Contact Us
800.227.0627

Comparison of various protein profiling methods

 
Print Print
03/07/2011

Comparison of various protein profiling methods

Additional Complementary Methods comparison
Method Labeling Separation Sample Comparison Limits Pros
DIGE* Cy fluoro- phores at primary amines or at cyteines 2D PAGE 3 sample compared in same gel multiple gels for > 3 samples: basic and hydrophobic proteins more challenging useful for protein isoform detection and PTM changes
2D LC* None 2D chromato- focusing & RP HPLC quantify pair wise RP fractions by UV best for comparison of 2 samples at >500μg ideal for serum/plasma discovery
iTRAQ Isobaric tags at N-terminus & ε-N of Lys CEX & LC-MS/MS 4 & 8-plex MS/MS quantitation based on intensity of reporter ions quantitation on MS/MS selected peptides only 8 plex allows greater multiplexing
ICAT C12/C13 at Cys CEX, Avidin & LC-MS/MS 2-plex MS quantitation only detects Cys-containing proteins simplifies complex mixtures; no PTMs
SILAC Stable isotope labeled peptides CEX & LC-MS/MS 2-plex MS quantitation difficulties with software quantitation Labeling occurs early on in the sample prep
Label Free Quantitation None LCMS LC-MS based disease biomarker discovery tool limited or no initial protein identification. Repeat run often used for identification countless samples can be compared
MudPIT None CEX & LC-MS/MS 2D LC approach used to catalogue proteins from complex samples additional pre-fractionation aids in identification of >proteins in the proteome no direct quantitation