Other resources
Alternatively to ProteoSuite, there is a large number of software packages for the analysis of quantitative proteomics data. In this page we provide a concensus of current commercial (Table 1) and free (Table 2) distributions. This list is intended to serve as a useful reference and guide to the selection and use of different pipelines to perform quantitative proteomics data analysis depending on the type of instrument, method or platform used.
The list is periodically updated by the ProteoSuite Consortium. If you want to suggest a new software to the existing list or wish to update the status of an existing software package, please contact us.
Tip: Try also our "Pipeline Configuration Tool", this tool allows users to examine the different pipelines available according to the type of experiment and resources.
Table 1 Commercial software packages for analysis of quantitative proteomics data
| Software | Company | SILAC | iTRAQ | 15N | 18O | ICPL | ICAT | Label Free | TMT | Other |
|---|---|---|---|---|---|---|---|---|---|---|
| BioWorksTM | Thermo | Y | Y | Y | Y | |||||
| Elucidator© | Rosetta | Y | Y | Y | ||||||
| Mascot Distiller | Matrix Science | Y | Y | Y | Y | Y | Y | Absolute quantitation (AQUA) | ||
| Mascot Server | Matrix Science | Y | Y | |||||||
| PEAKS® Q | Bioinformatics Solutions | Y | Y | Y | Y | Y | Y | Y | ||
| PLGSTM | Waters | Y | Absolute quantification (Hi3) | |||||||
| Progenesis LC-MSTM | NonLinear Dynamics | Y | ||||||||
| ProQuant | Applied Biosystems | Y | ||||||||
| ProteinPilotTM | AB SCIEX | Y | Y | Y | Y | |||||
| ProteinScape | Bruker | Y | Y | Y | Y | Y | Y | Y | ||
| ProteoIQ | Bioinquire | Y | Y | Y | Y | Y | Y | Y | ||
| Proteome Discoverer | Thermo | Y | Y | Absolute quantification (HeavyPeptide - AQUA) | ||||||
| SIEVE | Thermo | Y |
Last update: 30 April 2012. [Top]
Table 2 Free software packages for analysis of quantative proteomics data
| Software | Version | Date | Technique | Type of data | Instruments | Input files | Distribution | License | Language | OS | Ref |
|---|---|---|---|---|---|---|---|---|---|---|---|
| APEX |
1.1.0 |
Mar-10 | Improvement of SC | LC-MS/MS | Any via prot.xml files | .fasta, .oi, prot.xml | Free - Open Source | GNU GPL 3.0 | Java | Windows, OSX, Linux | (1) |
| Census |
1.72 |
Mar-10 | 15N, SILAC, iTRAQ, SC | MS1/MS2 | Any via mzXML | MS1/MS2, DTASelect, mzXML, pepXML | Free | - | Java | Windows, OSX, Linux | (2) |
| MapQuant |
2.1.1 |
Jan-06 | Label free image recognition | LC-MS | Thermo, Waters | OpenRaw | Free - Open Source | - | Visual C++ | Windows, Linux | (3) |
| MaXIC-Q | 0.9.2 | - | SILAC, ICAT | LC-MS | Any via mzXML | mzXML, Mascot/SEQUEST/ProteinProphet xml | Free | - | Visual C++ | Windows, Web | (4) |
| MaxQuant | 1.3.0.5 | - | SILAC, ICPL, Label free, iTRAQ, TMT | MS1/MS2 | LTQ, Orbitrap, FT-ICR (Thermo) | .raw (Thermo) | Free | - | C# | Windows | (5) |
| MFPaQ | 4.0.0 | - | SILAC, ICAT, label free (SC and MS signals) |
MS1/MS2 | QSTAR XL, QSTAR Elite (ABI) | .wiff (ABI) | Free - Open Source | - | Perl | Windows | (6) |
| mProphet | 1.0.4.1 | Dec-10 | SRM, AQUA, QconCAT, PSAQ | LC-MS/MS | Any via mzXML | .mzXML+.xls | Free - Open Source | Apache 2.0 | Perl / R | Windows, Linux | (7) |
