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63 Free Proteomics Tools - Software and Resources

63 Free Proteomics Tools - Software and Resources

mass spectrometer.


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  1. InSilicoSpectro
    • Description : InSilicoSpectro is a tool containing a comprehensive set of functions for proteomics data analyses. For example, conversion of file formats, digestion of protein sequences, theoretical peptide, and fragment mass computations, matching with experimental data, estimation of isoelectric points, peptide retention time prediction, and also a graphical display.
  2. PatternLab
    • Description : PatternLab is a tool for the analysis of proteomics data. The PatternLab package includes functions for formatting sequence databases, peptide spectrum matching, filtering and organizing, extraction of quantitative information from label-free and labeled data, statistics for differential proteomics, display of results in a variety of formats, similarity studies with de novo sequencing data, analysis of time-course experiments.
  3. ProteoWizard
    • Description : ProteoWizard is a software project that provides a modular and extensible set of cross-platform tools and libraries for proteomics. The also includes the following tools: msConvert (file format conversion), chainsaw (in-silico digestion of amino acid sequences), msAccess (extraction of data/metadata), idConvert (conversion between various file formats), msPicture (pseudo2d gels from mass spectra data), and more.
  4. ProteomeDigestSim
    • Description : ProteomeDigestSim is a collection of R scripts to predict a proteome coverage done using iterative digestion by MED-FASP.
  5. AESOP
    • Description : AESOP is a tool to examine electrostatics in protein Interactions. The AESOP algorithm uses PDB2PQR and Adaptive Poisson-Boltzmann Solver to compute grid-based electrostatic potentials. It can also quantitatively compare the similarity of sets of grid-based electrostatic potentials and generate ensembles of electrostatic potentials for a library of mutants to quantify the effects of disturbances.
  6. Fodis
    • Description : Fodis is a tool for visualization and analysis of force-distance spectroscopy curves of the unfolding of single Molecules from single-molecule force spectroscopy experiments.
  7. Structuprint
    • Description : Structuprint is a tool to represent two-dimensional surfaces of proteins. It can also generate animations and still images.
  8. PyFolding
    • Description : PyFolding is a tool to chart, simulate, and analyze the biophysical properties of proteins. See also a video tutorial (links).
  9. CATALYST
    • Description : CATALYST (Cytometry dATa anALYSis Tools) is a pipeline tool to pre-process cytometry data. The CATALYST package has functions for normalization using bead standards, single-cell deconvolution, and bead-based compensation.
  10. diffcyt
    • Description : diffcyt is an R tool to analyze flow cytometry, mass cytometry or CyTOF, and oligonucleotide-tagged cytometry. The diffcyt package uses a high-resolution clustering and empirical Bayes moderated tests.
  11. InterMineR
    • Description : InterMineR is an R tool to interface with FlyMine, modMine (modENCODE), RatMine, YeastMine, HumanMine, and TargetMine Databases.
  12. phosphonormalizer
    • Description : phosphonormalizer is a tool to normalize mass spectrometry-based label-free phosphoproteomics. The phosphonormalizer algorithm applies the median normalization and uses the overlap between enriched and non-enriched datasets for compensation for the bias caused by global phosphorylation.
  13. SBPKS2
    • Description : SBPKS2 is a web-based tool to analyze polyketide and non-ribosomal peptide synthetases based on structure. A new function to compare the chemical structure of a secondary metabolite to the chemical structures of intermediates and final products. In addition, to identify catalytic domains it uses HMM profile-based searches.
  14. SLiMSearch 4
    • Description : SLiMSearch 4 (Short Linear Motifs Search) is a tool to discover and annotate functional modules. The SLiMSearch algorithm scans a motif consensus, that represents the specificity determinants of a binding domain to discover novel motifs and uses various complementary approaches to exploit the common properties.
  15. CombiROC
    • Description : CombiROC is a web-based tool for selecting marker combinations of omics data. The CombiROC algorithm computes sensitivity and specificity for each markers combination, performances, and ROC curves. It also has an interface for visualization.
  16. SAMNetWeb
    • Description : SAMNetWeb is a tool for functional enrichment analysis and visualization of mRNA expression and global proteomics. SAMNetWeb can identify distinct and common pathways across experiments.
  17. d-Omix
    • Description : d-Omix (a Mixer of Protein Domain Analysis Tools) is a web-based tool to analyze, compare and visualize protein domain combinations. It can construct protein phylogenetic trees using distance matrices calculated from protein domain architectures, calculate and visualize the versatility, abundance, and co-presence of protein domains, compare the similarity of proteins based on domain architecture alignments, build a putative protein network based on domain-domain interactions from DOMINE.
  18. Alloscore
    • Description : Alloscore is a web-based tool to predict allosteric ligand-protein interactions.
  19. Heatmapper
    • Description : Heatmapper is a web-based tool to visualize data as heatmaps. It can generate heatmaps for a wide variety of data, for example, generate, cluster and visualize: (1) expression-based heat maps from transcriptomic, proteomic and metabolomic experiments; (2) pairwise distance maps; (3) correlation maps; (4) image overlay heat maps; (5) latitude and longitude heat maps and (6) geopolitical (choropleth) heat maps.
  20. BetaVoid
    • Description : BetaVoid is a tool to identify molecular voids in the van der Waals or the Lee-Richards, solvent-accessible surfaces. The BetaVoid algorithm also computes mass properties.
  21. AntiAngioPred
    • Description : AntiAngioPred is a web tool to predict anti-angiogenic peptides. The authors have collected the peptides from the literature and analyzed the residue preferences of the peptides.
  22. HUF-ZINC
    • Description : HUF-ZINC is a web-based tool for the prediction of zinc finger motifs in protein sequences. The HUF-ZINC algorithm uses a hidden Markov model (HMM).
  23. CAB-align
    • Description : CAB-align (contact area-based alignment) is a tool to align protein structures. The CAB-align algorithm uses the residue-residue contact area to identify similar regions.
  24. Unipept CLI
    • Description : Unipept CLI is a command-line interface to the Unipept web services (see links).
  25. SteinerNet
    • Description : SteinerNet is a web-based tool to integrate high-throughput omics data for the discovery of components of response pathways. The SteinerNet is replaced by Omics Integrator. See links.
  26. ISPIDER Central
    • Description : ISPIDER Central is a web-based tool to integrate search results from proteomic repositories, such as PRoteomics IDEntifications database (PRIDE), PepSeeker, PeptideAtlas, and the Global Proteome Machine.
  27. Bioverse
    • Description : Bioverse is a sequence annotation server to explore the relationships between molecular, genomic, proteomic, systems and organism information.
  28. xComb
    • Description : xComb is a web-based tool to compute all possible cross-links of a given set of proteins and includes data from, e.g., Phenyx, Mascot, Sequest, OMSSA, X!Tandem. The website doesn't seem to be working.
  29. OmicsIntegrator
    • Description : OmicsIntegrator is a tool to integrate omics data with molecular pathways. The OmicsIntegrator algorithm uses advanced network optimization algorithms.

