper - MRMMapper maps measured chromatograms (mzML) and the transitions used (TraML).

TOPPOpenSwathComponent

TOPP OpenSwath component - OpenSwath component of the TOPP software.

TOPPOpenSwathAnalyzer

TOPP OpenSwathAnalyzer - Picks peaks and finds features in an SRM experiment.

TOPPOpenSwathChromatogramExtractor

TOPP OpenSwathChromatogramExtractor - Extract chromatograms (XIC) from a MS2 map file.

TOPPOpenSwathDecoyGenerator

TOPP OpenSwathDecoyGenerator - Generates decoys according to different models for a specific TraML.

TOPPOpenSwathFeatureXMLToTSV

TOPP OpenSwathFeatureXMLToTSV - Converts a featureXML to a mProphet tsv (tab separated values).

TOPPOpenSwathRTNormalizer

TOPP OpenSwathRTNormalizer - Generates a transformation file for retention time space into normalized space.

TOPPProteinInference

TOPP ProteinInference - Infer proteins from a list of (high-confidence) peptides.

TOPPFalseDiscoveryRate

TOPP FalseDiscoveryRate - Estimates the false discovery rate on peptide and protein level using decoy searches.

ProteoWizardMsconvert

ProteoWizard msconvert - Converts, filters, and processes mass spectrometry data in variety of formats.

ProteoWizardIdconvert

ProteoWizard idconvert - Converts, filters, and processes identifications from shotgun proteomics experiments.

ProteoWizardChainsaw

ProteoWizard chainsaw - Filters and processes protein sequence databases.

ProteoWizardMsaccess

ProteoWizard msaccess - Filters, processes, and displays mass spectrometry data in a variety of ways.

ProteoWizardSeeMS

ProteoWizard SeeMS - An interactive GUI application to view and filter mass spectrometry data in a variety of formats.

IsobariQ

IsobariQ - A quantitative software package designed for analysis of IPTL, TMT and iTRAQ data.

MRMaid

MRMaid - A web-based SRM assay design tool whose transitions are generated by mining the millions of identified peptide spectra held in the EBI’s PRIDE database.

MzidLib

mzidLib - A library of Java routines for manipulating mzIdentML files.

MzidLibOmssa2Mzid

mzidLib:Omssa2Mzid - A converter for OMSSA OMX to mzIdentML.

MzidLibTandem2Mzid

mzidLib:Tandem2Mzid - A converter for Tandem XML to mzIdentML.

MzidLibCsv2Mzid

mzidLib:Csv2Mzid - A converter for CSV files (following OMSSA CSV style) to mzIdentML.

MzidLibProteoGrouper

mzidLib:ProteoGrouper - A generic and parameterizable protein inference algorithm for mzIdentML files.

MzidLibThresholder

mzidLib:Thresholder - A routine for keeping only identifications passing a given threshold or setting passThreshold to true or false for SpectrumIdentificationItem or ProteinDetectionHypothesis in mzIdentML files.

MzidLibPerformEmPAIOnMzid

mzidLib:Perform emPAI on mzid - A routine for adding emPAI quantitative values to an mzIdentML file.

MzidLibFalseDiscoveryRate

mzidLib:FalseDiscoveryRate - A routine for calculating local FDR, q-value and FDRScore for mzIdentML files, based on a decoy search.

MzidLibMzidentml2Csv

mzidLib:Mzidentml2Csv - A tool for converting mzIdentML files to CSV format.

MzidLibCombineSearchEngines

mzidLib:CombineSearchEngines - A tool for combining results analysed in parallel in two or three search engines into a single mzIdentML file.

MzidLibInsertMetaDataFromFasta

mzidLib:InsertMetaDataFromFasta - A tool for adding additional meta data from a FASTA file to DBSequence entries (sequence and description) in mzIdentML files.

Comet

Comet - Comet open-source sequence search engine developed at the University of Washington.

Byonic

Byonic - Byonic search engine from Protein Metrics.

TransProteomicPipeline

Trans-Proteomic Pipeline - A suite of open source tools for the processing of MS2 proteomics data developed by the Seattle Proteome Center at the Institute for Systems Biology.

TransProteomicPipelineSoftware

Trans-Proteomic Pipeline software - A software program that is a component of the Trans-Proteomic Pipeline.