| MSQuant | 2.0b6 | May-10 | 15N, SILAC, ICAT, 18O, label free |
MS1/MS2 | QSTAR (ABI), Q-ToF (Waters), LTQ, FT, Orbitrap (Thermo) | .raw (Thermo), .dat (Waters), .wiff (ABI) | Free - Open Source | - | C# and VB .NET | Windows | (8) |
| Multi-Q | 1.6.5.4 | Jul-10 | iTRAQ | LC-MS/MS | Any via mzXML | mzXML, .wiff (ABI) | Free | - | VB .NET | Windows, Web | (9) |
| OpenMS | 1.8 | Mar-11 | iTRAQ, SILAC, Label free | MS1/MS2 | Any via mzXML or mzML | .dta, mzData, mzXML, mzML | Free - Open Source | LGPL | C++ | Windows, Linux, OSX | (10) |
| PeakQuant | 1.5.42 | - | 15N, SILAC, iTRAQ | MS1/MS2 | Any via mzXML | mzXML | Free | - | Java | Windows, Linux, OSX | - |
| PEPPeR | - | - | Label free | MS1/MS2 | Any via mzXML | mzXML | Free | - | Perl | Windows | (11) |
| ProRata | 1.0 | Dec-05 | 15N, SILAC, ICAT, 18O | LC-MS | Any via mzXML | mzXML | Free - Open Source | GNU GLP 3.0 | C++ | Windows, Linux | (12) |
| Proteios | 2.16 | Jun-11 | iTRAQ, TMT | MS1/MS2 | Any via mzML | mzML | Free - Open Source | GPL v2 | Java | Windows, Linux, OSX | (13) |
| QUIL | - | - | 18O, ICAT | LC-MS | LCQ, LTQ, FT-ICR (Thermo) | - | Available on request | - | Visual C++ | Windows | (14) |
| Qupe | - | - | 15N | LC-MS | LTQ, Orbitrap (Thermo) | mzXML | Web based | - | Java | Web-based | (15) |
| Skyline | 1.2 | Mar-12 | SRM, label free | LC-MS | Any via mzXML | mzXML, pepXML | Free - Open Source | Apache 2.0 | C# | Windows | (16) |
| STEM | - | - | 18O | LC-MS | - | .pkl (Protein Lynx – Waters) | - | - | - | Windows | (17) |
| TPP | 4.5.0 | Aug-11 | ICAT, SILAC, iTRAQ | MS1/MS2 | See below | mzXML, mzML | Free | - | - | Windows, Linux, OSX | (18) |
| -ASAPRatio | - | - | ICPL, ICAT, SILAC | Any via mzXML or mzML | Via TPP | Free | - | C | Windows, Linux, OSX | (19) | |
| -Libra | - | - | iTRAQ | Any via mzXML or mzML | Via TPP | Free | - | C | Windows, Linux, OSX | (20) | |
| -SpecArray | - | - | Label free | Any via mzXML | Via TPP | Free | - | C++ | Linux | (21) | |
| -SuperHirn | - | - | Label free | Any via mzXML | Via TPP | Free | - | C | Linux, OSX | (22) | |
| -XPRESS | - | - | ICPL, ICAT, SILAC, 14N/15N | Any via mzXML or mzML | Via TPP | Free | - | C | Windows, Linux, OSX | (23) | |
| VIPER | 3.48.456 | Sep-11 | 18O, ICAT | MS1/MS2 | Any via mzXML | .pek, .CSV, .mzXML, .mzData, .raw (Thermo) | Free - Open Source | Apache 2.0 | - | Windows | (24) |
| X-Tracker | 1.3 | Jun-11 | iTRAQ, 15N | MS1/MS2 | Any via mzML | mzML, mzIdentML | Free - Open Source | GNU GPL 3.0 | Java | Windows, Linux, OSX, | - |
| -iTracker | 1.1 | May-05 | iTRAQ | MS2 | - | .mgf, .dta | Free | - | Perl | Windows, Linux | (25) |
| ZoomQuant | - | - | 18O | LC-MS | LTQ (Thermo) | .raw (Thermo) | Free | - | Perl | Windows, Linux, OSX | (26) |
Last update: 30 April 2012; Abbreviations: SC=Spectral Count, (-) Information not available. [Top]
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References
1. Braisted, J.C., Kuntumalla, S., Vogel, C., Marcotte, E.M., Rodrigues, A.R., Wang, R., et al., (2008). The APEX Quantitative Proteomics Tool: Generating protein quantitation estimates from LC-MS/MS proteomics results. Bmc Bioinformatics 9
2. Park, S.K., Venable, J.D., Xu, T., Yates, J.R., (2008). A quantitative analysis software tool for mass spectrometry-based proteomics. Nat Methods 5, 319-322.
