| Software |
Developer/Vendor |
Publication Date |
Relation to Proteomics |
Programming language |
Platform |
| 1. Data Formats |
| mzData[23] |
HUPO PSI |
2007 |
Standardized data-exchange format |
XML |
independent |
| mzXML[24] |
Seattle Proteome Center; Institute for Systems Biology |
2004 |
Standardized data-exchange format |
XML |
independent |
| mzML[23] (replacement of mzXML u. mzData) |
HUPO PSI |
2008 |
Standardized data-exchange format |
XML |
independent |
| TraML[23] |
HUPO PSI |
2010 |
Standardized data-exchange format |
XML |
independent |
| mzIdentML[23] |
HUPO PSI |
2009 |
Standardized data-exchange format |
XML |
independent |
| mzQuantML[23] |
HUPO PSI |
2011 |
Standardized data-exchange format |
XML |
independent |
| mz5[25] |
Boston Children's Hospital; Steen & Steen Laboratory |
2012 |
Storage-optimized data-exchange format |
XML, HDF5 |
independent |
| netCDF[26] |
UCAR |
1997 |
Standardized data-exchange format |
binary |
independent |
| 2. Commercial Software |
| Analyst |
ABSciex[27] |
- |
Automated MS a. MS/MS Detection, MRM Monitoring, Database-search possible |
C, C++ |
Windows |
| SWATH Acquisition |
ABSciex |
- |
Data-indepentend data capture, MRM, High resolution, MS/MS, labelfree Quantification |
C, C++ |
Windows |
| MetabolitePilot |
ABSciex |
- |
Detection and identification of metabolites (drug design) |
C, C++ |
Windows |
| ProteinPilot |
ABSciex |
- |
Protein-identification a. -quantification |
C, C++ |
Windows |
| MultiQuant |
ABSciex |
- |
MRM, Quantification |
C, C++ |
Windows |
| PeakView |
ABSciex |
- |
TripleTOF, Mass interpretation, Accurate mass, Protein structure |
C, C++ |
Windows |
| Masshunter |
Agilent[28] |
- |
MS-Detection platform of Agilent, Peak detection, -integration |
C, C++ |
Windows |
| LCMS ChemStation |
Agilent |
- |
High-throughput quantification, Peak detection, NIST-search |
C, C++ |
Windows |
| OpenLAB |
Agilent |
- |
Data center, Crosslinkage between analytical hardware and software of Agilent |
C, C++ |
Windows |
| Proteome Discoverer |
Thermo[29] |
- |
Extentable platform for qualitative a. puantitative Proteomics |
C, C++ |
Windows |
| Xcalibur |
Thermo Fisher Scientific Inc. |
- |
Data system for device control and data analysis |
C, C++ |
Windows |
| ProMass |
Thermo Fisher Scientific Inc. |
- |
Automated biomolecule deconvolution |
C, C++ |
Windows |
| MassLynx |
Waters[30] |
- |
Platform for MS-detection of Waters |
C, C++ |
Windows |
| OpenLynx |
Waters |
- |
Qualitative screening a. identification |
C, C++ |
Windows |
| QuanLynx |
Waters |
- |
Automated Quantification |
C, C++ |
Windows |
| ProteinLynx Global SERVER |
Waters |
- |
Platform for qualitative a. quantitative proteomics |
C, C++ |
Windows |
| Phenyx[31] |
GeneBio |
2006 |
MS/MS Protein identification, -quantification |
- |
web based |
| Seaquest[32][33] |
Yates Lab |
1993/1994 |
Protein identification algorithm throug MS-data |
- |
Windwos, Linux |
| PEAKS[34][35] |
Bioinformatics Solutions Inc. |
2003 |
De Novo sequencing, Data base search, PTMs, SPIDER-search, Quatnification, Protein/Peptid identification |
C, C++ |
Windows |
| 3. Free/Open Source Platforms and Software-Tools |
| Achroma[7][8] |
Weihenstephan-Triesdorf - University of Applied Sciences |
2012 |
LC-MS, Functional proteomics |
C++, C#, Microsoft NET Framework a. Visual Studio 2003 |
Windows |
| OpenChrom (free Community Edition)[9] |
University of Hamburg, Lablicate |
2010 |
