Software List
| platforms, pipelines and libraries | ||||
| CPFP | Central Proteomics Facilities Pipeline [1] (demo here) | |||
| GenePattern | platform for integrative genomics and proteomics (includes PEPPeR [2] and other tools for proteomics) | Java | ||
| InSilicoSpectro | open source proteomics library (of Perl functions) [3] | Perl | ||
| libmgf | a flex/bison-based Mascot Generic Format (MGF) parser library | C++ | ||
| MALDIquant | analysis pipeline for MALDI-TOF profiling [4] | C, R | ||
| Mass-up | utility with full GUI for proteomics data analysis, particularly MALDI-TOF [5] | Java | ||
| MASSyPup | a lightweight Linux live distribution prepackaged with a wide range of tools for MS and MS/MS data analysis | |||
| MetaProteomeAnalyzer | pipeline to analyze metaproteomics data, supporting MGF and X!Tandem, OMSSA and Mascot [6] | Java | ||
| mspire | MS data processing in Ruby, including mzML reader/writer, in-silico digestion, isotopic pattern calculation etc. [7] | Ruby | ||
| MSFileReader_Python_bindings | Python bindings for the (non-free) ThermoFisher Scientific MSFileReader | Python | ||
| mzAccess | Open source web-service software for remote interactive access to the large collections of mass spectrometry data [8] | C#, R | ||
| MzJava | library for the analysis of mass spectrometry data from large scale proteomics and glycomics experiments | Java | ||
| OpenMS | library for the analysis, reduction and visualization of LC-MS(/MS) data | C++ | ||
| PAPPSO | Plateforme d'Analyse Protéomique de Paris Sud-Ouest | Java | ||
| PatternLab | suite of pattern recognition software for interpretation of quantiative proteomics data [9] | .NET | ||
| pFind Studio | platform for mass spectrometry-based proteomics, including pFind [10], pNovo [11], pQuant [12] and pLink [13] | Java | ||
| PeptideShaker | platform for interpretation of proteomics identification results from multiple search engines [14] | Java | ||
| PRIDE Toolsuite | a selection of tools and libraries for interacting with data in PRIDE | Java | ||
| Proline | a free and open source software suite for mass spectrometry based proteomics. | |||
| Proteios | pipeline/LIMS for proteomics experiments and analysis | Java | ||
| Proteomatic | platform for creating MS/MS data analysis workflows using scripts [15] | C++ | ||
| ProteoWizard | open source library for proteomics tools development (supports mzML) [16] | C++ | ||
| pymzML | Python module to parse mzML data based on cElementTree [17] | Python | ||
| Pyteomics | framework for proteomics data analysis, supporting mzML, MGF, pepXML and more [18] | Python | ||
| QuanTP | resource for quantitative proteotranscriptomic data analysis [19] | R | ||
| QuPE | integrated environment for storage, analysis and integration of proteomics data (requires login) [20] | Java | web | |
| Rproteomics | set of routines for analyzing proteomics data, an XML database to store the results and a user interface | R | ||
| Ursgal | Python module providing a generalized interface to several common bottom-up proteomics tools [21] | Python | ||
| TPP | Institute for Systems Biology "Trans-Proteomic Pipeline" | |||
| XCMS | software package (in R) for metabolite profiling from LC-MS data | R | ||
| data visualization and analysis | ||||
| BatMass | platform for multiplexed LC–MS data visualization and exploration in proteomics and metabolomics [22] | Java | ||
| cdfread | a simple reader of mass spectra in netCDF | C | ||
| COMSPARI | compares two datasets in netCDF or ASCII format | C | ||
| imDEV | data exploration and visualization in Excel | |||
| Insilicos Viewer | basic viewer of LC-MS/MS data in mzXML format | |||
| LA-iMageS | generates 2D/3D images for elements in ICP-MS [23] | Java | ||
