3V

• Description : 3V (Voss Volume Voxelator) is a tool to compute internal volumes from RNA and protein structures, such as deep clefts, channels, and cavities. The 3V algorithm computes the internal volumes using the differences between two rolling-probe solvent-excluded surfaces, probe radiuses, and solvent radiuses.

AAstretch

• Description : AAstretch is a tool to extract pure and impure poly-residue stretches, such as position, flanking regions, annotations, GO terms, and various other information. The AAstretch package includes AAprepare tool, which links to the genomic EnsEMBL database and utilizes the BioMart services and prepares gene sets for AAstretch. The website contains files from different kingdoms. The CDS function of the AAstretch tool can analyze coding regions that AAexplore tool can visualize.

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.

Alloscore

• Description : Alloscore is a web-based tool to predict allosteric ligand-protein interactions.

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.

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.

Bioverse

• Description : Bioverse is a sequence annotation server to explore the relationships between molecular, genomic, proteomic, systems and organism information.

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.

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.

CHOP

• Description : CHOP is a tool to predict protein domain boundaries using Pfam, PDB, and SWISS-PROT databases. The CHOP algorithm includes a homology-based and neural network-based (CHOPnet) methods.

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.

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.

DAnTE

• Description : Dante is an R tool for general omics data analysis tasks. Dante has functions for Merge, sort, filter, apply arbitrary R commands, Normalization via eigenvalues, linear regression, LOESS, quantiles, Via medians, means or quantiles, Shapiro-Wilks, Kruskal-Wallis statistics, Matrix/Scatterplot, 3D plots using RGL, histogram, QQ, boxplots, ellipses, and Venn diagram. Note that Dante is superseded by InfernoRDN.

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.

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.

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.

HHrep

• Description : HHrep is a web-based tool to de novo identify divergent repeats in protein sequences by pair-wise comparison using hidden Markov models (HMMs). Note that the website (http://hhrep.tuebingen.mpg.de) is not available anymore or temporarily down.

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).

InfernoRDN

• Description : InfernoRDN is a tool to analyze proteomics data. InfernoRDN has functions for
  diagnostic plots, such as histograms, boxplots, correlation plots, qq-plots, peptide-protein rollup plots, MA plots, PCA plots,
  1. Log transforming.
  2. Rolling up to proteins
  3. LOESS normalization
  4. Linear Regression Normalization
  5. Mean Centering
  6. Median Absolute Deviation Adjustment
  7. Quantile Normalization
  8. Principal Component Analysis
  9. Partial Least Squares Analysis
  10. ANOVA
  11. Heatmaps with options for Hierarchical and K-means clustering
  

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.

InterMineR

• Description : InterMineR is an R tool to interface with FlyMine, modMine (modENCODE), RatMine, YeastMine, HumanMine, and TargetMine Databases.

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.

NetChop

• Description : NetChop is a tool to predict cleavage sites of the human proteasome. The NetChop algorithm uses a neural network trained on human proteasome data.

OmicsIntegrator

• Description : OmicsIntegrator is a tool to integrate omics data with molecular pathways. The OmicsIntegrator algorithm uses advanced network optimization algorithms.

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.

Pegasys

• Description : Pegasys is a web-based service containing numerous tools for sequence analyses, such as Agave, Alignment Tools, BRENDA, CpGAT, Edit Tools, Emboss, Information Tools, Kegg Search, Nucleic Tools, Phylogeny Tools, Protein Tools, Sabio - Rk, and Similarity Search Tools.
  
  A user can create custom analysis workflows with the Pegasys system using a graphical interface.

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.

ProteomeDigestSim

• Description : ProteomeDigestSim is a collection of R scripts to predict a proteome coverage done using iterative digestion by MED-FASP.

ProteoWizard

• Description : ProteoWizard toolkit consists of open-source software libraries and applications for proteomics research. The ProteoWizard toolkit includes the following tools: 1. Skyline: Multiple Reaction Monitoring methods and analysis of mass spectrometer data, 2. Filters, 3. idConvert, 4. msaccess: read M/S data files, spectrum binary and metadata, ion chromatograms, and pseudo-2D gel image creation, 5. msconvert, 6. mspicture: pseudo-2D gel image creation together with mapped peptide ID info, 7. qtofpeakpicker: peak detection in Q-TOF raw data.

