Software List
| platforms, pipelines and libraries | ||||
| CPAS | LIMS and analysis tools for proteomics data (includes msInspect) | |||
| 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 | ||
| libfbi | a fast implementation of box intersection for correspondence estimation in peak picking, alignment, etc. | C++ | ||
| mspire | MS data processing in Ruby, including mzML reader/writer, in-silico digestion, isotopic pattern calculation etc. [4] | Ruby | ||
| OpenMS | library for the analysis, reduction and visualization of LC-MS(/MS) data | C++ | ||
| PAPPSO | Plateforme d'Analyse Protéomique de Paris Sud-Ouest | Java | ||
| Proteios | pipeline/LIMS for proteomics experiments and analysis | Java | ||
| Proteomatic | platform for creating MS/MS data analysis workflows using scripts [5] | C++ | ||
| ProteoWizard | open source library for proteomics tools development (supports mzML) [6] | C++ | ||
| pymzML | Python module to parse mzML data based on cElementTree [7] | Python | ||
| Pyteomics | framework for proteomics data analysis, supporting mzML, MGF, pepXML and more [8] | Python | ||
| QuPE | integrated environment for storage, analysis and integration of proteomics data (requires login) [9] | Java | web | |
| Rproteomics | set of routines for analyzing proteomics data, an XML database to store the results and a user interface | R | ||
| TOPP | the OpenMS protein identification/quantitation pipeline | C++ | ||
| 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 | ||||
| cdfread | a simple reader of mass spectra in netCDF | C | ||
| COMSPARI | compares two datasets in netCDF or ASCII format | C | ||
| Insilicos Viewer | basic viewer of LC-MS/MS data in mzXML format | |||
| MapQuant | image analysis" of LC-MS features, deconvolution etc. [10] | C | ||
| massXpert | tool for analysis of polymer and peptide/protein mass spectra | |||
| mMass | analysis program data in Bruker .fid, mzData and mzXML formats | Python | ||
| MoverZ | free version of MoverZ for viewing and manipulating single mass spectra in many formats | |||
| msaccess | creates a psuedo-2D-gel representation [11] | 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 | |||
| MZmine | toolbox for visualization and analysis of LC-MS data in netCDF or mzXML [12] | |||
| 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 [13] | Java | ||
| Pep3D | plots LC-MS and LC-MS/MS data in a 2D m/z vs time plot [14] | |||
| 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 | ||
| Taverna | Taverna workflows for proteomics [15] | Java | ||
| 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 | ||||
| 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 (from the IonSource.com website | |||
| 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++ | ||
| MGF to .dta File Converter | converts MGF to .dta | |||
| 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 [16] | Python | ||
| msconvert | converts from RAW/WIFF/T2D/Agilent/Bruker/Waters/mzML/mzXML/MGF/MS2 to mzML/mzXML/MGF/MS2 [17] | 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++ | ||
| PyMS | tools for reading LC-MS data in the ANDI-MS and JCAMP-DX formats [18] | Python | ||
| ReAdW | converts Xcalibur native acquisition files to mzXML | VC++ | ||
| unfinnigan | reading Thermo .raw files without MsFileReader | Perl | ||
| wiff2dta | converts ABI WIFF to .dta [19] | |||
| X2XML | converts from almost any format (Thermo, Bruker, Agilent and Micromass) to mzXML | .NET | ||
| lipid analysis/lipidomics | ||||
| LipidXplorer (NEW) | high-throughput lipid identification from shotgun mass spectra in mzML, mzXML, CSV and .dta formats [20] | Python | ||
| peak picking/deconvolution | ||||
| DeconMSn | tool for accurate precursor ion monoisotopic mass determination for tandem mass spectra [21] | .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 [22] | 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 [23] | Python | web | |
| libmprc | library for analysis of high resolution mass spectrometry data (including THRASH) | C++ | ||
| massifquant (NEW) | Kalman filter based on binless peak picking and quantitation in XCMS | R | ||
| nontarget | R function for compound, adducts and ion series detection using isotopic distributions | R | ||
| Xtractor | extracts pre-defined peaks or regions into a uniform array | C | ||