| MapQuant | image analysis" of LC-MS features, deconvolution etc. [24] | C | ||
| mMass | user-friendly and free software to view MS data in a range of formats [25] | Python | ||
| MoverZ | free version of MoverZ for viewing and manipulating single mass spectra in many formats | |||
| msaccess | creates a psuedo-2D-gel representation [26] | C++ | ||
| MSGraph | an MS-DOS program to visualize LC-MS data in 2D and 3D (converter from mzXML available) | C | ||
| MSPicturePerfect | visualize mzXML data in 2D | |||
| msXpertSuite | tools for analysis of polymer and peptide/protein mass spectra, including ion mobility data | C++ | ||
| MZmine | toolbox for visualization and analysis of LC-MS data in netCDF or mzXML [27] | |||
| mzXMLplot | plots mzXML LC-MS data as virtual gels or heat maps | C | ||
| mzXML Viewer | mzXML viewer from Seattle Proteome Center | |||
| OpenChrom | open source tool for mass spectrometry and chromatography [28] | Java | ||
| Pep3D | plots LC-MS and LC-MS/MS data in a 2D m/z vs time plot [29] | |||
| Peppy | proteogenomic, proteomic search tool [30] | Java | ||
| ProteomicsDB | explorable, interactive human proteome database, including MS/MS data [31] | web | ||
| PROTICdb | proteomic database to store, track, query and compare proteome data [32] | Java | web | |
| Protter | interactive protein feature visualization and integration with experimental proteomic data [33] | Java | web | |
| Scaffold Viewer | free viewer to share and visualize Scaffold-analyzed data | |||
| Sirius | tool for metabolite identification using mass spectrometry | Java | ||
| Skyline | builds SRM/MRM methods and analyzes resulting data | C# | ||
| Spectrum Look | tool for viewing and annotating MS/MS spectra | C | ||
| TAPIR | visualization of targeted/SWATH proteomics LC-MS(/MS) data | Python | ||
| Taverna | powerful, scalable, open source and domain independent tools for designing and executing workflows [34] | Java | ||
| Taverna4Proteomics | Taverna workflows for integrated proteomics data analysis, a.k.a. Workflow4Proteomics [35] | Java, C/C++ | ||
| VIPER | visualizes features from LC-MS analyses, particularly AMTs | |||
| WinICR | reads and analyzes single FTICR and TOF spectra in various older vendor formats | |||
| format conversion | ||||
| APLToMGFConverter | converts MaxQuant APL (Andromeda peak lists) to MGF | C# | ||
| collect_mgf | collects MGF files and dd_results from an XMass setup_QDD.tcl experiment to a single MGF file | C | ||
| CompassXport | converts Bruker analysis.baf and analysis.yep files to mzXML or mzML | |||
| dat2mgf | converts Mascot results files back to MGF | |||
| DataAnalysis2TPP | converts MGF from Bruker DataAnalysis to TPP-friendly format for use with XPRESS and ASAPRatio | AWK | ||
| MassWolf | converts MassLynx format to mzXML | VC++ | ||
| .dta to MGF File Converter | converts .dta to MGF | |||
| MSD File Reader | read, display and save data from the original HP MSD based on the HP Pascal Chemstation (replaced with Quadfiles) | |||
| mspire/mspire-sequest | mzML to imzML and Bioworks Sequest results files (.srf) to pepXML (mspire-sequest) | Ruby | ||
| multiplierz | scriptable framework for access to manufacturers' formats via mzAPI [36] | Python | ||
| msconvert | converts from RAW/WIFF/T2D/Agilent/Bruker/Waters/mzML/mzXML/MGF/MS2 to mzML/mzXML/MGF/MS2 [37] | C++ | ||
| msgfdb2pepxml | converter from MS-GFDB output to pepXML | Python | ||
| mz2mgf | converts mzData files to MGF | |||
| mzBruker | converts Bruker analysis.baf files to mzXML | VC++ | ||
| mzStar | converts SCIEX/ABI Analyst format (WIFF) to mzXML | VC++ | ||
| mzXML2Other | converts mzXML to SEQUEST .dta, MGF, and Micromass .pkl | VC++ | ||