Protein mass spectrometry tools

  1. ProteinProphet
    • Description : ProteinProphet is a tool to identify proteins by tandem mass spectrometry. The ProteinProphet algorithm uses the expectation-maximization algorithm and learns from a subsequent dataset by how much peptide probabilities should be adjusted.
  2. CPFP
    • Description : CPFP (Central Proteomics Facilities Pipeline) is a tool for identification, validation, and quantitation of peptides and proteins from LC-MS/MS data.
  3. GenePattern
    • Description : GenePattern is a web-based tool that includes PEPPeR (Platform for Experimental Proteomics Pattern Recognition) and several other algorithms, such as 'Landmark Matching' and 'Peak Matching'. It also includes Jupyter Notebooks and analysis pipelines
  4. MASSyPup
    • Description : MASSyPup is a tool for the analysis and visualization of mass spectrometry data. MASSyPup identifies proteins using Peptide Mass Fingerprints (PMF) or LC-MS/MS data, and de novo sequencing.
  5. MzJava
    • Description : MzJava is a tool for the analysis of mass spectrometry data from proteomics and glycomics experiments. MzJava package includes functions for processing fragmentation mass spectra (MSn) and associated molecules, numerous functions for cleaning and transforming MSn spectra, clustering, computation of consensus spectra, contains classes to store peptides and glycans with modifications or substituents, mass calculations and matching to experimental, data import and export.
  6. pFind Studio
    • Description : pFind Studio is a tool to identify proteins using tandem mass spectrometry. The pFind Studio package has four automated workflows for varying requirements. Alternative name: Open-pFind.
  7. Proteomatic
    • Description : Proteomatic is a tool to construct and run MS/MS data analysis pipelines. The Proteomatic package can use both free and commercial software tools.
  8. Pyteomics
    • Description : Pyteomics Python library includes tools for MS analyses. The Pyteomics package includes functions for reading LC-MS/MS data, search engine output, protein sequence databases, the theoretical prediction of retention times, electrochemical properties of polypeptides, mass and m/z calculations, and sequence parsing.
  9. QuPE
    • Description : Rich Internet Application (RIA) QuPE is a tool for the analysis, integration, and storage of proteomics data. Among others, the QuPE has extensive data management and analysis functions for LC-MS/MS experiments. To request an account, contact QuPE _at_ CeBiTec.Uni-Bielefeld.DE.
  10. compareMS2
    • Description : compareMS2 is a tool to calculate overlaps between two LC-MS/MS datasets. The compareMS2 algorithm uses the distribution of spectra dot products of tandem mass spectra collected from two samples compute shared peptides and converts it to distance metric.
  11. enviPat
    • Description : enviPat is a tool to calculate isotope fine structures. The enviPat algorithm uses pruned transition trees. The enviPat package includes functions for instrument-specific envelope and centroid calculation, batch processing, molecular formula parsing for a variety of adducts commonly formed during electrospray ionization (ESI), user-defined inputs cover absolute and relative pruning thresholds, charge states, resolution-dependent envelope discretization, and enriched isotope tables, and more.
  12. OpenMZxy
    • Description : OpenMZxy is a tool for automatic and manual sampling, and the recording of position data for plasma ionization mass spectrometry imaging (LTP-MSI. The OpenMZxy works in various types of mass analyzers and uses Plug and Play components, connected to the Universal Serial Bus (USB).
  13. MSiReader
    • Description : MSiReader is a tool for the analysis and visualization of mass spectrometry data. The standalone version of MSiReader does not require a separate Matlab license.
  14. HX-Express
    • Description : HX-Express is a Microsoft Excel utility to semi-automatically process hydrogen exchange mass spectra. HX-Express produces deuterium uptake and peak width plots from mass spectra.
  15. HDX WorkBench