PyFolding

• Description : PyFolding is a tool to chart, simulate, and analyze the biophysical properties of proteins. See also a video tutorial (links).

RADAR

• Description : RADAR (Rapid Automatic Detection and Alignment of Repeats) is a tool to identify complicated repeat structures. The RADAR algorithm can identify approximate repeats and include gaps. RADAR is available online at EBI on an online web-based tool, through REST, SOAP, Open API Interfaces, Common Workflow Language, and the tool package is available for download, too.

REPPER

• Description : REPPER (REPeats and their PERiodicities) is a web-based tool to detect and analyze short identical repeats in protein sequences. The REPPER algorithm uses Fourier Transform and internal similarity analysis to find periodicities, computes values for properties (e.g., hydrophobicity), predict secondary structure prediction, and coiled-coil prediction.

REPRO

• Description : REPRO is a tool for identification distantly located repeated sequences in proteins. The REPRO algorithm first finds n (n specified by user) top-scoring non-overlapping local alignments by a modified Smith-Waterman method and clusters them using a graph-based process.

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.

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.

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.

SSRCalc

• Description : SSRCalc (Sequence-Specific Retention Calculator), SSRCalcQ (see links below) are a tools to predict peptides’ behavior in reversed-phase HPLC data, such as prediction of retention filtering, method development for targeted (SRM) and data-independent (SWATH, MSE) in LC-MS, and analytical applications of peptide RP-HPLC.
  The SSRCalc algorithm uses retention coefficients summation of the individual amino acids and computes retention coefficients for amino acids at the N-terminal of the peptide, at the C-terminal of the peptide, peptide lengths, hydrophobicity, the nearest-neighbor effect for charged residues, and peptide propensity to form amphipathic helical structures. And, can predict retention for the following chemical modifications: N-terminal cyclization for Gln and Cys alkylated with Iodoacetamide, Methionine oxidation, six types of alkylation chemistries for Cys, TMT, and iTRAQ labels.
  The model organisms include Human, E. Coli, Saccharomyces cerevisiae, Bos taurus, Mus musculus, Neurospora crassa, Canis lupus familiaris, Gallus gallus, Caldicelluosiruptor kristjanssonii, Thermotoga petrophilia, Clostridium termitidis, Pseudomonas aeruginosa, Caldicellulosiruptor saccharoylticus, Acinetobacter baumannii, Thermoanaerobacter thermohydrosulfuricus, Ralstonia eutropha, Clostridium butryricum, Pseudomonas putida, Thermobifida fusca, Yarrowia lioplytica, and Clostridium thermocellum.

StavroX

• Description : StavroX and MeroX are a single tool for the analysis of complex peptide-peptide cross-links. The Authors have evaluated the StavroX algorithm with 1. the complex between calmodulin and a peptide derived from Munc13, 2. an N-terminal beta-laminin fragment, and (3) the complex between guanylyl cyclase-activating protein-2 and a peptide derived from retinal guanylyl cyclase.

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.

Structuprint

• Description : Structuprint is a tool to represent two-dimensional surfaces of proteins. It can also generate animations and still images.

Tally

• Description : Tally is a tool to validate the quality of detection of tandem repeats in protein sequences. The Tally algorithm uses machine learning and outputs various scores, such as entropy, Psim, p-value-phylo, and parsimony.

TAPO

• Description : TAPO (TAndemPrOtein detector) is a web-based tool to identify elements repeated in tandem in protein sequences. The TAPO algorithm uses atomic coordinate periodicities, strings generated by conformational alphabets, residue contact maps, and arrangements secondary structure elements.

TRDistiller

• Description : TRDistiller is a tool to enrich protein data sets containing tandem repeats. The TRDistiller algorithm compares the composition and the order of adjacent sequence motifs. Available from the Authors upon request.

Unipept CLI

• Description : Unipept CLI is a command-line interface to the Unipept web services (see links).

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.

