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.
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.
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.
Q Exactive HF