| Out2Summary | collects Sequest and TurboSequest *.out files to HTML for use with INTERACT | VC/VC++ | ||
| PklFileMerger | merges individual Q-TOF .pkl files into a single file for database searching | C++ | ||
| ProCon | converts ProteomeDiscovere 1.X .msf to mzIdentML | Java | ||
| PyMS | tools for reading LC-MS data in the ANDI-MS and JCAMP-DX formats [38] | Python | ||
| pyteomics.pepxmltk | converts X!Tandem t.XML files to pepXML (without enzyme limitations) [39] | Python | ||
| Quadfiles | (formerly Mass Hunder File Reader) exports raw quadrupole MS data from Agilent Chemstation or MassHunter to plain text | |||
| RawTools | package to parse Thermo Orbitrap raw data [40] | C# | ||
| ReAdW | converts Xcalibur native acquisition files to mzXML | VC++ | ||
| T2D converter | converts ABI SCIEX 4700/4800 t2d files to mzXML | Python | ||
| unfinnigan | reading Thermo .raw files without MsFileReader | Perl | ||
| wiff2dta | converts ABI WIFF to .dta [41] | |||
| X2XML | converts from almost any format (Thermo, Bruker, Agilent and Micromass) to mzXML | .NET | ||
| small molecules/lipidomics | ||||
| CEU Mass Mediator | annotation of metabolites in MS1 spectra with R and REST APIs [42] | J2EE | web | |
| Chrombox D | identification and quantitation, particularly of polar lipids, from LC-MS or direct infusion data in most formats [43][44] | MATLAB | ||
| Chrombox Q | deconvolution, search and identification of peaks in GC-MS data [45] | MATLAB | ||
| LipidXplorer | high-throughput lipid identification from shotgun mass spectra in mzML, mzXML, CSV and .dta formats [46] | Python | ||
| MSC Pro | mass spectrometry calculator for interpreting mass spectra integrated with NIST MSSearch | |||
| msPurity | precursor purity evaluation for tandem mass spectrometry in metabolomics [47] | R | ||
| statTarget | statistical analysis of molecular profiles and signal drift correction [48] | R | ||
| SpiderMass | semantic chemical database generation, metabolite identification and de novo formula generation | Python/C/C++ | ||
| peak picking/deconvolution | ||||
| DeconMSn | tool for accurate precursor ion monoisotopic mass determination for tandem mass spectra [49] | .NET | ||
| DeconTools | advanced peak picking of MS and LC-MS(/MS) data using THRASH and other algorithms | .NET | ||
| esimsa | simple deconvolution of electrospray ionization peak lists [50] | C | ||
| esimsa2D | simple deconvolution and 2D peak picking of LC-MS data | C | ||
| ESIprot | charge state determination and molecular weight calculation for low resolution electrospray ionization data [51] | Python | web | |
| libmprc | library for analysis of high resolution mass spectrometry data (including THRASH) | C++ | ||
| massifquant | Kalman filter based on binless peak picking and quantitation in XCMS | R | ||
| MS-DIAL | data independent MS/MS deconvolution for metabolomics [52] | .NET | ||
| nontarget | R function for compound, adducts and ion series detection using isotopic distributions | R | ||
| UniDec | universal deconvolution and visualization of (ion mobility) mass spectra [53] | C/Python | ||
| Xtractor | extracts pre-defined peaks or regions into a uniform array | C | ||
| Y.A.D.A. | tool for deconvoluting MS/MS spectra [54] | .NET | ||
| calibration/alignment | ||||
| adjustPKL | adjust (recalibrate) PKL peak lists | Java | ||
| CPM | alignment of time-series data [as in LC-MS(/MS)] using Continuous Profile Models [55] | MATLAB | ||
| ID-Align | aligns metabolite data from multiple files to single spreadsheet | Python | ||
| msalign | aligns LC-MS and LC-MS/MS datasets using peptides identified by MS/MS and accurate mass MS [56] | C | ||
| msalign2 | aligns two CE-MS or LC-MS datasets using accurate mass information [57] | C | ||