    • Description : HDX WorkBench is a tool for the analysis of Hydrogen/deuterium exchange mass spectrometry (HDX-MS) data from Waters or Thermo instruments. The HDX WorkBench has functions for calculating the deuteration levels of peptides and visualization tools.
  16. ExMS
    • Description : ExMS is a tool for the analysis of hydrogen exchange-mass spectrometry (HX-MS) data. The ExMS algorithm finds individual isotopic peaks and isotopic envelopes of a list of peptides identified by MS/MS, makes various tests and can process data from many sequential HX time points with no operator intervention.
  17. AUTOHD
    • Description : AUTOHD is a tool to identify and characterize peptides from hydrogen/deuterium exchange experiments using isotopic distributions to fit a model for deuterium exchange with amide hydrogens.
  18. POSTMan
    • Description : POSTMan (POST-translational modification analysis) is a tool to identify post-translationally modified peptides. The POSTMan algorithm aligns LC-MS runs and detects pairs of peptides differing by a defined mass difference.
  19. VIPER (pnl)
    • Description : VIPER (Visual Inspection of Peak/Elution Relationships) is a tool to visualize and characterize the features from LC-MS analyses (FT, TOF, or Orbitrap).
  20. Sirius
    • Description : Sirius is a tool to decompose isotope patterns to de novo identify metabolites from measured isotope patterns in data from a high-resolution mass spectrometer.
  21. Protter
    • Description : Protter is a tool to interactively visualize and integrate annotated features and to generate hypotheses with experimental proteomics data. The Protter also has a function to produce publication-quality protein illustrations.
  22. MSpC
    • Description : Morpheus Spectral Counter (MSpC) is a tool for the calculation of normalized spectral abundance factor (NSAF) values from the output from Morpheus (see links), peptide-MS/MS matching tool.
  23. SDAMS
    • Description : SDAMS is an R tool for the semi-parametric differential abundance analysis using metabolomics and proteomics data from mass spectrometry.
  24. DEP
    • Description : DEP is an R tool for differential enrichment analysis of Proteomics data from e.g., MaxQuant or IsobarQuant.
  25. MSstatsQC
    • Description : MSstatsQC is an R tool for system suitability tests (SST) to verify that mass spectrometric instrumentation performs as specified.
  26. Doscheda
    • Description : Doscheda is an R tool to define protein interaction profiles of small molecules from the whole-cell and tissue lysates using Mass Spectrometry data.
  27. RAId
  28. xiSPEC
    • Description : xiSPEC is a web tool to analyze, visualize, and share mass spectrometry data. It supports both standard proteomics and cross-linking experiments. The web tool has a function for users to store their data either publicly or protected by a password. This gives a way to share the data with collaborators.
  29. Morpheus Spectral Counter
    • Description : Morpheus Spectral Counter is a tool to search high-resolution tandem mass spectra.
  30. MixGF
    • Description : MixGF is a tool for the computation of the statistical significance of peptides matched to a given MS/MS spectrum.
  31. xQuest
    • Description : xQuest is a web-based tool to search Lysine-specific cross-linked peptides and to identify cross-linking sites using LC-MS/MS and the xQuest/xProphet tools.
  32. Specialize
    • Description : Specialize is a tool to identify peptides with complex post-translational modifications from tandem mass spectra. It can identify, for example, UMOylation and Ubiquitylation.
  33. ProSight Lite
    • Description : ProSight Lite is a tool to match protein sequences against a set of mass spectrometric data. It reports multiple scores and a matching fragment list. Dependencies: MathNet.Numerics, DocumentFormat.OpenXML, GalaSoft.MvvmLight, SQLite, NHibernate, Fluent NHibernate, and Quadruple.
  34. LA-iMageS
    • Description : LA-iMageS is a tool to produce 2D and 3D images for the elements in a set from ICP-MS spectra.

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