3. Leptos, K.C., Sarracino, D.A., Jaffe, J.D., Krastins, B., Church, G.M., (2006). MapQuant: Open-source software for large-scale protein quantification. Proteomics 6, 1770-1782.
4. Tsou, C.C., Tsui, Y.H., Yian, Y.H., Chen, Y.J., Yang, H.Y., Yu, C.Y., et al., (2009). MaXIC-Q Web: a fully automated web service using statistical and computational methods for protein quantitation based on stable isotope labeling and LC-MS. Nucleic Acids Research 37, W661-W669.
5. Cox, J., Mann, M., (2008). MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification. Nat Biotechnol 26, 1367-1372.
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12. Pan, C.L., Kora, G., McDonald, W.H., Tabb, D.L., VerBerkmoes, N.C., Hurst, G.B., et al., (2006). ProRata: A quantitative proteomics program for accurate protein abundance ratio estimation with confidence interval evaluation. Analytical chemistry 78, 7121-7131.
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14. Wang, G.H., Wu, W.W., Pisitkun, T., Hoffert, J.D., Knepper, M.A., Shen, R.F., (2006). Automated quantification tool for high-throughput proteomics using stable isotope labeling and LC-MSn. Analytical chemistry 78, 5752-5761.
15. Albaum, S.P., Neuweger, H., Franzel, B., Lange, S., Mertens, D., Trotschel, C., et al., (2009). Qupe-a Rich Internet Application to take a step forward in the analysis of mass spectrometry-based quantitative proteomics experiments. Bioinformatics 25, 3128-3134.
16. Maclean, B., Tomazela, D.M., Shulman, N., et al. (2010). Skyline: an open source document editor for creating and analyzing targeted proteomics experiments. Bioinformatics 26, 966–968.
17. Shinkawa, T., Taoka, M., Yamauchi, Y., Ichimura, T., Kaji, H., Takahashi, N., et al., (2005). STEM: A software tool for large-scale proteomic data analyses. J Proteome Res 4, 1826-1831.
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20. Pedrioli, P.G.A., Eng, J.K., Hubley, R., et al. (2004). A common open representation of mass spectrometry data and its application to proteomics research. Nat Biotechnol 22, 1459–1466.
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22. Mueller, L.N., Rinner, O., Schmidt, A., et al. (2007). SuperHirn— a novel tool for high resolution LC-MS-based peptide/protein profiling. Proteomics 7, 3470–3480.
23. Han, D.K., Eng, J., Zhou, H.L., Aebersold, R., (2001). Quantitative profiling of differentiation-induced microsomal proteins using isotope-coded affinity tags and mass spectrometry. Nat Biotechnol 19, 946-951.
24. Monroe, M.E., Tolic, N., Jaitly, N., Shaw, J.L., Adkins, J.N., Smith, R.D., (2007). VIPER: an advanced software package to support high-throughput LC-MS peptide identification. Bioinformatics 23, 2021-2023.
25. Shadforth, I.P., Dunkley, T.P.J., Lilley, K.S., Bessant, C., (2005). i-Tracker: For quantitative proteomics using iTRAQ (TM). Bmc Genomics 6.
26. Halligan, B.D., Slyper, R.Y., Twigger, S.N., Hicks, W., Olivier, M., Greene, A.S., (2005). ZoomQuant: An application for the quantitation of stable isotope labeled peptides. J Am Soc Mass Spectr 16, 302-306.
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