Software List
| platforms, pipelines and libraries | ||||
| CPAS | LIMS and analysis tools for proteomics data (includes msInspect) | |||
| InSilicoSpectro | open source proteomics library (of Perl functions) [1] | Perl | ||
| GenePattern | platform for integrative genomics and proteomics (includes PEPPeR [2] and other tools for proteomics) | Java | ||
| OpenMS | library for the analysis, reduction and visualization of LC-MS(/MS) data | C++ | ||
| Proteios | pipeline/LIMS for proteomics experiments and analysis | Java | ||
| ProteoWizard (NEW) | open source library for proteomics tools development (supports mzML) [3] | C++ | ||
| Rprotoemics | 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. [4] | 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 | |||
| 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 [5] | |||
| mzXMLplot (NEW) | plots mzXML LC-MS data as virtual gels or heat maps | C | ||
| mzXML Viewer | mzXML viewer from Seattle Proteome Center | |||
| Pep3D | plots LC-MS and LC-MS/MS data in a 2D m/z vs time plot [6] | |||
| Sirius | tool for metabolite identification using mass spectrometry | Java | ||
| Spectrum Look | tool for viewing and annotating MS/MS spectra | 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 | ||||
| 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 | |||
| 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 | |||
| 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++ | ||
| ReAdW | converts Xcalibur native acquisition files to mzXML | VC++ | ||
| wiff2dta | converts ABI WIFF to .dta [7] | |||
| X2XML (NEW) | converts from almost any format (Thermo, Bruker, Agilent and Micromass) to mzXML | .NET | ||
| peak picking/deconvolution | ||||
| Decon2LS | advanced peak picking of MS and LC-MS(/MS) data using THRASH and other algorithms | .NET | ||
| esimsa | simple deconvolution of electrospray ionization peak lists [8] | C | ||
| esimsa2D | simple deconvolution and 2D peak picking of LC-MS data | C | ||
| libmprc | library for analysis of high resolution mass spectrometry data (including THRASH) | C++ | ||
| calibration/alignment | ||||
| CPM | alignment of time-series data [as in LC-MS(/MS)] using Continuous Profile Models [9] | MATLAB | ||
| msalign (NEW) | align LC-MS and LC-MS/MS datasets using peptides identified by MS/MS and accurate mass MS [10] | C | ||
| OBI-Warp | aligns multiple LC-MS(/MS) datasets in retention time by dynamic time warping [11] | C++ | ||
| recalibrate_using_MSMS | recalibrate LC-FTICRMS(/MS) datasets using peptides identified by MS/MS [12] | C | ||
| SpecArray | aligns multiple LC-MS datasets and much more [13] | C++ | ||
| retention time prediction | ||||
| rt | retention time prediction using LC-MS data [14] | C | ||
| SSRCalc | sequence-specific retention time calculator [15] | 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 [16] | C/Python | web | |
| lutefisk | de novo peptide sequencing from MS/MS data [17] | C | ||
| PEAKS Online | web-based de novo sequencing | web | ||
| PepNovo | de novo sequencing using probabilistic network modeling [18] | C++ | ||
| Popitam | searches for unknown post-translational modifications [19] | web | ||
| ProSight PTM | web portal for PTM search in top-down experiments [20] | 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 [21] | web | ||
| SPS | shotgun protein sequencing assembling multiple MS/MS spectra [22] | MATLAB | ||
| theospec | command line tool for predicting MS/MS spectra [23] | 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 | ||
| PepMAPPER | multi-experiment peptide mass fingerprinting | web | ||
| ProFound | free web version of ProFound (peptide mass fingerprinting) | web | ||
| ProteinProspector | the ProteinProspector suite of protein identification tools | web | ||
| tandem mass specrometry (MS/MS) | ||||
| MASCOT | free, web-based version of the MASCOT MS/MS Ions Search | web | ||
| OMSSA | mass spectrometry search algorithm from NIH (also searches ETD MS/MS data) [24] | web | ||
| Percolator (NEW) | semi-supervised learning for peptide identification from MS/MS data [25] | |||
| Phenyx | free version of the GeneBio Phenyx protein identification platform | web | ||