| Y.A.D.A. (NEW) | tool for deconvoluting MS/MS spectra [24] | .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 [25] | 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 [26] | C | ||
| msalign2 | aligns 2 CE-MS or LC-MS datasets using accurate mass information [27] | C | ||
| OBI-Warp | aligns multiple LC-MS(/MS) datasets in retention time by dynamic time warping [28] | C++ | ||
| recal2 | recalibrate LC-FTICRMS(/MS) datasets using peptides identified by MS/MS [29] | C | ||
| SpecArray | aligns multiple LC-MS datasets and much more [30] | C++ | ||
| retention time prediction | ||||
| BioLCCC | an analytic model of peptide retention [31] | web | ||
| hplcsimulator | a general tool for simulating and optimizing HPLC gradients | web | ||
| retentionprediction | a related web utility for projecting/predicting retention times [32] | web | ||
| rt | (legacy) retention time prediction using LC-MS data [33] | C | ||
| rt3 | latest version of rt (3.0) with improved user interface | C | web | |
| SSRCalc | sequence-specific retention time calculator [34] | web | ||
| de novo sequencing/PTMs | ||||
| Delta Mass | the ABRF database of protein post-translational modifications | web | ||
| GlycoMod | predicts oligosaccharide structures from experimental masses | web | ||
| InSpecT | "blind" spectral search of tandem mass spectra of peptides [35] | C/Python | web | |
| lutefisk | de novo peptide sequencing from MS/MS data [36] | C | ||
| MSNovo | de novo peptide sequencing from MS/MS data [37] | |||
| PEAKS De Novo | integrated de novo peptide sequencing [38], PTM finder [39], and homology search [40] (demo available) | Java | ||
| PepNovo | de novo sequencing using probabilistic network modeling [41] | C++ | ||
| Popitam | searches for unknown post-translational modifications [42] | web | ||
| POSTMan | post-translational modification software [43] | C++ | ||
| ProSight PTM | web portal for PTM search in top-down experiments [44] | web | ||
| ProSight PTM Ion Predictor | generate exact masses for CID/ECD fragments with PTMs | web | ||
| Sequit! | free (non-batch) version of a de novo/BLAST tool [45] | web | ||
| SPS | shotgun protein sequencing assembling multiple MS/MS spectra [46] | MATLAB | ||
| theospec | command line tool for predicting MS/MS spectra [47] | 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 | ||
| 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) | ||||
| 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 | ||
| MassWiz | peptide identification and FDR calculation [48] | Perl | ||
| MS-GFDB | peptide identification using a combination of de novo and database search [49] | Java | ||
| MSPolygraph | open source hybrid database and spectral library MS/MS search engine [50] | C | ||
| MyriMatch | another free MS/MS search engine | C++ | ||
| OMSSA | mass spectrometry search algorithm from NIH (also searches ETD MS/MS data) [51] | web | ||
| PEAKS DB | de novo-assisted database search [52] | Java | ||
| Percolator | semi-supervised learning for peptide identification from MS/MS data [53] | |||
| Phenyx | free version of the GeneBio Phenyx protein identification platform | web | ||
| PepProbe | web-based MS/MS search engine [54] | web | ||
| PepSplice | cache-optimized search algorithm [55] | C++ | ||
| 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 [56] | web | ||
| VEMS | platform for protein identification and characterization [57] | |||
| 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 [58] | web | ||
| SpectraST | matches peptide MS/MS spectra with library spectra | |||
| X! Hunter | matches tandem mass spectra with library spectra from same organism | C++ | ||
| accurate mass and time (AMT) | ||||
| msInspect | align data from multiple samples and identify peptides by AMT using LC-MS and LC-MS/MS [59] | Java | ||
| (result) parsers/validation/fragment spectrum processing | ||||
| goa_gubbar | sorts protein identifications under GOA slim terms | C | ||
| Mascot Parser | PDOM and MASCOT parser [60] | Java | ||
| libmgf | libmgf (formerly mgfp) - a flex/bison-based Mascot Generic Format (MGF) parser library [61] | C++ | ||
| ms2preproc | ms2preproc - MGF and dta fragment spectrum preprocessing [62] | C++ | ||
| mres2x | a tool to process MASCOT results [63] | 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 [64] | C++/Perl | ||