PeptideProphet

PeptideProphet - A program in the TPP that calculates PSM probabilities for MS2 proteomics data searched with any of the supported sequence or spectral library search engines via the pepXML format.

IProphet

iProphet - A program in the TPP that calculates distinct peptide probabilities based on several lines of corroborating evidence including search results from multiple search engines via the pepXML format.

ProteinProphet

ProteinProphet - A program in the TPP that calculates protein-level probabilities based on input PSM or peptide-level probabilities from PeptideProphet or iProphet. The output is written in the protXML format.

XPRESS

XPRESS - A program in the TPP that calculates PSM-level abundances based on 2-channel isotope-labelled data such as ICAT, SILAC, etc.

Libra

Libra - A program in the TPP that calculates PSM, peptide, and protein-level abundances based on N-channel isobaric label peptide data such as iTRAQ, TMT, etc.

PTMProphet

PTMProphet - A program in the TPP that calculates PTM localization probabilities by re-analyzing the peaks that are available to distinguish between possible modification sites.

ConversionSoftware

conversion software - Computer software primarily designed to convert data represented in one format to another format, sometimes with minor data alterations in the process.

ProCon

ProCon - Java software designed to convert one of several proteomics identification results formats into mzIdentML or PRIDE XML.

PRIDEConverter2

PRIDE Converter2 - Java software designed to convert one of several proteomics identification results formats into PRIDE XML.

Amanda

Amanda - Amanda scoring system for PSM identification.

Andromeda

Andromeda - Andromeda is a peptide search engine.

Mzmine

mzmine - A framework for differential analysis of mass spectrometry data.

Maltcms

Maltcms - Modular Application Toolkit for Chromatography Mass-Spectrometry is an application framework mainly for developers.

MALDISolutionsLCMALDI

MALDI Solutions LC-MALDI - Software for automated LC-MALDI analysis and reporting.

SCiLSSoftware

SCiLS software - SCiLS software for data acquisition and analysis.

SCiLSLab

SCiLS Lab - SCiLS Lab software.

PreprocessingSoftware

preprocessing software - Preprocessing software.

PIA

PIA - PIA - Protein Inference Algorithms, a toolbox for protein inference and identification analysis.

Anubis

Anubis - Anubis software for selected reaction monitoring data.

PostprocessingSoftware

postprocessing software - Postprocessing software.

Maui

Maui - The Maltcms Graphical User Interface.

PeptideShaker

PeptideShaker - PeptideShaker is a software for the interpretation of proteomics identification results.

PepFinder

PepFinder - Thermo Scientific PepFinder BioPharma analysis software.

XiFDR

xiFDR - Target/Decoy based FDR estimation for crosslinking peptide-identifications.

Xi

xi - Search engine for crosslinked peptides.

SkylineMzQuantMLConverter

Skyline mzQuantML converter - A software package to convert Skyline report to mzQuantML.

ASAPRatio

ASAPRatio - A program in the TPP that calculates PSM, peptide, and protein-level abundances based on 2-channel isotope-labelled data such as ICAT, SILAC, etc.

Tide

Tide - Tide open-source sequence search program developed at the University of Washington.

ProLuCID

ProLuCID - The SEQUEST-like sequence search engine ProLuCID, developed in the Yates Lab at the Scripps Research Institute.

DTASelect

DTASelect - Analysis software designed to reassemble the SEQUEST peptide identifications and to highlight the most significant matches.

MSDK

MSDK - Mass Spectrometry Development Kit (MSDK) is a Java library of algorithms for processing of mass spectrometry data.

Morpheus

Morpheus - Morpheus search engine.

OpenXQuest

OpenXQuest - Cross-Linking MS search engine.

FLASHDeconv

FLASHDeconv - Ultrafast, High-Quality Feature Deconvolution for Top-Down Proteomics.

WatersDATAConvert

Waters DATA Convert - Software for processing and exporting Waters MassLynx and waters_connect data.

MSPathFinder

MSPathFinder - PNNL top-down/bottom-up analysis software for identifying peptides and proteoforms in fragmentation mass spectra.

NISTMSPepSearch

NIST MSPepSearch - Search tool of the NIST (National Institute of Standards and Technology) for spectral library searches.

MetaMorpheus

MetaMorpheus - MetaMorpheus search engine.

MzR

mzR - Bioconductor package mzR for reading and writing mass spectrometry data files.