GC/MS, LC/MS, HPLC-MS, ICP-MS, MALDI-MS |
Java, Eclipse |
independent |
| Maltcms/Maui[20] |
University of Bielefeld |
2012 |
LC-MS-, GS-MS- u. GC-MS/MS-high-throughput metabolomics |
Java, NetBeans |
independent |
| polyXmass / massXpert [36] |
Filippo Rusconi |
2001 / 2009 |
Simulation of biological a. chemical reactions, Fragmentation |
C++, Qt-Bibliotheken |
independent |
| DeconLS[37] |
Pacific Northwest National Laboratory |
2009 |
Detection of molecule properties with MS-data and isotopes signatures, Deconvolution |
C++, C#, Microsoft NET Framework a. Visual Studio 2003 |
Windows |
| BioClipse[38][39] |
Dept. of Pharmaceutical Biosciences, Uppsala University; European Bioinformatics Institute |
2007 |
Tool box for bio- a. chemoinformatics |
Java, Eclipse |
independent |
| BioSunMS[40] |
Center of Computational Biology, Beijing Institute of Basic Medical Sciences |
2009 |
Peptide profiles via MS |
Java, R, SQL |
Windows, Linux |
| openMS[41] |
University of Tübingen, Free University of Berlin, ETH Zürich |
2008 |
LC-MS data management a. -analytics, Label-free quantification, SILAC, iTRAQ, SRM, SWATH, De-novo identification, Data base search |
C++ |
Windows, Linux |
| MetaQuant[42] |
Bioinformatics Organization |
2006 |
Automated quantification of GC/MS based Metabolome-data |
Java |
independent |
| intelliMS[43] |
Yonsei Proteome Research Center |
2008 |
Management a. Visualization of tandem-MS data |
PHP, MySQL |
web based |
| mMass[44] |
Martin Strohalm |
2008 |
Protein- a lipid-identification, Protein modification, Deconvolution, Data base search, Standard-MS evaluations, e.g. peak detection, Spectrum-Viewer,… |
Python, wxPython |
independent |
| MZMine2[45] |
Okinawa Institute of Science and Technology |
2010 |
Peak-identification of MS-data, Peak deconvolution, 3D-Visualization, Statistics, Data base search |
Java, Java3D |
independent |
| pymzML[46] |
University of Münster |
2012 |
High-throughput bioinformatics with MS-data |
Python |
independent |
| MS-Spectre[47] |
Netherlands Proteomics Centre |
2007 |
Spectra visualization, Filter, Peak detection, Peak matching |
Java, Eclipse |
independent |
| ProteoWizard [8] |
ProteoWizard Software Foundation |
2008 |
Proteomics a. MS software toolbox (msconvert converting tool for vendor formats into mzML) |
C++ |
independent |
| X!Tandem / X!!Tandem [48] |
The Global Proteome Machine Organization |
2004 |
Data base search (algorithm) for matching tandem-MS sequences with peptide sequences for protein identification |
C |
Linux |
Mascot (Server)[49][50]
(free search for 1200 spectra and limited functions) |
Matrix Science |
1993 |
Data base search (algorithm) for Protein identification, characterization a. quantification via MS-data |
- |
Windows, Linux |
| PRIDE[51] |
EMBL-EBI |
2005 |
Data base search (algorithm) for Protein identification |
Java, HTML; SQL, XML |
Windows, Linux a. web based |
| TOPP[11] |
University of Tübingen |
2007 |
OpenMS Proteomik Pipeline for batch processing of analytical tasks |
C++ |
Windows, Linux |
| MapQuant[52] |
Havard Molecular Technologies |
2006 |
Large-scale Protein quantification |
C++ |
Windows, Linux |
| SpecArray[53] |
Seattle Proteome Center |
2005 |
Comparison of peptide-arrays with LC-MS data |
C |
Linux |
| ATAQS[54] |
Seattle Proteome Center |
2011 |
Automated a. targeted analysis with quantitative SRM a. MS |
Java, R, mysql |
Linux |
| Skyline[55] |
MacCoss Lab Software |