Protein mass spectrometry tools

Andromeda

• Description : Andromeda is a tool to identify peptides from tandem mass spectrometry (MS/MS). The Andromeda algorithm uses probabilistic scoring, computes scores for complicated patterns of post-translational modifications, and handles high fragment mass accuracy. Andromeda comes as a standalone tool or as integrated into MaxQuant

APLToMGFConverter

• Description : APLToMGFConverter is a tool to convert MaxQuant APL peaklist files to MGF compatible peaklist files.

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.

BioLCCC

• Description : BioLCCC model is available as a web-based tool on TheorChromo.ru to predict the retention time of peptides and proteins in liquid chromatography. A comparison of the observed peptide retention times to the BioLCCC model provides extra validation of MS/MS-based peptide identification, reducing the false discovery rate and improves the fidelity of phosphoproteome profiling.

BRAIN

• Description : BRAIN (Baffling Recursive Algorithm for Isotope distributioN calculations) is an R tool to compute aggregated isotopic distribution and exact center-masses for chemical substances and the probabilities of consecutive aggregated isotopic peaks in mass spectral data. The BRAIN algorithm currently computes for C, H, N, O, and S. The BRAIN algorithm uses the Newton-Girard theorem and Viète's formulae for the polynomial coding of variants of aggregated isotopes.

Comet_ms

• Description : Comet is a tool to search tandem mass spectra (MS/MS) of peptides against databases. The Comet algorithm is multithreaded and includes functions for the analysis of post-translational modifications.

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.

COMSPARI

• Description : COMSPARI (COMparison of SPectral And Retention Information) is a tool to visualize mass spectrometry data. Mainly for GC/MS and LC/MS but is also usable for other technologies. The COMSPARI algorithm has a function to simultaneously visualize two separate M/S data to allow comparison.

CPFP

• Description : CPFP (Central Proteomics Facilities Pipeline) is a tool for identification, validation, and quantitation of peptides and proteins from LC-MS/MS data.

CPM

• Description : CPM (Continuous Profile Models) is a Matlab tool to normalize and align LC-MS(/MS) time-series data. The toolbox includes EM-CPM and HB-CPM models.

CrossTalkDB

• Description : CrossTalkDB is a web-based database for mass spectrometry (MS) data of multiply modified proteins. Users can store, analyze, and compare histone modifications discovered by MS.

Crux

• Description : Crux is a mass spectrometry analysis toolkit that combines state-of-the-art computational, machine learning, and statistical methods. The Crux toolkit includes the following tools:
  
  1. bullseye
  2. tide-index
  3. tide-search
  4. cascade-search
  5. comet
  6. percolator
  7. q-ranker
  8. barista
  9. search-for-xlinks
  10. spectral-counts
  11. pipeline
  
  Utilities:
  1. assign-confidence
  2. generate-peptides
  3. get-ms2-spectrum
  4. hardklör
  5. make-pin
  6. param-medic
  7. predict-peptide-ions
  8. print-processed-spectra
  9. psm-convert
  10. subtract-index
  11. xlink-assign-ions
  12. xlink-score-spectrum
  13. localize-modification
  
  Text file utilities:
  1. extract-columns
  2. extract-rows
  3. stat-column
  4. sort-by-column
  

Datacube Explorer

• Description : Datacube Explorer is a tool to visualize mass spectrometry (M/S) data in 2-D and 3-D. The Datacube Explorer provides image and spectral view, user-definable regions-of-interest, Mass bin size between 1.0 and 0.001 m/z, loading of volumes-of-interests for large datasets, and Hierarchical presentation of imzML metadata.

DeconMSn

• Description : DeconMSn is a tool to determine the monoisotopic mass and charge state of parent ions in high-resolution tandem mass spectrometry (MS/MS) data. The DeconMSn algorithm detects charge using a support-vector-machine method.

DeconTools

• Description : DeconTools (Decon2LS) is a software tool package for de-isotoping and feature detection in mass spectrometry (MS) data. The DeconTools algorithm includes functions for peak detection, noise reduction, prediction of a theoretical isotopic envelope, and scoring functions.DeconTools is available as graphical user interphase (GUI) version (DeconToolsAutoProcessor) and as a command-line version (DeconConsole).