| mzRecal | recalibrate LC-MS datasets using peptides identified by MS/MS [58] | Go | ||
| OBI-Warp | aligns multiple LC-MS(/MS) datasets in retention time by dynamic time warping [59] | C++ | ||
| recal2 | recalibrate LC-FTICRMS(/MS) datasets using peptides identified by MS/MS [60] | C | ||
| SpecArray | aligns multiple LC-MS datasets and much more [61] | C++ | ||
| retention time prediction | ||||
| BioLCCC | an analytic model of peptide retention [62] | web | ||
| hplcsimulator | a general tool for simulating and optimizing HPLC gradients | web | ||
| retentionprediction | a related web utility for projecting/predicting retention times [63] | web | ||
| rt | retention time prediction using LC-MS data with improved user interface [64] | C | ||
| SSRCalc | sequence-specific retention time calculator [65] | web | ||
| de novo sequencing/PTMs | ||||
| CrossTalkDB | histone modification database designed to store, analyze and compare histone modifications determined by MS [66] | Java | web | |
| Delta Mass | the ABRF database of protein post-translational modifications | web | ||
| DeNovoGUI | A nice GUI for running the PepNovo and DirecTag under Windows, Mac or Linux [67] | Java | ||
| GlycoMod | predicts oligosaccharide structures from experimental masses | web | ||
| InSpecT | "blind" spectral search of tandem mass spectra of peptides [68] | C/Python | web | |
| lutefisk | de novo peptide sequencing from MS/MS data [69] | C | ||
| MSNovo | de novo peptide sequencing from MS/MS data [70] | |||
| Novor | fast, real-time peptide de novo sequencing engine [71] | Java | web | |
| PEAKS De Novo | integrated de novo peptide sequencing [72], PTM finder [73], and homology search [74] (demo available) | Java | ||
| PepNovo | de novo sequencing using probabilistic network modeling [75] | C++ | ||
| Popitam | searches for unknown post-translational modifications [76] | web | ||
| POSTMan | post-translational modification software [77] | C++ | ||
| ProSight PTM | web portal for PTM search in top-down experiments [78] | web | ||
| ProSight PTM Ion Predictor | generate exact masses for CID/ECD fragments with PTMs | web | ||
| ProteoSushi | transformation of peptide-centric PTM data into annotated PTM-site output | Python | ||
| Sequit! | free (non-batch) version of a de novo/BLAST tool [79] | web | ||
| SPS | shotgun protein sequencing assembling multiple MS/MS spectra [80] | MATLAB | ||
| theospec | command line tool for predicting MS/MS spectra | C | ||
| UniMod | database of simple protein modifications | web | ||
| protein identification | ||||
| peptide mass fingerprinting | ||||
| aldente | web based peptide mass fingerprinting | web | ||
| MASCOT | free version of the Matrix Science MASCOT Peptide Mass Fingerprinting | web | ||
| ms1searchpy | an open-source Python proteomics search engine for the LC-MS spectra (also LC-MS/MS data can be used) [82] | Python | ||
| MS-Fit | peptide mass fingerpriting tool in the ProteinProspector suite | C++ | web | |
| PepMAPPER | multi-experiment peptide mass fingerprinting | web | ||
| ProFound | free web version of ProFound (peptide mass fingerprinting) | web | ||
| ProteinGuru | several on-line tools, including OLMAT for peptide mass fingerprinting | web | ||
| ProteinProspector | the ProteinProspector suite of protein identification tools | web | ||
| tandem mass spectrometry (MS/MS) | ||||
| Comet | open source tandem mass spectrometry (MS/MS) sequence database search tool [83] | C++ | ||
| EasyProt | graphical and software platform for the analysis of MS/MS data | |||
| greylag | free MS/MS search engine | Python/C++ | ||
| MASCOT | free, web-based version of the MASCOT MS/MS Ions Search | web | ||
