Untargeted Quantitative Peptide Proteomics

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)


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