Untargeted Quantitative Peptide Proteomics

Quantitation always requires a consultation to help design the experiment. Depending on the problem, we can use a variety of methods to perform the analysis.

Metabolic Label: SILAC (Stable Isotope Labelling of Amino Acids in Cell Culture)

Best for cell lines, few states to compare

Isobaric Label: iTraq/TMT

Best for many states. Fewer runs, expensive reagents.

Label-Free Peptide Quantitation

More runs required, no reagent needed.

Related Publications

Rauniyar N, Yates JR 3rd “Isobaric labeling-based relative quantification in shotgun proteomics.” J Proteome Res, 2014, 13(12) p. 5293-309.

Summary | Full Text (PMC) | Full Text (DOI)

Ong SE, Blagoev B, Kratchmarova I, Kristensen DB, Steen H, Pandey A, Mann M “Stable isotope labeling by amino acids in cell culture, SILAC, as a simple and accurate approach to expression proteomics.” Mol Cell Proteomics, 2002, 1(5) p. 376-86.

Summary | Full Text (DOI)

Wiese S, Reidegeld KA, Meyer HE, Warscheid B “Protein labeling by iTRAQ: a new tool for quantitative mass spectrometry in proteome research.” Proteomics, 2007, 7(3) p. 340-50.

Summary | Full Text (DOI)



Instruments Used

Orbitrap Elite

Q Exactive HF