| MassMatrix | web based tools for peptide identification and quantitation | web | ||
| MassAI | free (Windows/WINE) tool for analysis of MS/MS, bottom-up proteomics data, including non-standard PTMs and more | Delphi | ||
| MassWiz | peptide identification and FDR calculation [84] | Perl | ||
| MS Amanda | algorithm optimized for high accuracy tandem mass spectra [85] | C# | ||
| MSFragger | ultrafast database search for peptide identification, including from TIMS-TOF data [86] | Java | ||
| MS-GFDB | peptide identification using a combination of de novo and database search [87] | Java | ||
| MS-GF+ | latest version of MS-GFDB above [88] | |||
| MSPolygraph | open source hybrid database and spectral library MS/MS search engine [89] | C | ||
| MyriMatch | another free MS/MS search engine | C++ | ||
| OMSSA | mass spectrometry search algorithm from NIH (also searches ETD MS/MS data) [90] | web | ||
| PEAKS DB | de novo-assisted database search [91] | Java | ||
| Percolator | semi-supervised learning for peptide identification from MS/MS data [92] | |||
| PepProbe | web-based MS/MS search engine [93] | web | ||
| PepSplice | cache-optimized search algorithm [94] | C++ | ||
| ProLuCID | improved SEQUEST-like algorithm with enhanced sensitivity and specificity [95] | Java | ||
| ProLuCID GUI | user-friendly graphical user interface for the ProLuCID database search engine | Python, Java | ||
| ProteinProspector | the ProteinProspector suite of protein identification tools | web | ||
| Proteome ARTworks | predicts detectability and tandem mass spectra of peptides and addresses the protein inference problem [96] | web | ||
| SearchGUI | graphical user interface to several common search engines, such as X!Tandem, Mascot and OMSSA. [97] | Java | ||
| TopPIC | proteoform identification/characterizaion at the proteome level using database search [98][99][100] | C++ | web | |
| VEMS | platform for protein identification and characterization [101] | |||
| X!Tandem | matches tandem mass spectra with peptide sequences | C++ | ||
| MS/MS library search | ||||
| ProMEX | matches tandem mass spectra against A. thaliana and M. truncatula libraries | web | ||
| SpectraST | matches peptide MS/MS spectra with library spectra | |||
| X! Hunter | matches tandem mass spectra with library spectra from same organism | C++ | ||
| (result) parsers/validation/fragment spectrum processing | ||||
| goa_gubbar | sorts protein identifications under GOA slim terms | C | ||
| Mascot Parser | PDOM and MASCOT parser [103] | Java | ||
| Mayu | estimates protein identification false discovery rates | Perl/R | ||
| libmgf | libmgf (formerly mgfp) - a flex/bison-based Mascot Generic Format (MGF) parser library [104] | C++ | ||
| ms2preproc | ms2preproc - MGF and dta fragment spectrum preprocessing [105] | C++ | ||
| mres2x | a tool to process MASCOT results [106] | C | ||
| PAnalyzer | rearranges Waters PLGS XML or mzIdentML peptide data into inferred proteins | C# | ||
| PeptideProphet (TPP) | validation of peptide identifications by MS/MS and database searches [107] | C++/Perl | ||
| ProteinProphet (TPP) | validation of protein identifications by MS/MS and database searches [108] | C/Perl | ||
| XTandem Parser | Java-based parser for X!Tandem result files [109] | Java | ||
| X!TandemPipeline | filter, edit and group peptide/protein identifications from X!Tandem (and MASCOT) | Java | ||
| data-independent acquisition (DIA) | ||||
| DIA-Umpire | computational framework for data-independent acquisition proteomics [110] | Java | ||
| EncylcopeDIA | library searching for DIA data [111] | Java | ||
| OpenSWATH | Workflow for targeted data analysis of data-independent acquisition (DIA) or SWATH-MS proteomics data [112] | C++ | ||