DeNovoGUI

• Description : DeNovoGUI is a tool to run PepNovo+, DirecTag, PepNovo+, and pNovo+de novo MS/MS spectra sequencing tools.

DEP

• Description : DEP is an R tool for differential enrichment analysis of Proteomics data from e.g., MaxQuant or IsobarQuant.

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.

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.

esimsa

• Description : esimsa is a tool to deconvolute electrospray ionization peak lists. The esimsa algorithm uses only mass differences between isotopic peaks, can separate overlapping and isotopic distributions without modeling the distributions.

ESIprot

• Description : ESIprot is a tool to deconvolute low-resolution electrospray ionization (ESI) mass spectrometry (MS) data of proteins. The ESIprot algorithm includes functions to determine the charge state and molecular weight of proteins.

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.

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

GlycoMod

• Description : GlycoMod is a tool to predict the compositions of oligosaccharide structures in proteins using experimentally determined masses. The GlycoMod algorithm works for free, derivatized oligosaccharides and glycopeptides. If the protein is in either the SWISS-PROT or TrEMBL database, GlycoMod computes the experimentally determined masses against all the predicted protease-produced peptides.

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.

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.

ICPLQuant

• Description : ICPLQuant is a tool to analyze large mass-spectrometric data sets from ICPL, LC-MALDI based experimental proteomics data. The ICPLQuant algorithm 1. Executes ICPL multiplex detection, quantification, and lists peptides to be subsequently identified by MS/MS, 2. Couples MASCOT MS/MS protein identification with the quantitative data and provides a protein/peptide list containing the relevant information.

idconvert

• Description : idconvert is a tool to convert between various file formats. See also ProteoWizard.

LA-iMageS

• Description : LA-iMageS is a tool to produce 2D and 3D images for the elements in a set from ICP-MS spectra.

LFQuant

• Description : LFQuant is a tool to analyze label-free LC-MS/MS quantitative proteomics data (SDS-PAGE and 2D LC), compatible with high-resolution mass spectrometers (Thermo RAW data) and SEQUEST and MASCOT database search engines using the target-decoy search strategy.

MASCOT

• Description : Mascot is a web-based tool to identify proteins by integrating 1. peptide molecular weights from the digestion of a protein by an enzyme, 2. tandem mass spectrometry (MS/MS) data, 3. combine mass data with amino acid sequence data. Mascot supports AB Sciex, Agilent, Bruker, Jeol, Shimadzu, Thermo Scientific, and Waters instruments.

MassWiz

• Description : MassWiz is a tool to score peptides in tandem mass spectroscopy (MS/MS) data. The MassWiz algorithm computes weights to major ions, continuity of b-y ions, intensities, the supporting neutral losses based on the instrument type, and integrated target-decoy based FDR.

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.

MaxQuant

• Description : MaxQuant is a tool for the analysis of large mass-spectrometric data sets. The MaxQuant algorithm can manage large high-resolution data sets, uses many labeling procedures, and label-free quantification. MaxQuant has a viewer module to visualize 3-D graphical models. See also Perseus framework for statistical analysis of MaxQuant output.

MetaProteomeAnalyzer

• Description : MetaProteomeAnalyzer (MPA) is a tool for the analysis and interpretation of metaproteomics and proteomics data. The MetaProteomeAnalyzer supports X!Tandem, OMSSA, and Mascot.
  The MetaProteomeAnalyzer includes functions for project management for MS/MS experiments, shotgun proteomics data analysis, integration of search algorithms of Comet, MS-GF+ and X!Tandem, re-analysis of results in mzIdentML format, analysis of taxa, ontologies, pathways and enzymes, grouping of redundant protein hits, label-free quantification, among others.

MFPaQ

• Description : MFPaQ (Mascot File Parsing and Quantification) is a tool to parse, validate, quantify Mascot results and isotopic labeling, SILAC/ICAT, and spectral counting, MS signal comparison. The MFPaQ algorithm has functions for retrieving the Mascot list of proteins, validation, sorting by scores, and by user-defined criteria.

MixGF

• Description : MixGF is a tool for the computation of the statistical significance of peptides matched to a given MS/MS spectrum.

