CalibraCurveA highly useful and flexible tool for calibration of targeted MS‐based measurements. CalibraCurve enables an automated batch-mode determination of dynamic linear ranges and quantification limits for both targeted proteomics and similar assays. The software uses a variety of measures to assess the accuracy of the calibration and provides intuitive visualizations.https://github.com/mpc-bioinformatics/CalibraCurvecalibracurvebiotools:calibracurve2.0WorkflowScriptDesktop applicationPlug-inhttp://edamontology.org/topic_0121Proteomicshttp://edamontology.org/topic_3678Experimental design and studiesLinuxWindowsMacRBSD-3-ClauseBioInfra.Protde.NBICUBiMed.RUBMatureFree of chargeOpen accessToolsProteomicsGermanyhttp://edamontology.org/operation_2945Analysishttp://edamontology.org/data_2526Text datahttp://edamontology.org/format_3752CSVhttp://edamontology.org/operation_0337Visualisationhttps://github.com/mpc-bioinformatics/CalibraCurveRepositoryhttps://github.com/mpc-bioinformatics/CalibraCurveDownloads page2.0https://github.com/mpc-bioinformatics/CalibraCurveInstallation instructionsCitation instructionsGeneralUser manualTraining materialTerms of use10.1002/pmic.20190014332086983Primary2.0PD Dr. Martin Eisenachermartin.eisenacher@rub.dePersonProviderPrimary contactIf contacting use "SPARROW" in subject line to avoid mail deluge.de.NBIhttps://www.denbi.de/ProjectProviderMaintainerSupportService provision and maintenance funded by de.NBI.Dr. Michael Kohlmichael.kohl@rub.dePersonDeveloperMetaProteomeAnalyzer-CloudThe MetaProteomeAnalyzer Cloud (MPA Cloud) is an intuitive, open-source tool for metaproteomics data analysis and interpretation, designed to analyse comprehensive metaproteomics data from tandem mass spectrometry experiments through a web interface.https://mdoa-tools.bi.denbi.de/mpacloud/mpa-cloudbiotools:mpa-cloudWeb servicehttp://edamontology.org/topic_0078Proteinshttp://edamontology.org/topic_4060Metaproteomicshttp://edamontology.org/topic_0121ProteomicsJavaTypeScriptGPL-3.0MatureFree of chargeOpen accessGermanyhttps://gitlab.com/mdoa-group/mpa-websiteRepositoryhttps://gitlab.com/mdoa-group/mpa-cloud-serverRepositoryhttps://mdoa-tools.bi.denbi.de/mpacloud/documentationUser manualmetaproteomeanalyzerisNewVersionOfmpa_portableisNewVersionOf10.1038/s41596-020-0368-73285998410.3389/fmicb.2019.0188331474963PMC670742510.1021/acs.analchem.7b0354429215871PMC575722010.1021/pr501246w25660940Kay SchallertDaniel KautznerBenjamin J. SaalfeldProf. Dr.-Ing. Robert HeyerLudwig KnocheMalte BöttcherPolySTestRobust statistical testing of quantitative proteomics data. The tool comprises and combines different tests and includes a new method for combined statistics of quantitative and missing values.http://computproteomics.bmb.sdu.dk/app_direct/PolySTestPolySTestbiotools:PolySTestWeb applicationhttp://edamontology.org/topic_0121Proteomicshttp://edamontology.org/topic_3520Proteomics experimenthttp://edamontology.org/topic_2269Statistics and probabilityLinuxMacRGPL-2.0MatureFree of chargeOpen accessDenmarkhttp://edamontology.org/operation_3664Statistical modellinghttp://edamontology.org/operation_3741Differential protein expression profilinghttp://edamontology.org/data_2603Expression datahttp://edamontology.org/format_3751DSVhttp://edamontology.org/format_3752CSVhttps://github.com/computproteomics/PolySTestRepository10.1074/mcp.RA119.00177732424025PMC8015005PrimaryDigestedProteinDBDigestedProteinDB provides a scalable computational infrastructure for indexing and querying peptide cleavage data. Designed for seamless integration into high-throughput mass spectrometry pipelines, it enables low-latency searches and advanced filtering of digested protein datasets to accelerate experimental spectra cross-referencing.https://digestedproteindb.pbf.hrdigestedproteindbbiotools:digestedproteindbDatabase portalhttp://edamontology.org/topic_0121ProteomicsPyProphetPyProphet is a tool for semi-supervised learning and scoring of OpenSWATH results in mass-spectrometry based proteomics.https://github.com/PyProphet/pyprophetpyprophetbiotools:pyprophet3.0.14Command-line toolhttp://edamontology.org/topic_0121Proteomicshttp://edamontology.org/topic_0091BioinformaticsLinuxPythonBSD-3-ClauseMatureFree of chargehttp://edamontology.org/operation_3631Peptide identificationhttp://edamontology.org/operation_3630Protein quantificationhttp://edamontology.org/operation_2238Statistical calculationhttp://edamontology.org/data_0943Mass spectrumhttp://edamontology.org/format_2333Binary formathttps://pyprophet.readthedocs.io/API documentationUser manual10.1038/nmeth.158421423193Primary10.1038/nmeth.439828825704PMC5581544MethodProteoPyProteoPy is a lightweight Python library for protein- and peptide-level quantitative proteomics analysis, built around the AnnData class as its core data structure. It streamlines data import, preprocessing, and differential analysis while preserving all metadata within a single object.https://proteopy.readthedocs.io/en/latest/proteopybiotools:proteopy0.1.1Libraryhttp://edamontology.org/topic_0091Bioinformaticshttp://edamontology.org/topic_3520Proteomics experimentWindowsMacLinuxPythonApache-2.0mass spectrometryproteomicsEmergingFree of chargeOpen accesshttps://github.com/UKHD-NP/proteopyRepositoryhttps://github.com/UKHD-NP/proteopy/discussionsDiscussion forumhttps://github.com/UKHD-NP/proteopy/issuesIssue trackerhttps://proteopy.readthedocs.io/en/latest/OtherDocumentationhttps://github.com/UKHD-NP/proteopy/archive/refs/heads/main.zipSource codehttps://proteopy.readthedocs.io/en/latest/Generalanndatauses10.64898/2026.03.31.715273PreprintIsabell Bludauisabell.bludau@med.uni-heidelberg.dehttps://orcid.org/0000-0002-2601-238XPersonPrimary contactJunior Group Leader at the Department of Neuropathology, University Hospital HeidelbergIan Dirk FichtnerIanDirk.Fichtner@med.uni-heidelberg.dehttps://orcid.org/0009-0002-3000-2907PersonDeveloperPhD student at the Department of Neuropathology, University Hospital Heidelberg and Division of Artificial Intelligence in Oncology, German Cancer Research Center (DKFZ)Omics StudioOmics Studio is a bioinformatics platform designed to support the exploration, contextualization, interpretation, and presentation of omics data. It provides guided workflows, visualization, annotation, database search, and analysis tools that help researchers work more efficiently with complex biological datasets.