| PECAN | library-free peptide detection for DIA data [113] | Python | ||
| protein quantitation | ||||
| APEX | protein abundance estimate from LC-MS/MS data [114] | Java | ||
| ASAPRatio (TPP) | statistical analysis of protein ratios from ICAT, cICAT or SILAC experiments | VC++ | ||
| DAnTE | protein quantitation, statistical analysis and visualization | .NET | ||
| Diffprot | non-parametric statistical analysis of differential proteomics data [115] | Perl | ||
| FlashLFQ | label-free quantification algorithm for mass spectrometry-based proteomics [116] | C# | ||
| ICPLQuant | tool for processing and analyzing ICPL LC-MALDI data [117] | Java | ||
| ICPL_ESIQuant | tool for processing and analyzing ICPL LC-MS/MS (ESI) data [118] | Java | ||
| isobar | quantitation of TMT and iTRAQ data and LaTeX report generation [119] | R | ||
| IsobariQ | quantitation of IPTL, iTRAQ and TMT-labeled peptides [120] | C++ | ||
| Libra (TPP) | analyzes 4- and 8-channel iTRAQ data [121] | |||
| MassChroQ | XIC extraction and quantitation from LC-MS data [122] | C++ | ||
| MaxQuant | quantitation from SILAC data from Thermo Orbitrap and FTICR | |||
| MFPaQ | Mascot file parsing and quantitation using ICAT and SILAC [123] | Perl/.NET | ||
| MSQuant | protein quantitation combining Mascot results and raw data from stable isotope labeling | .NET | ||
| MS-Spectre | quantitiave analysis of multiple LC-MS(/MS) analyses in mzXML | Java | ||
| MSstats | statistical tool for quantitative mass spectrometry-based proteomics [124] | R | ||
| Multi-Q | tool for multiplexed iTRAQ-based quantitation [125] | .NET/Perl | ||
| muxQuant | multiplexed quantitiave proteomics using differential stable isotope labeling [126] | C | ||
| PeakQuant | an integrated platform of quantitative proteomics tools, including for SILAC and metabolic labeling | Java | ||
| PEAKS Q | peptide/protein quantification by iTRAQ, ICAT, SILAC or label-free | Java | ||
| pepXML2Excel | converts output from PeptideProphet to protein level information in Excel | AWK | ||
| ProRata | differential proteomics analysis using for various stable isotope labeling schemes [127] | |||
| ProteoClade | taxonomic-based annotation and quantification of bottom-up metaproteomics data [128] | Python | ||
| PVIEW | isotope labeled, label-free, and XIC-based quantitation for high resolution LC-ESI-MS/MS data [129] | C++ | ||
| pyQms | generalized mass spectrometry data quantification module using isotopic distributions [130] | Python | ||
| Quant | MATLAB program for protein quantitation by iTRAQ [131] | MATLAB | ||
| QUIL | another program for relative quantitation using stable isotope labeling [132] | |||
| RAAMS | algorithm for interpreting O-16/O-18 differential proteomics data | C++ | ||
| RelEx | calculation of ion current ratios from LC-MS data (requires Xcalibur) [134] | |||
| XINA | network integration of kinetic proteomics data [135] | R | ||
| XPRESS (TPP) | calculates relative abundances from ICAT, cICAT, SILAC and other N-14/N-15 experiments [136] | VC++ | ||
| protein structure | ||||
| Cross-linking | ||||
| ASAP | automatic peptide identification in crosslinking experiments [137] | web | ||
| CCdigest | digest proteins with intact disulfide bridges | Perl | web | |
| CCfind | find peptides with disulfide bridges from ETD data | Perl | web | |
| Crosslinx | identify cross-linked peptides from mzML files feasible for larger databases with a two-step approach [138] | Python | ||
| Kojak | application for identification of cross-linked peptides from mass spectra [139] | C++ | ||
| MassMatrix | MassMatrix also allows cross-linked peptide identification | web | ||