MSnbase

MSnbase - Bioconductor package MSnbase provides infrastructure for manipulation, processing and visualization of mass spectrometry and proteomics data, ranging from raw to quantitative and annotated data.

CAMERA

CAMERA - Bioconductor package CAMERA for annotation of peak lists generated by xcms, rule based annotation of isotopes and adducts, isotope validation, EIC correlation based tagging of unknown adducts and fragments.

SmallMoleculeAnalysisSoftware

small molecule analysis software - Software for the analysis of small molecules.

ProgenesisQI

Progenesis QI - Metabolomics analysis software for LC-MS data from Nonlinear Dynamics.

CompoundDiscoverer

Compound Discoverer - Metabolomics analysis software from Thermo Fisher Scientific.

MyCompoundID

MyCompoundID - Metabolite identification tool MyCompoundID.

TopPIC

TopPIC - TopPIC: a software tool for top-down mass spectrometry-based proteoform identification and characterization.

TopFD

TopFD - Top-down mass spectral feature detection.

TopMG

TopMG - A mass graph-based approach for the identification of modified proteoforms using top-down tandem mass spectra.

LipidomicsAnalysisSoftware

lipidomics analysis software - Lipidomics analysis software.

LipidDataAnalyzer

Lipid Data Analyzer - Lipid Data Analyzer software for lipid quantification.

LipidHunter

LipidHunter - Software for identification of phospholipids by high-throughput processing of LC-MS and shotgun lipidomics datasets.

LipidXplorer

LipidXplorer - Software for consensual cross-platform lipidomics.

LipidMatch

LipidMatch - An automated workflow for rule-based lipid identification using untargeted high-resolution tandem mass spectrometry data.

Greazy

Greazy - Open-source software for automated phospholipid tandem mass spectrometry identification.

LipidBlast

LipidBlast - LC-MS-based lipidomics and automated identification of lipids using the LipidBlast in-silico MS/MS library.

LipidPro

Lipid-Pro - A computational lipid identification solution for untargeted lipidomics on data-independent acquisition tandem mass spectrometry platforms.

LipidFinder

LipidFinder - A computational workflow for the discovery of lipids for the identification of eicosanoid-phosphoinositides in platelets.

LipiDex

LipiDex - An integrated software package for high-confidence lipid identification.

LIQUID

LIQUID - An-open source software for identifying lipids in LC-MS/MS-based lipidomics data.

ALEX

ALEX - Analysis of lipid experiments, a calculator for m/z values of intact lipid molecules (MS1).

ALEX123

ALEX123 - Analysis of lipid experiments 123, a calculator with m/z values of intact lipid molecules (MS1) and their fragment ions at the MS2 and MS3 level.

LIMSA

LIMSA - Software tool for the quantitative analysis of mass spectrometric lipidome data.

LOBSTAHS

LOBSTAHS - Adduct-Based lipidomics software for the discovery and identification of oxidative stress biomarkers.

LipidQA

LipidQA - Lipid qualitative/quantitative analysis software for identification and quantitation of complex lipid molecular species.

Proline

Proline - The Proline software suite for mass spectrometry based proteomics.

PepNovo

PepNovo - PepNovo tool for de novo peptide sequencing.

PNovo

pNovo - pNovo tool for de novo peptide sequencing and identification using HCD spectra.

Novor

Novor - Novor real-time peptide de novo sequencing software tool.

IdentiPy

IdentiPy - IdentiPy.

MsDeisotope

ms_deisotope - ms_deisotope, a library for deisotoping and charge state deconvolution of mass spectra.

PythonPsims

python-psims - python-psims, a library for generating mzML and mzIdentML.

LPPtiger

LPPtiger - Software for lipidome-specific prediction and identification of oxidized phospholipids from LC-MS datasets.

PFind

pFind - Sequence-tag-based search engine pFind.

I3tms

i3tms - i3-tms search engine and data-analysis software.

MSFragger

MSFragger - A database search-based peptide identification tool.

Philosopher

Philosopher - General proteomics processing toolkit for shotgun proteomics.

OpenPepXL

OpenPepXL - Cross-Linking MS search engine.

MSDIAL

MS-DIAL - Data processing software for untargeted metabolomics and lipidomics that supports multiple instruments and MS vendors.

PatternLab

PatternLab - PatternLab for Proteomics is an integrated computational environment for analyzing shotgun proteomic data.