Morpheus Spectral Counter

• Description : Morpheus Spectral Counter is a tool to search high-resolution tandem mass spectra.

MPA Portable

• Description : MPA (MetaProteomeAnalyzer) Portable is a tool to identify and analyze proteins in metaproteomics and proteomics data. The MPA Portable supports MGF input files and X!Tandem, Comet, MS-GF+ database search engines. You can also run MPA Portable using the command-line interface MetaProteomeAnalyzerCLI.
  See also MetaProteomeAnalyzer.

MS Amanda

• Description : MS Amanda is a tool to identify peptide sequences in tandem mass spectra (MS/MS). The MS Amanda algorithm can use HCD, ETD, CID data, and can work as a plugin for the Proteome Discoverer platform.

msaccess

• Description : msaccess is a tool to extract data and metadata from data files, a part of the ProteoWizard toolkit.

msconvert

• Description : msconvert is a tool to convert between various file formats, such as mzML, mz5, mgf, text, ms1, cms1, ms2, cms2, with many options.

MSGF+

• Description : MS-GF+ is an R tool to interface MS-GFplus. The MS-GF+ algorithm has functions to run a computation in batches, construct parameter sets using a command-line or a GUI.

msgfdb2pepxml

• Description : msgfdb2pepxml is a tool to convert MS-GFDB output to pepXML-format. The msgfdb2pepxml algorithm uses regular expressions to recognize enzyme uses and cleavage rules and supports PSI-MS controlled vocabulary version 3.10 (2011-08-24). The msgfdb2pepxml converter recalculates peptide and post-translational modification masses with specified precision.

MSGFgui

• Description : MSGFgui is an R tool to use MSGFplus through a graphical user interface (GUI). The MSGFgui has functions for interactive plots, summary statistics, filtering, and seamless integration to pipelines.

MSGFplus

• Description : MSGFPlus (MSGF+ or MSGFPlus) is a tool to identify peptide from tandem mass spectra (MS/MS) data. The MSGFPlus algorithm scores MS/MS spectra against a protein sequence database to identify peptides. MSGFPlus algorithm is optimal for various combinations of fragmentation methods, instruments, enzymes, and experimental protocols. See also an R interface for MSGFPlus and MSGFgui.

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.

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.

MSstats

• Description : MSstats is an R tool to analyze quantitative mass spectrometry data and proteomics. The MSstats algorithm includes functions for the differential detection of proteins in mass spectrometry (MS) with chromatography-based quantification, characterization of MS assays, quality control, and system suitability testing.

MSstatsQC

• Description : MSstatsQC is an R tool for system suitability tests (SST) to verify that mass spectrometric instrumentation performs as specified.

MSstatsTMT

• Description : MSstatsTMT is an R tool to detect differentially abundant proteins in shotgun mass spectrometry using the tandem mass tagging. The MSstatsTMT algorithm has functions for protein summarization based on peptide quantification data and visualization and model-based group comparison for the detection of changes in abundance. MSstatsTMT works with isobaric labeling quantitative proteomics, such as iTRAQ and TMT.

Multi-Q

• Description : Multi-Q is a tool to analyze multiplexed iTRAQ data. The Multi-Q has functions for calculation of peptide ratios, detection and processing iTRAQ’s signature peaks, background subtraction, isotope correction, normalization, and data filtering using empirical or statistical models. Multi-Q works with various input formats from different search engines and mass spectrometers.

muxQuant

• Description : muxQuant is a tool to multiplex relative quantitation of peptides and proteins from mass LC-MS data in mzXML. The muxQuant algorithm uses the same code as the FFTW library, which is used by AUTOHD, the Random Access Minimal Parser (RAMP) library to read data in mzXML, selects isotopic envelopes for peptides, fits computed envelopes using the weighted isotopic distributions for each level of stable isotopes and peptides.

MyriMatch

• Description : MyriMatch is a tool for the analysis of shotgun proteomics data. The MyriMatch algorithm uses the multivariate hypergeometric distribution to compare peptide sequences against a protein database and computes the probabilities for each match occurring by random chance.

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.

