International Journal of Proteomics

Review Article

Current Status and Advances in Quantitative Proteomic Mass Spectrometry

Table 1

Overview of the main approaches for quantitative proteomics. Modified from Schulze and Usadel [4] and Ly and Wasinger [4, 7].


Method	Dynamic range^a	Coverage	Quant accuracy, (throughput) R = relative, A = absolute	Associated software	Link

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

Orders of magnitude.
APEX: absolute protein expression profiling. emPAI: exponentially modified protein abundance index. SILAC: stable isotope labelling by amino acids. DIGE: Difference Gel Electrophoresis. ICAT: isotope-coded affinity tags. ITRAQ: isobaric tags for absolute and relative quantitation. TMT: tandem mass tags. MRM: multiple reaction monitoring.
Few target proteins can be selected efficiently in a single LC-MS/MS experiment.
MS²: MSMS