| MS2Pro | assigns crosslinked or non-crosslinked fragments in whole protein MS/MS (top-down) spectra [140] | web | ||
| MeroX | tool for protein-protein cross-linking using MS-cleavable cross-linking reagents (DSBU, DSSO, CDI or PIR) [141] | Java | ||
| MS2Assign | assigns crosslinked or non-crosslinked peptides in MS/MS spectra [142] | web | ||
| MS-Studio | analysis of crosslinking, H/D exchange and covalent labeling data [143][144] | |||
| SIM-XL | Spectrum Identification Machine for Cross-Linked Peptides [145] | |||
| StavroX | analyses peptide-peptide cross-links for protein-protein interaction or protein structure analysis [146] | Java | ||
| xComb | interogate protein-protein interactions and protein structure using cross-links FASTA databases [147] | Perl | web | |
| Xilmass | algorithm for identifying cross-linked peptides [148] | Java | ||
| XLink (TPP) | set of tools for analysis of data from crosslinked and digested protein complexes | |||
| xQuest/xProphet | analysis of lysine-specific cross-linking [149] | |||
| H/D exchange | ||||
| AUTOHD | analysis of H/D-exchange data using isotopic distributions [150] | C | ||
| Deuterator | web based software platform for determining backbone amide H/D ratios | Java/JSP | web | |
| DEX | another program (similar to AUTOHD) for analysis of H/D-exchange spectra [152] | C/C++ | ||
| ExMS | MATLAB program for analyzing H/D-exchange data [153] | MATLAB | ||
| HDX WorkBench | integrated software platform for HDX data analysis [154] | Java/JSP | web | |
| hydrogen_bondifier | PyMOL script for retrieving hydrogen bond characteristics from protein structures | PyMOL | ||
| HX-Express | an Excel spreadsheet for analysis of H/D exchange mass spectra [155] | Excel | ||
| in silico digestion | ||||
| bash | sed 1d|tr -d '\n'|awk 'BEGIN{RS="[RK]"}(NR==1)&&/.{5,}/{print $1 RT;next}/[^P].{4,}/{print $1 RT}' | bash | ||
| dig | digests or fragments protein sequences [156] | C | ||
| dig2 | updated version of dig | C | ||
| InDigestion | iOS app for in-silico digestion and more | mobile app | ||
| MS-Digest | digests a protein sequence | web | ||
| PChopper | multiple-enzyme in silico digester for experimental design | web | ||
| PeptideCutter | another web based protein digestion applet | web | ||
| Protein Digestion Simulator Basic | calculates theoretical enzymatic peptides and AMTs | |||
| ProteomeDigestSim | R classes for prediction of proteome coverage based on iterative digestion by MED-FASP or similar [157] | R | ||
| mass spectrometry imaging (MSI) | ||||
| Axima2Analyze | converts imaging data from the Axima formats to the Analyze format used in BioMap | |||
| BioMap | biomedical image analysis software (also MSI) | IDL™ | ||
| Cardinal | a MSI toolbox for statistical analysis [158] | C++ | ||
| Datacube Explorer | vendor-neutral visualization program for mass spectrometry imaging data (including imzML) [159] | C# (.NET) | ||
| massPix | R package for annotation and interpretation of lipidomics mass spectrometry imaging data [160] | R | ||
| microMS | Python platform for image-guided mass spectrometry profiling [161] | Python | ||
| MSImageView | generate images from WIFF data and export to imzML | |||
| msIQuant | fast access, visualization, and analysis of MSI data in imzML [162] | C++ (.NET) | ||
| MSI.R | Collection of R scripts for processing mass spectrometry imaging [163] | R | ||
| MSiReader | vendor-neutral MATLAB program to view analyze mass spectrometry imaging data [164] | MATLAB | ||
| OpenMZxy | open mass spectrometry imaging control software [165] | Python | ||
| pyImagingMSpec | Python library for processing imaging mass spectrometry data | Python | ||
| rMSI | R package for mass spectrometry imaging data handling and visualization [166] | R | ||