Omics Studio is intended for use in applications such as biomarker discovery, systems biology, and precision medicine.https://omicsstudio.comomics_studiobiotools:omics_studio1.0Web applicationhttp://edamontology.org/topic_0091Bioinformaticshttp://edamontology.org/topic_0121Proteomicshttp://edamontology.org/topic_3172Metabolomicshttp://edamontology.org/topic_3308Transcriptomicshttp://edamontology.org/topic_4021MultiomicsMacLinuxWindowsOtherProprietaryProteomicsTranscriptomicsmetabolomic platformMatureCommercialhttp://edamontology.org/operation_2945Data analysishttp://edamontology.org/operation_0226Annotationhttp://edamontology.org/operation_0337Visualisationhttp://edamontology.org/operation_3501Enrichment analysishttp://edamontology.org/operation_3928Pathway analysishttps://platform.omicsstudio.comServiceIf you already have an account, or would like to sign up, please use this link. If you do not yet have access, contact support@omicsstudio.com.https://help.omicsstudio.com/Quick start guideESIprotCharge state determination and molecular weight calculation for low resolution electrospray ionization data.https://nube-gran.de/esiprotesiprotbiotools:esiprotWeb applicationDesktop applicationhttp://edamontology.org/topic_0121Proteomicshttp://edamontology.org/topic_3520Proteomics experimentLinuxWindowsMacPythonGPL-3.0ms-utilsProteomicshttp://edamontology.org/operation_0398Protein molecular weight calculationhttp://edamontology.org/operation_2929Protein fragment weight comparisonhttp://edamontology.org/operation_3629Deisotopinghttp://edamontology.org/data_0944Peptide mass fingerprinthttp://edamontology.org/format_3245Mass spectrometry data formathttp://www.bioprocess.org/esiprot/esiprot_form.phpMirrorhttp://ms-utils.orgSoftware cataloguehttp://www.bioprocess.org/esiprot/esiprot.zipSource codehttp://www.bioprocess.org/esiprot/esiprot.zipSource codehttp://www.lababi.bioprocess.org/index.php/lababi-software/84-esiprotGeneral10.1002/rcm.438420049890Robert Winklerrobert.winkler@ira.cinvestav.mxPersonMaintainerwebmaster@ms-utils.orghttp://ms-utils.orgPersonDocumentorPyxisPyxis is a vendor-neutral desktop application for ion mobility spectrometry imaging (IMS-MSI) data analysis, supporting both untargeted and targeted analysis workflows. The software is designed to address the challenges of analyzing complex IM-MSI datasets.https://mass-analytica.com/products/pyxis/pyxisbiotools:pyxishttp://edamontology.org/topic_3172Metabolomicshttp://edamontology.org/topic_3931Chemometricshttp://edamontology.org/topic_3520Proteomics experimenthttp://edamontology.org/topic_3382Imaginghttp://edamontology.org/topic_0121Proteomicshttp://edamontology.org/operation_3803Natural product identificationhttp://edamontology.org/operation_3215Peak detectionhttp://edamontology.org/operation_3891Essential dynamics10.1007/S00216-025-06281-541420743Sara Tortorellasara.tortorella@mass-analytica.comhttps://orcid.org/0000-0001-9691-8323PersonJens SoltwischJens.Soltwisch@ukmuenster.dehttps://orcid.org/0000-0002-0258-1561PersonProTransDeconvProTransDeconv is an R package designed for deconvolving cell-type-specific protein expression from bulk mass spectrometry proteomics data. It integrates data transformation, deconvolution, and quality checks and provides practical guidance for researchers.https://github.com/HuangLabAtUAB/ProTransDeconvprotransdeconvbiotools:protransdeconvhttp://edamontology.org/topic_0121Proteomicshttp://edamontology.org/topic_3922Proteogenomicshttp://edamontology.org/topic_0080Sequence analysishttp://edamontology.org/topic_2640Oncologyhttp://edamontology.org/topic_3520Proteomics experimentRhttp://edamontology.org/operation_3799Quantificationhttp://edamontology.org/operation_0314Gene expression profilinghttp://edamontology.org/operation_3629Deisotoping10.1021/ACS.JPROTEOME.5C0098041328725PMC12772123Chen Huanghuangc@uab.eduhttps://orcid.org/0000-0003-2777-7365PersonMMSA (Multiple Mass Spectral Alignment)MMSA is an interactive web-based tool that improves the interpretability of molecular networks by visualizing detailed spectral alignment information. It enables users to explore and analyze the global alignment of molecular networks, providing insights into structural relationships within molecular families.https://wang-bioinformatics-lab.github.io/GNPS2_Documentation/mmsa/mmsabiotools:mmsahttp://edamontology.org/topic_3172Metabolomicshttp://edamontology.org/topic_3520Proteomics experimenthttp://edamontology.org/topic_0081Structure analysishttp://edamontology.org/operation_0492Multiple sequence alignmenthttp://edamontology.org/operation_3925Network visualisationhttp://edamontology.org/operation_0496Global alignmenthttp://edamontology.org/operation_3803Natural product identification10.1021/JASMS.5C0023741328747PMC12724678Xianghu WangPersonMingxun Wangmingxun.wang@cs.ucr.eduPersonIHMValidationIHMValidation is a pipeline for assessing integrative hybrid structure models, providing quality assessments and data fit evaluations for PDB-IHM entries. It incorporates recommendations from various structural biology communities and offers reports in PDF and HTML formats.https://github.com/salilab/IHMValidationihmvalidationbiotools:ihmvalidationhttp://edamontology.org/topic_3382Imaginghttp://edamontology.org/topic_0081Structure analysishttp://edamontology.org/topic_0078Proteinshttp://edamontology.org/topic_3520Proteomics