2010 |
Document editor for designing a. analysing targeted proteomic experiments |
C#, Windwos Forms |
Windows |
| msInspect[56] |
Fred Hutchinson Cancer Research Center |
2006 |
Analysing complex protein mixtures with LC-MS |
Java |
independent |
| SuperHirn[57] |
Seattle Proteome Center |
2007 |
LC-MS peptide-/protein-profiling |
C++ |
Linux, MacOS X |
| MassSorter[58] |
FUGE Bioinformatics Platform |
2006 |
Analysing of MS protein experiments mit knowns amino acids |
Java, NetBeans, Java3D |
independent |
| PASSEL[59] |
Institute of System Biology, Seattle |
2012 |
PeptideAtlas SRM experiment library |
- |
web based |
| jTraML[60] |
CompOmics |
2011 |
Java API of TraML-Standard of the Proteome Standards Initiative, SRM experiments |
Java |
independent |
| HDX-analyzer[61] |
Texas A&M University |
2011 |
Package for statistical analysis of protein structure dynamics |
Python, R |
independent |
| PeptidePicker[62] |
Genome British Columbia Proteomics Center |
2014 |
Toolbox for selction of possible peptides for targeted proteomics |
- |
web based |
| TPP (Trans-Proteomic Pipeline) [10] |
Seattle Proteome Center |
2005 |
MS/MS based "shotgun"-proteomics, Identification, Quantification |
C++, Python |
independent |
| SpectraST[63] |
Institute of System Biology, Seattle |
2007 |
Search algorithm for spectra libraries for identification of peptides via MS/MS |
a spart of TPP in Python |
independent |
| OMSSA (Open Mass Spectrometry Search Algorithm)[64] |
National Center of Biotechnology Information |
2004 |
Data base search algorithm for peptide identification via MS/MS |
- |
independent |
| Andromeda[65] (Part of MaxQuant) |
Max Planck Institute of Biochemistry |
2011 |
Data base search engine for peptide identification via MS/MS |
C# |
web based, local installation: Windows |
| MaxQuant[66] |
Max Planck Institute of Biochemistry |
2008 |
Quantitative proteomics via MS |
C# |
Windows |
| Proteios SE[67] |
University Lund |
2005 |
Platform for storing, organizing, analyzing a. annotation of protein experiments |
Java |
independent |
| MyriMatch [68] |
Vanderbilt University Medical Center |
2006 |
Data base search engine for peptide identification via MS/MS |
C++ |
Windows, Linux |
| PAGIT[69] |
Sanger Institute |
2012 |
Tools to generate automatically high quality sequence by ordering contigs, closing gaps, correcting sequence errors and transferring annotation |
C++ |
Linux, virtual machine ( for other operating systems) |
| MUMmer[70] |
J. Craig Venter Institute |
1999,2004 |
Ultra-fast alignment of large-scale DNA and protein sequences |
C++, Python |
Linux |
| VeSPA[71] |
Computational Biology and Bioinformatics, Pacific Northwest National Laboratory |
2012 |
Facilitation of genomic annotation of prokaryotic organisms through integration of proteomic and transcriptomic data |
Python |
independent |
| MINT[72] |
University of Rome |
2006 |
Molecular interaction database, focus on experimentally verified protein-protein interactions |
Java |
web based |
| Mass Bank[73] |
Institute for Advanced Biosciences, Keio University |
2010 |
Data base for mass spectra of small chemical compounds for life sciences (<3000 Da) |
Java |
web based |
| MSEA[74] |
University of Alberta |
2010 |
Tool to identify biologically patterns in quantitative metabolomic data |
Java, R |
web based |
| XANNpred [75] |
University of Dundee |
2010 |
Crystallisation propensity predictor |
Perl |
web based |