| SPUTNIK | R package for filtering spatially correlated peaks in MSI data [167] | R | ||
| isotopic distributions | ||||
| BRAIN | algorithm for calculating aggregated isotope distributions and corresponding center-masses (R package) | C++ | ||
| enviPat | batch fine structure, profile and centroid calculation with resolution settings provided | R | web | |
| IDCalc | isotope distribution and theoretical spectrum calculation with GUI | VB | ||
| iso2l | calculates the isotopic distribution of a chemical formula or a amino acid chain | Java | ||
| IsoSpec | calculates isotopic fine structure (with bindings for C, Python and R) | C++ | ||
| isotop | MATLAB code for calculating the isotopic distribution of a molecule (e.g. insulin) [168] | MATLAB | ||
| isotop | the same program in R | R | ||
| Isotope calculator | console application for calculating isotope distributions based on Yergey's method [169] | |||
| isotop_fs | MATLAB code for calculating isotopic fine structure | MATLAB | ||
| isotope.py | the same program in Python | Python | ||
| libipaca | Isotopic PAttern CAlculation library (MIT license) | C++ | ||
| Molecular Weight Calculator | calculates molecular masses and isotopic distributions | VB | ||
| MS-Isotope | calculates the isotopic distribution from a peptide sequence | C++/Java | web | |
| Prot pi | online calculator of physicochemical parameters of peptides/proteins, including isotopic distributions | VB | web | |
| random database generation | ||||
| Database Manager | sequence database manager, including random database generation | Java | ||
| decoy.pl | decoy database generator from Matrix Science | Perl | ||
| make_random | generate random database through Markov process | C | ||
| simulation/other | ||||
| compareMS2 | calculates overlap between two LC-MS/MS datasets in MGF [170] | C | ||
| Graph Extract | tool for digitizing data from images, similar to the classic Data Grabber, DataThief and WebPlotDigitizer | |||
| mspire-simulator | simulates peptide retention times and chromatographic profiles | Ruby | ||
| NGP | simulation of next-generation proteomics experiments | R | ||
| Prot pi | online calculation (simulation) of many physicochemical parameters of peptides/proteins | VB | web | |
The categorization of the software and algorithms here is somewhat arbitrary and may change over time. Many programs belong to multiple categories. If you have any suggestions on how to better organize this website - please let us know (see below).
The goal is to continuously improve the website while not moving too far beyond being a classic link collection and repository of free software for data analysis in mass spectrometry-based proteomics and protein analysis. The idea is to maximize the usefulness to anyone facing an analytical or computational problem in proteomics who first would like to know if a solution to the problem already exists and is in the public domain. The list will therefore always be an eclectic mix of full software suites with advanced graphical user interfaces, web-based software, libraries, scripts and pieces of source code to accomplish anything from reading a file in a particular format to providing a complete package for a proteomic analysis pipeline, from sample tracking to storing, viewing and comparing results from protein identification search engines.
The ambition should be to maintain only functional links to tested, useful and gratis software.
IMPORTANT - BY INSTALLING, COPYING OR USING ANY OF THE SOFTWARE YOU (EITHER AN INDIVIDUAL OR A SINGLE ENTITY) AGREE THAT YOU HAVE READ THESE TERMS, UNDERSTAND THEM AND AGREE TO BE LEGALLY BOUND BY THEM. IF YOU DO NOT AGREE TO ALL OF THE TERMS, DO NOT INSTALL, USE OR COPY ANY OF THE SOFTWARE.