experimentSAShttp://edamontology.org/operation_3907Information extractionhttp://edamontology.org/operation_3431Data depositionhttp://edamontology.org/operation_0477Protein modelling10.1016/J.JMB.2025.16959841421450Arthur O Zalevskyarthur.zalevsky@rcsb.orgPersonBrinda Vallatbrinda.vallat@rcsb.orgPersonAndrej Salisali@salilab.orgPersonProtrec2Protrec2 is a probabilistic framework for missing protein recovery in proteomics that integrates tissue-specific protein complex annotations with Bayesian inference. It outperforms existing methods and has been validated on HeLa and A549 proteomes, demonstrating biological and clinical relevance.https://github.com/miaomiao6606/Protrec2protrec2biotools:protrec2http://edamontology.org/topic_0121Proteomicshttp://edamontology.org/topic_0080Sequence analysishttp://edamontology.org/topic_0108Protein expressionhttp://edamontology.org/topic_2640Oncologyhttp://edamontology.org/topic_4021Multiomicshttp://edamontology.org/operation_2489Subcellular localisation predictionhttp://edamontology.org/operation_3557Imputationhttp://edamontology.org/operation_3767Protein identificationhttp://edamontology.org/operation_2436Gene-set enrichment analysis10.1093/BIB/BBAF69241451539PMC12741561Wilson Wen Bin Gohwilsongoh@ntu.edu.sghttps://orcid.org/0000-0003-3863-7501PersonLimsoon Wongwongls@comp.nus.edu.sghttps://orcid.org/0000-0003-1241-5441PersonReXReX is an R package that infers residue-level hydrogen deuterium exchange (HDX) patterns from HDX-MS data by recasting the analysis as a change-point detection problem. It provides a Bayesian non-parametric model for improved resolution and statistical significance of HDX data.https://ococrook.github.io/RexMS/articles/ReX.htmlrexbiotools:rexhttp://edamontology.org/topic_3520Proteomics experimenthttp://edamontology.org/topic_0154Small moleculeshttp://edamontology.org/topic_3332Computational chemistryhttp://edamontology.org/topic_3306Biophysicshttp://edamontology.org/topic_3068Literature and languagehttp://edamontology.org/operation_3891Essential dynamicshttp://edamontology.org/operation_0404Protein hydrogen exchange rate calculationhttp://edamontology.org/operation_3435Standardisation and normalisationhttp://edamontology.org/operation_3935Dimensionality reductionhttp://edamontology.org/operation_2939Principal component visualisationhttps://olivercrook.shinyapps.io/BRD4-ReX/Otherhttps://ococrook.github.io/RexMS/Other10.1038/S42004-025-01719-441214241PMC12603136Oliver M. Crookoliver.crook@chem.ox.ac.ukhttps://orcid.org/0000-0001-5669-8506PersonGlycoGeniusGlycoGenius is an open-source program offering an automated workflow for glycomics data analysis, featuring a graphical interface to reduce manual effort and facilitate data visualization and quantification.https://github.com/LoponteHF/GlycoGenius_GUIglycogeniusbiotools:glycogeniushttp://edamontology.org/topic_3292Biochemistryhttp://edamontology.org/topic_3520Proteomics experimenthttp://edamontology.org/topic_0769Workflowshttp://edamontology.org/topic_0121Proteomicshttp://edamontology.org/topic_0154Small moleculeshttp://edamontology.org/operation_3860Spectrum calculationhttp://edamontology.org/operation_0337Visualisationhttp://edamontology.org/operation_3215Peak detection10.1038/S41467-025-65265-241285743PMC12644503Hector F. Lopontehectorfloponte@gmail.comhttps://orcid.org/0009-0000-0372-4723PersonKoinaKoina is an open-source model repository and client that democratizes machine learning for proteomics research, enabling remote execution of models via HTTP requests and simplifying model integration into data analysis pipelines.https://koina.wilhelmlab.orgkoinabiotools:koinahttp://edamontology.org/topic_0121Proteomicshttp://edamontology.org/topic_3474Machine learninghttp://edamontology.org/topic_0080Sequence analysishttp://edamontology.org/topic_0154Small moleculeshttp://edamontology.org/topic_0769WorkflowsRApache-2.0http://edamontology.org/operation_3631Peptide identificationhttp://edamontology.org/operation_3435Standardisation and normalisationhttp://edamontology.org/operation_3633Retention time predictionhttps://bioconductor.org/packages/koinar/Repositoryhttps://koina.wilhelmlab.org/docsUser manual10.1038/S41467-025-64870-541219230PMC12606132Alexey I. Nesvizhskiinesvi@med.umich.eduhttps://orcid.org/0000-0002-2806-7819PersonMathias Wilhelmmathias.wilhelm@tum.dehttps://orcid.org/0000-0002-9224-3258PersonLipidQMapLipidQMap is an open-source platform for processing omics-scale quantitative mass spectrometry imaging (qMSI) lipidomics data. It uses one-point calibration and generates concentration heat maps, supporting centroided data import, recalibration, and lipid identification.https://github.com/swinnenteam/LipidQMaplipidqmapbiotools:lipidqmaphttp://edamontology.org/topic_0153Lipidomicshttp://edamontology.org/topic_3520Proteomics experimenthttp://edamontology.org/topic_3382Imaginghttp://edamontology.org/operation_3435Standardisation and normalisationhttp://edamontology.org/operation_3799Quantificationhttp://edamontology.org/operation_0337Visualisation10.1101/2025.10.15.682422Giotto SuiteGiotto Suite is a multiscale and technology-agnostic ecosystem for spatial multiomics data analysis, integration, and visualization. It provides scalable and extensible solutions for processing diverse spatial datasets and integrating molecular, morphology, spatial, and annotated feature information.http://giottosuite.comgiotto_suitebiotools:giotto_suitehttp://edamontology.org/topic_4021Multiomicshttp://edamontology.org/topic_3308Transcriptomicshttp://edamontology.org/topic_0121Proteomicshttp://edamontology.org/topic_0769Workflowshttp://edamontology.org/topic_3382Imaginghttp://edamontology.org/operation_3891Essential dynamicshttp://edamontology.org/operation_0314Gene expression profilinghttp://edamontology.org/operation_0337Visualisation10.1038/S41592-025-02817-W41034612PMC12510873Guo-Cheng