Novor

• Description : Novor is a tool to analyze peptide de novo sequences. The Novor algorithm uses decision trees computed from a peptide spectral library with over 300,000 spectra, dynamic programming, and its refinement to calculate the scores.

OMSSA

• Description : OMSSA (Open Mass Spectrometry Search Algorithm) is a tool to identify peptides in tandem mass spectrometry (MS/MS) data. The OMSSA algorithm uses a classic probability score to compute specificity. See also The NCBI C++ Toolkit and The NCBI C++ Toolkit Book.

OMSSA Parser

• Description : OMSSA Parser is a tool to parse OMSSA (Open Mass Spectrometry Search Algorithm) omx files. The OMSSA Parser algorithm parses omx files and creates functional object models.

OMSSAGUI

• Description : OMSSAGUI is a graphical user interface (GUI) for the OMSSA MS/MS search engine. NOTE, this project is not maintained anymore. See SearchGUI and OMSSA Parser.

OMSSAPercolator

• Description : OMSSAPercolator is a tool to re-score the OMSSA (Open Mass Spectrometry Search Algorithm) database search results. The OMSSAPercolator uses a machine learning method for scoring.

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).

PepArML

• Description : PepArML is a web-based tool to identify peptides using tandem mass spectra (MS/MS). The PepArML has functions for unsupervised, model-free, machine learning-based result combiner to identify peptides for each spectrum and estimation of false-discovery rate.

PeptideShaker

• Description : PeptideShaker is a tool to interpret, validate, map, GO enrich, plot, and re-analyze results from peptide identification platform tools, such as X!Tandem, MS Amanda, MS-GF+, MyriMatch, Andromeda, Comet, Tide, Mascot, OMSSA, and mzIdentML. The PeptideShaker algorithm has functions for
  1. Detailed overview,
  2. Comparison of search tools performance,
  3. Inspection of originating fractions,
  4. view post-translational modifications,
  5. Mapping peptides to PDB structures,
  6. Finding GO terms,
  7. Finetuning the validation,
  8. QC plotting,
  9. Re-analyze public datasets in PRIDE.

Perseus

• Description : Perseus is a tool for the statistical analysis of omic data. The Perseus framework contains functions for normalization, pattern recognition, time-series analysis, cross-omics comparisons, multiple-hypothesis testing, prediction of protein signatures, classification and validation of patient groups. The Perseus framework can directly analyze the output from MaxQuant.

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.

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.

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.

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.

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.

ProteoWizard

• Description : ProteoWizard toolkit consists of open-source software libraries and applications for proteomics research. The ProteoWizard toolkit includes the following tools: 1. Skyline: Multiple Reaction Monitoring methods and analysis of mass spectrometer data, 2. Filters, 3. idConvert, 4. msaccess: read M/S data files, spectrum binary and metadata, ion chromatograms, and pseudo-2D gel image creation, 5. msconvert, 6. mspicture: pseudo-2D gel image creation together with mapped peptide ID info, 7. qtofpeakpicker: peak detection in Q-TOF raw data.

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.

PVIEW

• Description : PVIEW is a tool to analyze and visualize high-resolution LC-MS/MS Data. The PVIEW algorithm has functions for
  1. Isotope-labeled heavy vs. light quantification,
  2. 5N heavy vs. light quantification,
  3. Isotope-labeled heavy vs. medium vs. light (e.g., pulsed SILAC) quantification,
  4. Nonlinear alignment label-free quantification,
  5. Label-free XIC-based quantification,
  6. XIC-based quantification (XICs are cross-referenced based on peptide sequence),
  7. MS/MS database search,
  8. Internal reverse concatenated decoy database construction,
  9. FDR and q-value estimation utilizing a reverse decoy database,
  10. Support for external search engines, such as Mascot, SEQUEST, X! Tandem,
  11. Protein grouping of isoforms and peptides,
  12. Support for data from Orbitrap, FTICR, and high resolution QTOF instruments.
  PVIEW is multi-threaded.

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.

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.