SIMXL

SIM-XL - Identifying crosslinked peptides in complex protein mixtures

QUINXL

QUIN-XL - Quantification of crosslinked peptides in complex protein mixtures

EPIFANY

EPIFANY - A Method for Efficient High-Confidence Protein Inference. The tool is part of the OpenMS framework

ProSight

ProSight - ProSight: Database search engine for top-down proteomics.

TDPortal

TDPortal - TDPortal: Database search engine for top-down proteomics.

ThermoRawFileParser

ThermoRawFileParser - Cross-platform software to convert Thermo RAW files to a number of open formats.

Pyteomics

pyteomics - Python module that helps handling various proteomics data analysis tasks.

PTXQC

PTX-QC - Proteomics (PTX) - QualityControl (QC) software for QC report generation and visualization.

QuaMeterIDFree

QuaMeter IDFree - QuaMeter IDFree software for QC metric calculation.

IMonDB

iMonDB - iMonDB software to extract, store, and manage mass spectrometry instrument parameters from raw data files.

BiblioSpec

BiblioSpec - A suite of software tools for creating and searching MS/MS peptide spectrum libraries, developed at the University of Washington

LibraryCreationSoftware

library creation software - Library creation software

PeakForest

PeakForest - comprehensive infrastructure to organize, curate and share a multi- instrument spectral library for metabolomics data annotation developed and distributed by the French National infrastructure in metabolomics and fluxomics (MetaboHUB).

DIANN

DIA-NN - A universal software for data-independent acquisition (DIA) proteomics data processing

Casanovo

Casanovo - Casanovo is a deep learning-based de novo spectrum identification tool. Official website https://github.com/Noble-Lab/casanovo/.

Goslin

Goslin - The Goslin implementations parse common lipid name dialects and normalize them to the recent lipid shorthand nomenclature based on grammars on succinct lipid nomenclature.

ANNSoLo

ANN-SoLo - ANN-SoLo (Approximate Nearest Neighbor Spectral Library) is a spectral library search engine for fast and accurate open modification searching. ANN-SoLo uses approximate nearest neighbor indexing to speed up open modification searching by selecting only a limited number of the most relevant library spectra to compare to an unknown query spectrum. This is combined with a cascade search strategy to maximize the number of identified unmodified and modified spectra while strictly controlling the false discovery rate and the shifted dot product score to sensitively match modified spectra to their unmodified counterpart.

ChemClipse

ChemClipse - ChemClipse is part of the Eclipse Science project. Primarily developed by Lablicate GmbH.

OpenChrom

OpenChrom - OpenChrom is an Open Source software for data processing and analysis. Based upon Eclipse ChemClipse.

WatersConnect

waters_connect - Waters Corporation waters_connect software for liquid chromatography and mass spectrometry acquisition and processing.

Spectra

Spectra - Bioconductor package Spectra for mass spectrometry data representation and processing.

MetaboAnnotation

MetaboAnnotation - Bioconductor package MetaboAnnotation for annotation of untargeted metabolomics data.

CompoundDb

CompoundDb - Bioconductor package CompoundDb for creation, usage and maintenance of public or library-specific annotation databases and spectra libraries.

QualityControlSoftware

quality control software - Software that creates or manipulates QC-related data.

Rmzqc

rmzqc - An R package for reading, validating, and writing mzQC files.

Jmzqc

jmzqc - A Java package for reading, validating, and writing mzQC files.

Pymzqc

pymzqc - A Python package for reading, validating, and writing mzQC files.

MzRecal

mzRecal - MS1 recalibration using identified peptides as internal calibrants.

SpectrumClusteringSoftware

spectrum clustering software - Software designed to group multiple mass spectra by high similarity, generally with the goal of grouping replicate spectra derived from the same analyte.

Scout

Scout - Identifying crosslinked peptides in complex protein mixtures

Kojak

Kojak - Kojak open-source crosslinked peptide sequence search engine developed at the Institute for Systems Biology.

Quantms

quantms - Cloud-based pipeline for quantitative proteomics that enables the reanalysis of public proteomics data.

XQuestXProphet

xQuest/xProphet - A software to identify cross-linked peptides from LC-MS/MS spectra.

PeakView

PeakView - A software for spectral analysis and data interrogation in qualitative review of LC-MS and MS/MS data.

Perseus

Perseus - A software for interpreting protein quantification, interaction and post-translational modification data.