Yuanguo-cheng.yuan@mssm.eduhttps://orcid.org/0000-0002-2283-4714PersonRuben Driesrdries@bu.eduhttps://orcid.org/0000-0001-7650-7754PersonMS2extractMS2extract is an R package for creating MS/MS spectral libraries by importing mass spectrometry data, extracting desired spectra, and exporting them in .msp format. It facilitates the creation of in-house libraries suitable for compound identification and is compatible with GNPS2.https://www.cooperstonelab.com/MS2extract/ms2extractbiotools:ms2extracthttp://edamontology.org/topic_3343Compound libraries and screeninghttp://edamontology.org/topic_3520Proteomics experimenthttp://edamontology.org/topic_3172MetabolomicsRhttp://edamontology.org/operation_3803Natural product identificationhttp://edamontology.org/operation_3860Spectrum calculationhttp://edamontology.org/operation_3646Peptide database searchhttp://edamontology.org/operation_3644de Novo sequencing10.1101/2025.10.05.680545Jessica L. CooperstonePersonProteomeGenerator3ProteomeGenerator3 is a proteogenomics workflow for discovering cryptic and non-canonical cancer proteoforms, integrating long-read transcriptomics and multi-dimensional proteomics. It is available open-source and designed for identifying disease biomarkers and therapeutic targets.https://github.com/kentsislab/proteomegenerator3proteomegenerator3biotools:proteomegenerator3http://edamontology.org/topic_3922Proteogenomicshttp://edamontology.org/topic_3520Proteomics experimenthttp://edamontology.org/topic_0121Proteomicshttp://edamontology.org/topic_0080Sequence analysishttp://edamontology.org/topic_4056Long-read sequencinghttp://edamontology.org/operation_3258Transcriptome assemblyhttp://edamontology.org/operation_3799Quantificationhttp://edamontology.org/operation_0337Visualisation10.1101/2025.08.23.671943MBC PathNetMBC PathNet integrates and visualizes networks of functionally related pathways predicted from transcriptomic and proteomic datasets. The tool utilizes the Molecular Biology of the Cell Ontology and other ontologies to facilitate exploration of shared and distinct mechanisms across datasets.http://iyengarlab.org/mbcpathnetmbc_pathnetbiotools:mbc_pathnethttp://edamontology.org/topic_0602Molecular interactions, pathways and networkshttp://edamontology.org/topic_0121Proteomicshttp://edamontology.org/topic_3308Transcriptomicshttp://edamontology.org/topic_0089Ontology and terminologyhttp://edamontology.org/topic_2229Cell biologyhttp://edamontology.org/operation_3925Network visualisationhttp://edamontology.org/operation_3501Enrichment analysishttp://edamontology.org/operation_3926Pathway visualisationhttp://edamontology.org/operation_3929Metabolic pathway prediction10.1093/BIOADV/VBAF19740917650PMC12413227Jens Hansenjens.hansen@mssm.eduhttps://orcid.org/0000-0002-1362-6534PersonMassVisionMassVision is an open-source platform built on 3D Slicer for AI-driven mass spectrometry imaging analysis. It provides an end-to-end workflow to address the complexities of MSI data, integrating visualization, segmentation, and statistical analysis.https://SlicerMassVision.readthedocs.io/massvisionbiotools:massvisionhttp://edamontology.org/topic_3520Proteomics experimenthttp://edamontology.org/topic_3382Imaginghttp://edamontology.org/topic_0769Workflowshttp://edamontology.org/topic_3500Zoologyhttp://edamontology.org/topic_3474Machine learninghttp://edamontology.org/operation_0337Visualisationhttp://edamontology.org/operation_3443Image analysishttp://edamontology.org/operation_3214Spectral analysis10.1021/ACS.ANALCHEM.5C0401840966530NuXLNuXL is a tool for identifying RNA- and DNA-protein interaction sites using chemical crosslinking and mass spectrometry. It is available as a standalone tool, Proteome Discoverer community node, or web application for robust and fast identification of crosslinks at amino acid resolution.https://openms.de/applications/nuxl/nuxlbiotools:nuxlhttp://edamontology.org/topic_0154Small moleculeshttp://edamontology.org/topic_3520Proteomics experimenthttp://edamontology.org/topic_0121Proteomicshttp://edamontology.org/topic_0099RNAhttp://edamontology.org/topic_0769Workflowshttp://edamontology.org/operation_3631Peptide identificationhttp://edamontology.org/operation_3900DNA-binding protein predictionhttp://edamontology.org/operation_0420Nucleic acids-binding site predictionhttp://edamontology.org/operation_3634Label-free quantificationhttp://edamontology.org/operation_3901RNA-binding protein prediction10.1093/NAR/GKAF72740823814PMC12359043Oliver Kohlbacheroliver.kohlbacher@uni-tuebingen.dehttps://orcid.org/0000-0003-1739-4598PersonJuliane Liepejuliane.liepe@mpinat.mpg.dePersonTimo Sachsenbergtimo.sachsenberg@uni-tuebingen.dePersonHenning Urlaubhenning.urlaub@mpinat.mpg.dehttps://orcid.org/0000-0003-1837-5233PersonMASSyPupXMASSyPupX is a Linux distribution designed for mass spectrometry data processing and analysis. It provides a ready-to-use environment with pre-loaded tools for proteomics and metabolomics workflows, enabling decentralized and cost-effective research.https://codeberg.org/LabABI/MASSyPupXmassypupxbiotools:massypupxhttp://edamontology.org/topic_3520Proteomics experimenthttp://edamontology.org/topic_0121Proteomicshttp://edamontology.org/topic_3172Metabolomicshttp://edamontology.org/topic_0080Sequence analysishttp://edamontology.org/topic_0154Small moleculesPythonRBashhttp://edamontology.org/operation_3799Quantificationhttp://edamontology.org/operation_3803Natural product identificationhttp://edamontology.org/operation_3645PTM identificationhttp://edamontology.org/operation_3767Protein identificationhttps://doi.org/10.5281/zenodo.14618430Other10.1016/J.JPROT.2025.10549440754233Robert Winklerrobert.winkler@cinvestav.mxhttps://orcid.org/0000-0001-6732-1958PersonIsoBayesIsoBayes is a Bayesian method for single-isoform proteomics inference, integrating mass spectrometry proteomics and transcriptomics data. The software is