RAId

• Description : RAId (Robust Accurate Identification) is a set of tools to analyze tandem mass spectrometry (MS/MS) data. A web-based version is available at https://www.ncbi.nlm.nih.gov/CBBresearch/Yu

rTANDEM

• Description : rTANDEM is a tool to identify proteins in MS/MS data interfacing the X!Tandem protein identification algorithm. The rTANDEM interface extends the command syntax and has functions to optimize analyses, converts results, parameters, and taxonomy to and from R. The rTANDEM algorithm can run multi-threaded. See associated tools: shinyTANDEM and X!Tandem.

SDAMS

• Description : SDAMS is an R tool for the semi-parametric differential abundance analysis using metabolomics and proteomics data from mass spectrometry.

SearchGUI

• Description : SearchGUI is a graphical user interface for X!Tandem, MS Amanda, MyriMatch, MS-GF+, Tide, Comet, OMSSA, Novor, Andromeda, and DirecTag proteomics identification search engines and de novo sequencing algorithms.

shinyTANDEM

• Description : shinyTANDEM is an R tool to visualize rTANDEM MS/MS protein identification results. shinyTANDEM has GUI functions to construct parameter objects, launch searches, and convert among R objects and XML files.

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.

Skyline

• Description : Skyline is a tool to build selected reaction, parallel reaction and multiple reaction monitoring, data-independent acquisition, and DDA with MS1 quantitative methods, and to analyze the resulting mass spectrometer (MS) data. See also ProteoWizard.

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.

TopPIC

• Description : TopPIC Suite contains the following tools:
  1. TopFD (TOP-Down Mass Spectrometry-Based Proteoform Identification and Characterization) is a tool to deconvolute spectrum grouping spectral peaks into isotopomers to monoisotopic neutral masses and to compute proteoform features from LC-MS or CE-MS data.
  2. TopPIC (Top-down mass spectrometry-based Proteoform Identification and Characterization) is a tool for the identification and characterization of proteoforms by searching a protein sequence database. The TopPIC algorithm uses spectral alignment, a generation function, and indices to increase the speed.
  3. TopMG (Top-down mass spectrometry-based proteoform identification using Mass Graphs) is a tool to identify ultra-modified proteoforms using protein sequence database searches in tandem mass spectra (MS/MS) data. The TopMG algorithm uses mass graphs, approximate spectrum-based filtering methods, a Markov chain Monte Carlo method, and can identify proteoforms with multiple variable PTMs and other alterations, for example, histone proteoforms and phosphorylations.
  4. TopDiff (Top-down mass spectrometry-based identification of Differentially expressed proteoforms) is a tool to compare proteoform abundances and to find differentially expressed proteoforms.

UniMod

• Description : Unimod is a public domain database of protein modifications for mass spectrometry (M/S) purposes. The data in the Unimod database includes the mass differences introduced by all types of natural and artificial alterations and mass change, neutral loss, occurring in MS/MS analysis and site-specificity.

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).

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.

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.

XTandem

• Description : X!Tandem is a tool to identify proteins in tandem mass spectra (MS/MS) data. The X!Tandem algorithm computes the statistical confidence for spectrum to sequence alignments and alignments to known protein sequences. The X!Tandem package has a graphical user interface (GUI) for visualization. See also 1. XTandem Parser, 2. rTANDEM, 3. shinyTANDEM.

XTandem Parser

• Description : XTandem Parser is a tool to extract information from X!Tandem output XML files to a object model. XTandem Parser is available for use in Maven projects. For visualization, see PetideShaker.

XTandemPipeline

• Description : X!TandemPipeline is a pipeline tool to filter and group proteins and peptides from tandem mass spectra (MS/MS) data. The X!TandemPipeline reads X!Tandem XML, MASCOT, TPP pepXML, PSI mzIdentML results. The X!TandemPipeline algorithm includes several filters based on statistics on protein levels, a filter to groups redundancy, handling of phosphoproteomic datasets, search and sort, XIC browser, comparison of theoretical isotope patterns to measured MS1 XIC area, and can export data to MS Office 2010.

YADA

• Description : YADA is a tool for deisotoping, de-charging high-resolution mass spectra (M/S) from large peptides, linking precursor monoisotopic peaks to the spectrum, and in multiplexed spectra estimation of co-fragmenting ion species. The YADA algorithm has functions for pipelining ProLuCID and DTASelect.

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