International Journal of Proteomics / 2013 / Article / Tab 1

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].

MethodDynamic rangeaCoverageQuant accuracy, (throughput)
R = relative, A = absolute
Associated softwareLink

Label-free
 2D gels1 to 4,
stain dependent
MediumMedium (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 MS13GoodMedium, (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 MS23, Inaccurate for low abundance.GoodPoor, (medium to high)
R
LC dependent
Scaffold [24]
Elucidator
ProteoIQ
http://www.proteomesoftware.com/
http://www.rosettabio.com/
http://www.bioinquire.com/
 APEX,emPAI3 or 4GoodPoor, (high)
R,within sample only.
APEX [25]
Mascot
http://pfgrc.jcvi.org/index.php/bioinformatics/apex.html
http://www.matrixscience.com/
Metabolic labeling
15N1 to 2MediumPrecise, (low).
R, between 2 conditions.
Scaffold
MSQuant [26]
http://www.proteomesoftware.com/
http://msquant.sourceforge.net/
 SILAC1 to 2MediumPrecise, (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 2Poor 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
MediumMedium, (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.
Poor1Precise, (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