available as a Bioconductor R package and accompanied by an example usage vignette.https://figshare.com/projects/IsoBayes_paper_data/183988isobayesbiotools:isobayeshttp://edamontology.org/topic_0121Proteomicshttp://edamontology.org/topic_0154Small moleculeshttp://edamontology.org/topic_0080Sequence analysishttp://edamontology.org/topic_2269Statistics and probabilityhttp://edamontology.org/topic_3520Proteomics experimentRGPL-3.0http://edamontology.org/operation_3630Protein quantificationhttp://edamontology.org/operation_3631Peptide identificationhttp://edamontology.org/operation_3767Protein identificationhttps://bioconductor.org/packages/IsoBayesRepository10.1093/BIOINFORMATICS/BTAF45040796134PMC12377908Gloria M Sheynkmanhttps://orcid.org/0000-0002-4223-9947PersonSimone Tiberisimone.tiberi@unibo.ithttps://orcid.org/0000-0002-3054-9964PersonLLPS DatasetsThe LLPS Datasets resource provides confident protein datasets and benchmarking for liquid-liquid phase separation studies. It offers an intuitive interface and datasets available both as a website and a data repository.https://llpsdatasets.ppmclab.comllps_databases_generate_confident_datasetsbiotools:llps_databases_generate_confident_datasetshttp://edamontology.org/topic_0078Proteinshttp://edamontology.org/topic_3474Machine learninghttp://edamontology.org/topic_2229Cell biologyhttp://edamontology.org/topic_0121Proteomicshttp://edamontology.org/topic_0154Small moleculeshttp://edamontology.org/operation_3216Scaffoldinghttp://edamontology.org/operation_3454Phasinghttp://edamontology.org/operation_3904Protein disorder predictionhttps://doi.org/10.5281/zenodo.15118996Other10.1186/S13059-025-03668-640629388PMC12239342Michał Burdukiewiczmichalburdukiewicz@gmail.comPersonSalvador VenturaSalvador.Ventura@uab.catPersonGlycoAnnotateRGlycoAnnotateR is an R package for *de novo* annotation of glycans in mass spectrometry data, enabling rapid and accurate identification of glycan compositions using a combinatorial, rule-based approach.https://margotbligh.github.io/GlycoAnnotateR/glycoannotaterabiotools:glycoannotaterahttp://edamontology.org/topic_0152Carbohydrateshttp://edamontology.org/topic_3520Proteomics experimenthttp://edamontology.org/topic_3292Biochemistryhttp://edamontology.org/topic_3172Metabolomicshttp://edamontology.org/topic_0102MappingRhttp://edamontology.org/operation_3629Deisotopinghttp://edamontology.org/operation_3860Spectrum calculationhttp://edamontology.org/operation_3627Mass spectra calibration10.1021/JASMS.5C0009340605194PMC12333352Margot Blighmbligh@mpi-bremen.dehttps://orcid.org/0000-0002-7945-7956PersonStatialStatial is an R package on Bioconductor that identifies changes in cell state relative to spatial associations, quantifying the impact of spatial proximity on cell phenotype and uncovering changes in marker expression associated with varying levels of localisation.https://bioconductor.org/packages/release/bioc/html/Statial.htmlstatialbiotools:statialhttp://edamontology.org/topic_0625Genotype and phenotypehttp://edamontology.org/topic_3308Transcriptomicshttp://edamontology.org/topic_0121Proteomicshttp://edamontology.org/topic_2229Cell biologyhttp://edamontology.org/topic_0080Sequence analysisRGPL-3.0http://edamontology.org/operation_0314Gene expression profilinghttp://edamontology.org/operation_3799Quantificationhttp://edamontology.org/operation_3659Regression analysis10.1093/BIOINFORMATICS/BTAF40940674581PMC12343047Ellis Patrickellis.patrick@sydney.edu.auhttps://orcid.org/0000-0002-5253-4747Personhyper.gamhyper.gam is an R package providing a supervised learning framework for deriving biomarkers based on single-cell distribution quantiles, enabling the estimation of quantile index predictors from immunohistochemistry images.https://CRAN.R-project.org/package=hyper.gamhypergambiotools:hypergamhttp://edamontology.org/topic_3360Biomarkershttp://edamontology.org/topic_3474Machine learninghttp://edamontology.org/topic_0625Genotype and phenotypehttp://edamontology.org/topic_0121Proteomicshttp://edamontology.org/topic_3308TranscriptomicsRGPL-2.0http://edamontology.org/operation_3630Protein quantificationhttp://edamontology.org/operation_0337Visualisationhttp://edamontology.org/operation_3659Regression analysishttps://CRAN.R-project.org/package=hyper.gam/vignettes/applications.htmlUser manual10.1093/BIOINFORMATICS/BTAF43040737436PMC12342988Tingting Zhantingting.zhan@jefferson.eduhttps://orcid.org/0000-0001-9971-4844PersoniDOMiDOM is an R package designed for statistical analysis and visualization of dissolved organic matter (DOM) data, particularly derived from Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS). It provides functions for various analyses and aims to bridge the gap between chemical characterization and ecological interpretation.https://github.com/jianjunwang/iDOMiidombiotools:iidomhttp://edamontology.org/topic_0610Ecologyhttp://edamontology.org/topic_3520Proteomics experimenthttp://edamontology.org/topic_0621Model organismshttp://edamontology.org/topic_3047Molecular biologyhttp://edamontology.org/topic_3314ChemistryRhttp://edamontology.org/operation_0310Sequence assemblyhttp://edamontology.org/operation_2238Statistical calculationhttp://edamontology.org/operation_0337Visualisation10.1002/MLF2.7000240600061PMC12207904Jianjun Wangjjwang@niglas.ac.cnhttps://orcid.org/0000-0001-7039-7136PersonCircadian Ontogenetic Metabolomics Atlas (COMA)COMA is an interactive resource providing insights into circadian metabolic rhythms across 16 rat anatomical structures during development. It integrates data from liquid chromatography-mass spectrometry analyses of metabolites across various developmental stages, enabling exploration of circadian metabolic regulation.https://coma.metabolomics.fgu.cas.czcircadian_ontogenetic_metabolomics_atlasbiotools:circadian_ontogenetic_metabolomics_atlashttp://edamontology.org/topic_3172Metabolomicshttp://edamontology.org/topic_0154Small