FragPipe

FragPipe - A computational platform for analyzing mass spectrometry-based proteomics data.

OpenMS

OpenMS - A software for LC-MS data management and analysis.

PLink

pLink - A tool for the analysis of chemically cross-linked proteins using mass spectrometry.

PLink2

pLink2 - Upgraded version of pLink tool, provides a graphical user interface and faster with newly designed index structure.

SCIEXOS

SCIEX OS - SCIEX OS software.

SCIEXMSDataConverter

SCIEX MS Data Converter - A software for converting SCIEX wiff or wiff2 format to mzML.

TimsControl

timsControl - Bruker software for data acquisition.

MetaboScape

MetaboScape - Bruker software for untargeted metabolomics and lipidomics data analysis.

TASQ

TASQ - Bruker software for target screening and quantitation.

InstaNovo

InstaNovo - InstaNovo is a deep learning based tool using a Transformer architecture for de novo peptide sequencing.

InstaNovoplus

InstaNovo+ - InstaNovo+ is a deep learning based tool using a Diffusion architecture for de novo peptide sequencing.

MsQuality

MsQuality - MsQuality – an interoperable open-source package for the calculation of standardized quality metrics of mass spectrometry data.

DIAMetric

DIAMetric - DIAMetric is a Data-Independent Acquisition Quality Metric Generator.

Implementations

impl SoftwareTerm

These methods are part of the controlled vocabulary mapping

pub const fn accession(&self) -> u32

Retrieve the accession number for this term, independent of its controlled vocabulary

pub const fn controlled_vocabulary(&self) -> ControlledVocabulary

Retrieve the controlled vocabulary this term belongs to

pub const fn name(&self) -> &'static str

Retrieve the plain text human readable name for this term

pub fn from_name(name: &str) -> Option<SoftwareTerm>

Attempt to map a string by name to retrieve one of the terms from this set.

If no match is found, None is returned.

pub const fn from_accession(accession: u32) -> Option<SoftwareTerm>

Attempt to map the numeric accession number to retrieve one of the terms from this set.

If no match is found, None is returned.

pub const fn to_param(self) -> ParamCow<'static>

Convert this term into a ParamCow without a value.

pub const fn from_curie(curie: &CURIE) -> Option<SoftwareTerm>

Convert a CURIE by accession.

If no match is found, None is returned.

pub const fn from_param(p: &ParamCow<'static>) -> Option<SoftwareTerm>

Attempt to convert a ParamCow to a term from this set.

If no match is found, None is returned.

Note

This method can be called in const contexts, requiring the type be ParamCow with a 'static lifetime parameter, but the regular From trait is implemented for all ParamLike types.

pub fn flags(&self) -> SoftwareType

Retrieve a term set specific set of flags

pub fn parents(&self) -> Vec<SoftwareTerm>

Retrieve the list of zero or more terms in the set which are parents of this term.

Trait Implementations

impl Clone for SoftwareTerm

fn clone(&self) -> SoftwareTerm

Returns a duplicate of the value.

fn clone_from(&mut self, source: &Self)

Performs copy-assignment from source.

impl Debug for SoftwareTerm

fn fmt(&self, f: &mut Formatter<'_>) -> Result<(), Error>

Formats the value using the given formatter.

impl From<&SoftwareTerm> for Param

fn from(value: &SoftwareTerm) -> Param

Converts to this type from the input type.

impl From<&SoftwareTerm> for ParamCow<'static>

fn from(value: &SoftwareTerm) -> ParamCow<'static>

Converts to this type from the input type.

impl<P> From<P> for SoftwareTerm

where P: ParamLike,

fn from(value: P) -> SoftwareTerm

Converts to this type from the input type.

impl From<SoftwareTerm> for Param

fn from(value: SoftwareTerm) -> Param

Converts to this type from the input type.

impl From<SoftwareTerm> for ParamCow<'static>

fn from(value: SoftwareTerm) -> ParamCow<'static>

Converts to this type from the input type.

impl PartialEq for SoftwareTerm

fn eq(&self, other: &SoftwareTerm) -> bool

Tests for self and other values to be equal, and is used by ==.

fn ne(&self, other: &Rhs) -> bool

Tests for !=. The default implementation is almost always sufficient, and should not be overridden without very good reason.

impl Copy for SoftwareTerm

impl Eq for SoftwareTerm

impl StructuralPartialEq for SoftwareTerm