| PepProbe | web-based MS/MS search engine [26] | web | ||
| PepSplice (NEW) | cache-optimized search algorithm [27] | C++ | ||
| ProteinProspector | the ProteinProspector suite of protein identification tools | web | ||
| Proteome ARTworks (NEW) | predicts detectability and tandem mass spectra of peptides and addresses the protein inference problem [28] | web | ||
| VEMS | platform for protein identification and characterization [29] | |||
| X! Tandem | matches tandem mass spectra with peptide sequences | C++ | ||
| MS/MS library search | ||||
| ProMEX (NEW) | matches tandem mass spectra against A. thaliana and M. truncatula libraries [30] | 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 [31] | Java | ||
| result parsers/validation | ||||
| goa_gubbar | sorts protein identifications under GOA slim terms | C | ||
| Mascot Parser | PDOM and MASCOT parser [32] | Java | ||
| mres2x | a tool to process MASCOT results [33] | C | ||
| PeptideProphet (TPP) | validation of peptide identifications by MS/MS and database searches [34] | C++/Perl | ||
| ProteinProphet (TPP) | validation of protein identifications by MS/MS and database searches [35] | C/Perl | ||
| protein quantitation | ||||
| APEX (NEW) | protein abundance estimate from LC-MS/MS data [36] | Java | ||
| ASAPRatio (TPP) | statistical analysis of protein ratios from ICAT, cICAT or SILAC experiments | VC++ | ||
| Libra (TPP) | analyzes 4-channel iTRAQ data | |||
| MFPaQ (NEW) | Mascot file parsing and quantitation using ICAT and SILAC [37] | 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 [38] | .NET/Perl | ||
| muxQuant (NEW) | multiplexed quantitiave proteomics using differential stable isotope labeling [39] | C | ||
| pepXML2Excel | converts output from PeptideProphet to protein level information in Excel | AWK | ||
| ProRata | differential proteomics analysis using for various stable isotope labeling schemes [40] | |||
| Quant (NEW) | MATLAB program for protein quantitation by iTRAQ [41] | MATLAB | ||
| QUIL | another program for relative quantitation using stable isotope labeling [42] | |||
| RAAMS | algorithm for interpreting O-16/O-18 differential proteomics data [43] | C++ | ||
| RelEx | calculation of ion current ratios from LC-MS data (requires Xcalibur) [44] | |||
| XPRESS (TPP) | calculates relative abundances from ICAT, cICAT, SILAC and other N-14/N-15 experiments [45] | VC++ | ||
| protein structure | ||||
| ASAP | automatic peptide identification in crosslinking experiments [46] | web | ||
| AUTOHD | analysis of H/D-exchange data using isotopic distributions [47] | C | ||
| Deuterator | web based software platform for determining backbone amide H/D ratios [48] | Java/JSP | web | |
| DEX | another program (similar to AUTOHD) for analysis of H/D-exchange spectra [49] | C/C++ | ||
| HX-Express | an Excel spreadsheet for analysis of H/D exchange mass spectra [50] | Excel | ||
| MS2Pro | assigns crosslinked or non-crosslinked fragments in whole protein MS/MS (top-down) spectra [51] | web | ||
| MS2Assign | assigns crosslinked or non-crosslinked peptides in MS/MS spectra [52] | 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 [53] | C | ||
| MS-Digest | digests a protein sequence | web | ||
| PeptideCutter | another web based protein digestion applet | web | ||
| Protein Digestion Simulator Basic | calculates theoretical enzymatic peptides and AMTs | |||
| isotopic distributions | ||||
| isotop | MATLAB code for calculating the isotopic distribution of a molecule (e.g. insulin) [54] | MATLAB | ||
| isotop_fs | MATLAB code for calculating isotopic fine structure [55] | MATLAB | ||
| isotope | simple command line isotopic distribution calcultor | C | ||
| Molecular Weight Calculator | calculates molecular masses and isotopic distributions | VB | ||
| MS-Isotope | calculates the isotopic distribution from a peptide sequence | Java | web | |
| random database generation | ||||
| decoy.pl | decoy database generator from Matrix Science | Perl | ||
| make_random | generate random database through Markov process | C | ||
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 enigines.
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.
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