moleculeshttp://edamontology.org/topic_3407Endocrinology and metabolismhttp://edamontology.org/topic_0121Proteomicshttp://edamontology.org/topic_3064Developmental biologyhttp://edamontology.org/operation_3891Essential dynamicshttp://edamontology.org/operation_3435Standardisation and normalisationhttp://edamontology.org/operation_3432Clusteringhttps://circadiomics.igb.uci.eduOther10.1007/S00018-025-05783-W40580317PMC12206216Alena Sumovaalena.sumova@fgu.cas.czPersonTomas Cajkatomas.cajka@fgu.cas.czhttps://orcid.org/0000-0002-9728-3355PersonPathway VolcanoPathway Volcano is an R Shiny application designed to filter and visualize differential expression data by specific pathways, enhancing biological interpretation and facilitating the identification of pathway-related changes. It utilizes the Reactome API to enable pathway-guided data filtering.https://bioconductor.org/packages/ReactomeContentService4R/pathway_volcanobiotools:pathway_volcanohttp://edamontology.org/topic_0602Molecular interactions, pathways and networkshttp://edamontology.org/topic_0203Gene expressionhttp://edamontology.org/topic_0121Proteomicshttp://edamontology.org/topic_3407Endocrinology and metabolismRhttp://edamontology.org/operation_2943Box-Whisker plot plottinghttp://edamontology.org/operation_0571Expression data visualisationhttp://edamontology.org/operation_3926Pathway visualisation10.1093/BIOINFORMATICS/BTAF36740581591PMC12263102Thomas M O’Connellthoconne@iu.eduhttps://orcid.org/0000-0003-4342-9539PersonCasanovoCasanovo is a deep learning model for *de novo* peptide sequencing from mass spectrometry proteomics data. It provides workflows and visualization tools to facilitate adoption and interpretation of results, and is available as open-source software.https://panoramaweb.org/Casanovo_v5.urlcasanovobiotools:casanovohttp://edamontology.org/topic_4060Metaproteomicshttp://edamontology.org/topic_0154Small moleculeshttp://edamontology.org/topic_0769Workflowshttp://edamontology.org/topic_3520Proteomics experimenthttp://edamontology.org/topic_3168Sequencinghttp://edamontology.org/operation_3646Peptide database searchhttp://edamontology.org/operation_3643Tag-based peptide identificationhttp://edamontology.org/operation_3860Spectrum calculationhttp://edamontology.org/operation_3644de Novo sequencinghttps://nf-ms-dda-casanovo.readthedocs.io/User manual10.1101/2025.07.25.666826PepMapVizPepMapViz is an R package for peptide mapping and visualization, enabling import, mapping, and comparative analysis of peptide data from mass spectrometry tools. It aids in visualizing peptide clusters for immunogenicity prediction and exploring protein modifications.https://github.com/Genentech/PepMapVizpepmapvizbiotools:pepmapvizhttp://edamontology.org/topic_0154Small moleculeshttp://edamontology.org/topic_3930Immunogeneticshttp://edamontology.org/topic_0601Protein modificationshttp://edamontology.org/topic_3520Proteomics experimenthttp://edamontology.org/topic_0121ProteomicsRhttp://edamontology.org/operation_0252Peptide immunogenicity predictionhttp://edamontology.org/operation_0416Epitope mappinghttp://edamontology.org/operation_3637Spectral countinghttp://edamontology.org/operation_0337Visualisationhttp://edamontology.org/operation_3645PTM identification10.1093/BIOINFORMATICS/BTAF40440663387PMC12303863Corey E Bakalarskibakalarski.corey@gene.comhttps://orcid.org/0000-0003-1085-7828PersonMassCubeMassCube is an open-source Python framework for MS data processing designed to improve accuracy in metabolomics workflows. It benchmarks against existing algorithms and offers comprehensive reporting for quality assurance, demonstrating ability to handle large datasets and detect batch effects.https://huaxuyu.github.io/masscubedocsmasscubebiotools:masscubehttp://edamontology.org/topic_3172Metabolomicshttp://edamontology.org/topic_3520Proteomics experimenthttp://edamontology.org/topic_0625Genotype and phenotypehttp://edamontology.org/topic_3393Quality affairshttp://edamontology.org/topic_0121ProteomicsPythonhttp://edamontology.org/operation_3628Chromatographic alignmenthttp://edamontology.org/operation_3215Peak detectionhttp://edamontology.org/operation_3283Anonymisation10.1038/S41467-025-60640-540593600PMC12216001Oliver Fiehnofiehn@ucdavis.eduhttps://orcid.org/0000-0002-6261-8928PersoncytoKernelcytoKernel is an R package implementing a kernel-based score test for differential expression analysis of single-cell data, designed to detect subtle variations often missed by traditional methods. It’s available from Bioconductor and offers comprehensive documentation and installation options.http://bioconductor.org/packages/cytoKernelcytokernelbiotools:cytokernelhttp://edamontology.org/topic_3934Cytometryhttp://edamontology.org/topic_0203Gene expressionhttp://edamontology.org/topic_3170RNA-Seqhttp://edamontology.org/topic_4028Single-cell sequencinghttp://edamontology.org/topic_0121ProteomicsRGPL-3.0http://edamontology.org/operation_3223Differential gene expression profilinghttp://edamontology.org/operation_3436Aggregationhttp://edamontology.org/operation_0337Visualisation10.1093/BIOINFORMATICS/BTAF39940658464PMC12312792Tusharkanti Ghoshtusharkanti.ghosh@cuanschutz.eduhttps://orcid.org/0000-0002-7537-6374PersonFragPipeFragPipe is a comprehensive computational platform for analyzing mass spectrometry-based proteomics data, leveraging MSFragger at its core, and integrated with TMT-Integrator for isobaric quantitative proteomic data analysis. It provides extensive documentation and Docker container options for streamlined workflows.https://fragpipe.nesvilab.org/fragpipe_tmt-integratorbiotools:fragpipe_tmt-integratorhttp://edamontology.org/topic_0121Proteomicshttp://edamontology.org/topic_0080Sequence analysishttp://edamontology.org/topic_0601Protein modificationshttp://edamontology.org/topic_0769Workflowshttp://edamontology.org/topic_0154Small