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]

 

 

Pipeline configurator tool

Customise your own experiment by selecting one of the options below:


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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.

 

6. Bouyssie, D., de Peredo, A.G., Mouton, E., Albigot, R., Roussel, L., Ortega, N., et al., (2007). Mascot file parsing and quantification (MFPaQ), a new software to parse, validate, and quantify proteomics data generated by ICAT and SILAC mass spectrometric analyses. Mol Cell Proteomics 6, 1621-1637.

 

7. Reiter, L., Rinner, O., Picotti, P., Huttenhain, R., Beck, M., Brusniak, M.Y., et al., (2011b). mProphet: automated data processing and statistical validation for large-scale SRM experiments. Nat Methods 8, 430-U485.

 

8. Mortensen, P., Gouw, J.W., Olsen, J.V., Ong, S.E., Rigbolt, K.T.G., Bunkenborg, J., et al., (2010). MSQuant, an Open Source Platform for Mass Spectrometry-Based Quantitative Proteomics. J Proteome Res 9, 393-403.

 

9. Lin, W.T., Hung, W.N., Yian, Y.H., Wu, K.P., Han, C.L., Chen, Y.R., et al., (2006). Multi-Q: A fully automated tool for multiplexed protein quantitation. J Proteome Res 5, 2328-2338.

 

10. Kohlbacher, O., Reinert, K., Gropl, C., et al. (2007). TOPP—the OpenMS proteomics pipeline. Bioinformatics 23, e191–197.

 

11. Jaffe, J.D., Mani, D.R., Leptos, K.C., Church, G.M., Gillette, M.A., Carr, S.A., (2006). PEPPeR, a platform for experimental proteomic pattern recognition. Mol Cell Proteomics 5, 1927-1941.

 

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.

 

13. Hakkinen, J., Vincic, G., Mansson, O., Warell, K., Levander, F., (2009). The Proteios Software Environment: An Extensible Multiuser Platform for Management and Analysis of Proteomics Data. J Proteome Res 8, 3037-3043.

 

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.

 

18. Deutsch, E.W., Mendoza, L., Shteynberg, D., Farrah, T., Lam, H., Tasman, N., et al., (2010). A guided tour of the Trans-Proteomic Pipeline. Proteomics 10, 1150-1159.

 

19. Li, X.J., Zhang, H., Ranish, J.A., Aebersold, R., (2003). Automated statistical analysis of protein abundance ratios from data generated by stable-isotope dilution and tandem mass spectrometry. Analytical chemistry 75, 6648-6657.

 

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.

 

21. Li, X.J., Yi, E.C., Kemp, C.J., Zhang, H., and Aebersold, R. (2005). A software suite for the generation and comparison of peptide arrays from sets of data collected by liquid chromatographymass spectrometry. Mol Cell Proteomics 4, 1328–1340.

 

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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