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Method | Dynamic rangea | Coverage | Quant accuracy, (throughput) R = relative, A = absolute | Associated software | Link |
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Label-free | | | | | |
2D gels | 1 to 4, stain dependent | Medium | Medium (low) R Requires MS identification. | PDQuest Progenesis SameSpots Melanie [18] Phoretix | http://www.bio-rad.com/ http://www.nonlinear.com/ http://www.genebio.com/ http://www.perkinelmer.com/ |
Ion intensities MS1 | 3 | Good | Medium, (medium to high) R, LC dependent. | Progenesis LCMS msInspect [19] MSight [20] TOPP [21] PEPPeR [22] SuperHirn [23] DeCyder MS SIEVE ProteinLynx | http://www.nonlinear.com/ http://proteomics.fhcrc.org http://web.expasy.org http://open-ms.sourceforge.net/ http://www.broadinstitute.org/ http://www.waters.com/ http://www.gelifesciences.com/ http://thermo.com/ http://www.waters.com/ |
Spectrum count MS2 | 3, Inaccurate for low abundance. | Good | Poor, (medium to high) R LC dependent | Scaffold [24] Elucidator ProteoIQ | http://www.proteomesoftware.com/ http://www.rosettabio.com/ http://www.bioinquire.com/ |
APEX,emPAI | 3 or 4 | Good | Poor, (high) R,within sample only. | APEX [25] Mascot | http://pfgrc.jcvi.org/index.php/bioinformatics/apex.html http://www.matrixscience.com/ |
Metabolic labeling | | | | | |
15N | 1 to 2 | Medium | Precise, (low). R, between 2 conditions. | Scaffold MSQuant [26] | http://www.proteomesoftware.com/ http://msquant.sourceforge.net/ |
SILAC | 1 to 2 | Medium | Precise, (low). R Between 2 and 3 samples. | Scaffold MSQuant Elucidator ASAPRatio | http://www.proteomesoftware.com/ http://msquant.sourceforge.net/ http://www.rosettabio.com/ http://tools.proteomecenter.org/ |
Isotopic labeling | | | | | |
ICAT, 18O, ICPL
| 1 to 2 | Poor | Precise, (low). R Between 2 conditions. | Elucidator XPRESS [27] MSQuant ASAPRatio [28] ZoomQuant [29] | http://www.rosettabio.com/ http://tools.proteomecenter.org/ http://msquant.sourceforge.net/ http://tools.proteomecenter.org/ http://proteomics.mcw.edu/zoomquant.html |
Isobaric labeling | | | | | |
ITRAQ, TMT, DIGE | 2 3 | Medium | Medium, (low). R or A Between 2 and 8 conditions. | ProteinPilot Multi-Q [30] iTracker [31] MSQuant | http://www.absciex.com/ http://ms.iis.sinica.edu.tw/Multi-Q-Web/ http://www.cranfield.ac.uk/ http://msquant.sourceforge.net/ |
Targeted | | | | | |
MRM Isotope dilution +/− heavy label | 5 Attomolar detection. | Poor1 | Precise, (high). R or A Requires intensive method development. | Skyline [32] MaxQuant ATAQS [33] MRMer [34] | https://brendanx-uw1.gs.washington.edu http://maxquant.org/ http://tools.proteomecenter.org/ATAQS/ATAQS.html http://proteomics.fhcrc.org/CPL/MRMer.html |
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