moleculeshttp://edamontology.org/operation_0417Post-translational modification site predictionhttp://edamontology.org/operation_3639iTRAQhttp://edamontology.org/operation_3638SILAChttp://edamontology.org/operation_3634Label-free quantification10.1101/2025.05.27.656447WHOOPERWHOOPER is a web application designed to facilitate the analysis of protein co-occurrence across taxa, utilizing HHblits and HMMER to identify remote homologs. It provides an intuitive interface for exploring and analyzing alignment data.https://whooper.migale.inrae.frwhooperbiotools:whooperhttp://edamontology.org/topic_0121Proteomicshttp://edamontology.org/topic_0080Sequence analysishttp://edamontology.org/topic_0160Sequence sites, features and motifshttp://edamontology.org/topic_3168Sequencinghttp://edamontology.org/topic_0114Gene structurehttp://edamontology.org/operation_3767Protein identificationhttp://edamontology.org/operation_2421Database searchhttp://edamontology.org/operation_2422Data retrieval10.1101/2025.06.19.660341SynaptopathyDBSynaptopathyDB is a database integrating data on genes, diseases, mutations, and publications related to synaptic dysfunction and nervous system disorders. It serves as a resource for studying the genetic and synaptic basis of these conditions.http://www.synaptopathyDB.orgsynaptopathydbbiotools:synaptopathydbhttp://edamontology.org/topic_3334Neurologyhttp://edamontology.org/topic_0199Genetic variationhttp://edamontology.org/topic_0625Genotype and phenotypehttp://edamontology.org/topic_0634Pathologyhttp://edamontology.org/topic_0121Proteomicshttp://edamontology.org/operation_3501Enrichment analysishttp://edamontology.org/operation_2421Database searchhttp://edamontology.org/operation_3227Variant calling10.1101/2025.06.27.661932Seth G.N. GrantPersonKETCHUPKETCHUP is a tool for parameterizing kinetic models of cell-free systems using time-series data. It extends existing methods to incorporate temporal data, improving accuracy and predictive power for metabolic simulations.https://github.com/maranasgroup/KETCHUPketchupbiotools:ketchuphttp://edamontology.org/topic_0821Enzymeshttp://edamontology.org/topic_0154Small moleculeshttp://edamontology.org/topic_3172Metabolomicshttp://edamontology.org/topic_3407Endocrinology and metabolismhttp://edamontology.org/topic_0121Proteomicshttp://edamontology.org/operation_2426Modelling and simulationhttp://edamontology.org/operation_3660Metabolic network modellinghttp://edamontology.org/operation_3799Quantification10.1101/2025.06.06.658289MAFcounterMAFcounter is a tool for counting k-mers in Multiple Alignment Format (MAF) files, designed to address a previously unmet need in bioinformatics. The software is multithreaded, fast, and memory efficient, making it suitable for large-scale sequence alignment analysis.https://github.com/Georgakopoulos-Soares-lab/MAFcountermafcounterbiotools:mafcounterhttp://edamontology.org/topic_0121Proteomicshttp://edamontology.org/topic_0080Sequence analysishttp://edamontology.org/topic_0081Structure analysisC++GPL-3.0http://edamontology.org/operation_3182Genome alignmenthttp://edamontology.org/operation_3472k-mer countinghttp://edamontology.org/operation_0335Data formattinghttp://edamontology.org/operation_0492Multiple sequence alignmenthttp://edamontology.org/operation_2479Protein sequence analysis10.1186/S12859-025-06172-740448014PMC12125892Ioannis Mouratidisioannis.mouratidis@psu.eduPersonIlias Georgakopoulos-Soaresizg5139@psu.eduPersonDANGODANGO is a software tool for the automated annotation of glycolipidomic datasets, supporting processing and annotation of mass spectrometry data to characterize glycan and lipid moieties. It integrates with the GRITS Toolbox and proposes candidate structures to the user based on experimental data.http://www.ms-dango.org/dangobiotools:dangohttp://edamontology.org/topic_3520Proteomics experimenthttp://edamontology.org/topic_0219Data curation and archivalhttp://edamontology.org/topic_0621Model organismshttp://edamontology.org/topic_0769Workflowshttp://edamontology.org/topic_0121Proteomicshttp://edamontology.org/operation_3646Peptide database searchhttp://edamontology.org/operation_3860Spectrum calculationhttp://edamontology.org/operation_3215Peak detection10.1016/J.BBADVA.2025.10016140485743PMC12143841Kazuhiro Aokikaoki@mcw.eduPersonRDMSRDMS is a tool for rapid variant prioritization in mitochondrial and other rare diseases, employing untargeted proteomics to quantify proteins and support pathogenicity assessments. It facilitates diagnosis and offers a paradigm shift for functional validation of genetic variants.https://rdms.app/ultra-rapid_genome_sequencingbiotools:ultra-rapid_genome_sequencinghttp://edamontology.org/topic_0121Proteomicshttp://edamontology.org/topic_3325Rare diseaseshttp://edamontology.org/topic_0080Sequence analysishttp://edamontology.org/topic_0821Enzymeshttp://edamontology.org/topic_3520Proteomics experimenthttp://edamontology.org/operation_3891Essential dynamicshttp://edamontology.org/operation_3920DNA testinghttp://edamontology.org/operation_3226Variant prioritisation10.1186/S13073-025-01467-Z40400026PMC12096736Daniella H. Hockdaniella.hock@unimelb.edu.auPersonDavid R. Thorburndavid.thorburn@mcri.edu.auPersonDavid A. Strouddavid.stroud@unimelb.edu.auPersonEndoMAP.v1EndoMAP.v1 is a resource providing a systematic human endosomal structural interactome, combining crosslinking and native gel mass spectrometry with AlphaFold predictions to chart the structural landscape of human early endosome complexes. It offers structural models and a network viewer for understanding organellar structural interactomes.https://endomap.hms.harvard.edu/endomapv1biotools:endomapv1http://edamontology.org/topic_0602Molecular interactions, pathways and networkshttp://edamontology.org/topic_0121Proteomicshttp://edamontology.org/topic_2229Cell biologyhttp://edamontology.org/topic_0080Sequence