| ProteinProphet (TPP) | validation of protein identifications by MS/MS and database searches [65] | C/Perl | ||
| XTandem Parser | Java-based parser for X!Tandem result files [66] | Java | ||
| protein quantitation | ||||
| APEX | protein abundance estimate from LC-MS/MS data [67] | Java | ||
| ASAPRatio (TPP) | statistical analysis of protein ratios from ICAT, cICAT or SILAC experiments | VC++ | ||
| DAnTE | protein quantitation, statistical analysis and visualization | .NET | ||
| ICPLQuant | tool for processing and analyzing ICPL LC-MALDI data [68] | Java | ||
| ICPL_ESIQuant (NEW) | tool for processing and analyzing ICPL LC-MS/MS (ESI) data [69] | Java | ||
| isobar | quantitation of TMT and iTRAQ data and LaTeX report generation [70] | R | ||
| IsobariQ | quantitation of IPTL, iTRAQ and TMT-labeled peptides [71] | C++ | ||
| Libra (TPP) | analyzes 4- and 8-channel iTRAQ data | |||
| MaxQuant | quantitation from SILAC data from Thermo Orbitrap and FTICR | |||
| MFPaQ | Mascot file parsing and quantitation using ICAT and SILAC [72] | 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 | ||
| Multi-Q | tool for multiplexed iTRAQ-based quantitation [73] | .NET/Perl | ||
| muxQuant | multiplexed quantitiave proteomics using differential stable isotope labeling [74] | C | ||
| 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 [75] | |||
| PVIEW | isotope labeled, label-free, and XIC-based quantitation for high resolution LC-ESI-MS/MS data [76] | C++ | ||
| Quant | MATLAB program for protein quantitation by iTRAQ [77] | MATLAB | ||
| QUIL | another program for relative quantitation using stable isotope labeling [78] | |||
| RAAMS | algorithm for interpreting O-16/O-18 differential proteomics data [79] | C++ | ||
| RelEx | calculation of ion current ratios from LC-MS data (requires Xcalibur) [80] | |||
| XPRESS (TPP) | calculates relative abundances from ICAT, cICAT, SILAC and other N-14/N-15 experiments [81] | VC++ | ||
| protein structure | ||||
| ASAP | automatic peptide identification in crosslinking experiments [82] | web | ||
| AUTOHD | analysis of H/D-exchange data using isotopic distributions [83] | C | ||
| Deuterator | web based software platform for determining backbone amide H/D ratios [84] | Java/JSP | web | |
| DEX | another program (similar to AUTOHD) for analysis of H/D-exchange spectra [85] | C/C++ | ||
| ExMS | MATLAB program for analyzing H/D-exchange data [86] | MATLAB | ||
| hydrogen_bondifier (NEW) | PyMOL script for retrieving hydrogen bond characteristics from protein structures | PyMOL | ||
| HX-Express | an Excel spreadsheet for analysis of H/D exchange mass spectra [87] | Excel | ||
| MassMatrix | MassMatrix also allows cross-linked peptide identification | web | ||
| MS2Pro | assigns crosslinked or non-crosslinked fragments in whole protein MS/MS (top-down) spectra [88] | web | ||
| MS2Assign | assigns crosslinked or non-crosslinked peptides in MS/MS spectra [89] | web | ||
| xComb | interogate protein-protein interactions and protein structure using cross-links FASTA databases [90] | Perl | web | |
| XLink (TPP) | set of tools for analysis of data from crosslinked and digested protein complexes | |||
| in silico digestion | ||||
| dig | digests or fragments protein sequences [91] | C | ||
| dig2 | updated version of dig | C | ||
| 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 | |||
| isotopic distributions | ||||
| 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 | ||
| isopat | R function for calculating isotopic distributions | R | ||
| isotop | MATLAB code for calculating the isotopic distribution of a molecule (e.g. insulin) [92] | MATLAB | ||
| isotop | the same program in R | R | ||
| isotop_fs | MATLAB code for calculating isotopic fine structure [93] | MATLAB | ||
| isotope.py | the same program in Python | Python | ||
| libipaca (NEW) | 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 | |
| SmileMS molecule toolkit | web utilities for isotopic distributions, elemental compositions and PubChem lookup by accurate mass | 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 | ||||
| mspire-simulator (NEW) | simulates peptide retention times and chromatographic profiles | Ruby | ||
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.
Please send an e-mail to webmaster@ms-utils.org for comments, suggestions or encouragements!