analysishttp://edamontology.org/topic_0820Membrane and lipoproteinshttp://edamontology.org/operation_0417Post-translational modification site predictionhttp://edamontology.org/operation_0310Sequence assemblyhttp://edamontology.org/operation_0474Protein structure prediction10.1038/S41586-025-09059-Y40437099PMC12222028J. Wade Harperwade_harper@hms.harvard.eduhttps://orcid.org/0000-0002-6944-7236PersonpubCounteRpubCounteR is an R package and web-based interface designed to screen publications for experimentally-derived gene lists within a user-defined biological context, facilitating the biological interpretation of gene lists.https://pubcounter.mpimp-golm.mpg.de/pubcounterbiotools:pubcounterhttp://edamontology.org/topic_3173Epigenomicshttp://edamontology.org/topic_3172Metabolomicshttp://edamontology.org/topic_0218Natural language processinghttp://edamontology.org/topic_0121Proteomicshttp://edamontology.org/topic_3308TranscriptomicsRhttp://edamontology.org/operation_0306Text mininghttp://edamontology.org/operation_0305Literature searchhttp://edamontology.org/operation_2436Gene-set enrichment analysis10.3389/FBINF.2025.152318440438466PMC12118352Marina Leermarina.leer@dife.dePersonTim J. Schulztim.schulz@dife.dePersonbenchmarKINbenchmarKIN is an R package enabling comprehensive evaluation of kinase activity inference methods by combining classical perturbation experiments with a tumor-based benchmarking approach utilizing multi-omics data. The tool helps researchers select reliable methods for identifying deregulated kinases.https://benchmarkin.readthedocs.io/benchmarkinbiotools:benchmarkinhttp://edamontology.org/topic_4021Multiomicshttp://edamontology.org/topic_0121Proteomicshttp://edamontology.org/topic_0601Protein modificationshttp://edamontology.org/topic_0749Transcription factors and regulatory siteshttp://edamontology.org/topic_0080Sequence analysisRhttp://edamontology.org/operation_3891Essential dynamicshttp://edamontology.org/operation_3896Active site predictionhttp://edamontology.org/operation_0417Post-translational modification site prediction10.1038/S41467-025-59779-Y40404650PMC12098709Bing Zhangbing.zhang@bcm.eduhttps://orcid.org/0000-0001-8676-2425PersonJulio Saez-Rodriguezsaezlab@ebi.ac.ukhttps://orcid.org/0000-0002-8552-8976PersonPSIA: Plant Self-Incompatibility AtlasPSIA is a comprehensive knowledgebase providing genomic resources, S gene annotations, and comparative genomic analyses for plant self-incompatibility species. It offers an interactive platform for data retrieval and comparative genomic studies.http://www.plantsi.cnpsiabiotools:psiahttp://edamontology.org/topic_0780Plant biologyhttp://edamontology.org/topic_3293Phylogeneticshttp://edamontology.org/topic_0196Sequence assemblyhttp://edamontology.org/topic_0194Phylogenomicshttp://edamontology.org/topic_0121Proteomicshttp://edamontology.org/operation_3478Phylogenetic reconstructionhttp://edamontology.org/operation_0310Sequence assemblyhttp://edamontology.org/operation_2422Data retrieval10.1093/GPBJNL/QZAF04640397480PMC12396629Yongbiao Xue (薛勇彪)ybxue@genetics.ac.cnhttps://orcid.org/0000-0002-6895-8472PersonTopLibTopLib is a software package designed for building and searching top-down mass spectral libraries for proteoform identification, utilizing an efficient spectral representation to improve performance compared to conventional methods.https://github.com/toppic-suite/toplibtoplibbiotools:toplibhttp://edamontology.org/topic_0121Proteomicshttp://edamontology.org/topic_3520Proteomics experimenthttp://edamontology.org/topic_0080Sequence analysishttp://edamontology.org/topic_3172Metabolomicshttp://edamontology.org/operation_2421Database searchhttp://edamontology.org/operation_3627Mass spectra calibrationhttp://edamontology.org/operation_3860Spectrum calculationhttp://edamontology.org/operation_3801Spectral library searchhttp://edamontology.org/operation_3755PTM localisation10.1021/ACS.ANALCHEM.4C0662740440726PMC12163883Xiaowen Liuxwliu@tulane.eduPersonLipidINLipidIN is a framework for flash platform-independent annotation and reverse lipidomics, offering a large lipid fragmentation library and a fast querying module for improved annotation accuracy and depth.https://github.com/LinShuhaiLAB/LipidINlipidinbiotools:lipidinhttp://edamontology.org/topic_0153Lipidomicshttp://edamontology.org/topic_3520Proteomics experimenthttp://edamontology.org/topic_3474Machine learninghttp://edamontology.org/topic_3360Biomarkershttp://edamontology.org/topic_3407Endocrinology and metabolismhttp://edamontology.org/operation_0224Query and retrievalhttp://edamontology.org/operation_3633Retention time predictionhttp://edamontology.org/operation_4034Multiple testing correction10.1038/S41467-025-59683-540379655PMC12084368Jun Zengjunzeng@jmu.edu.cnhttps://orcid.org/0000-0003-2103-4536PersonZongwei Caizwcai@hkbu.edu.hkhttps://orcid.org/0000-0002-8724-7684PersonShu-Hai Linshuhai@xmu.edu.cnhttps://orcid.org/0000-0002-4782-5320PersonDICED (Database of Identified Cleavage Sites Endemic to Diseases States)DICED is a web interface providing access to proteolytic peptides identified in disease tissues using N-terminomics. The database is searchable and designed to promote collaboration and knowledge sharing in degradomics.https://diced.lerner.ccf.org/dicedbiotools:dicedhttp://edamontology.org/topic_0121Proteomicshttp://edamontology.org/topic_0080Sequence analysishttp://edamontology.org/topic_0154Small moleculeshttp://edamontology.org/topic_0634Pathologyhttp://edamontology.org/topic_4045CybersecuritySQLPythonJavaScripthttp://edamontology.org/operation_2421Database searchhttp://edamontology.org/operation_0366Protein sequence cleavagehttp://edamontology.org/operation_2422Data retrievalhttp://edamontology.org/operation_3755PTM localisation10.1002/PMIC.20250000740351053PMC12246766Jayadev Joshijoshij@ccf.orgPersonSumit Bhutadabhutads@ccf.orgPerson