Targeted Quantitative Peptide Proteomics

If you know which peptides or proteins that you want to quantitate, this method offers high throughput and low cost (after the protocol is established). In this method, we use all the trappings of analytical chemistry to develop an assay to reliably and reproducibly quantitate a peptide (or set of peptides) within a complex sample. There is an up-front cost to establish the assay that varies depending on the number of analytes and whether or not you want absolute quantitation (i.e. There are exactly 10.25 picomoles of your peptide in this tube) or relative quantitation (i.e The level of your peptide in tube A is four-fold higher than in tube B).

Typically discovery experiments using untargeted methods lead to these methods which require less sample and can be performed on more samples in less time.

Related Publications

MacLean B, Tomazela DM, Shulman N, Chambers M, Finney GL, Frewen B, Kern R, Tabb DL, Liebler DC, MacCoss MJ “Skyline: an open source document editor for creating and analyzing targeted proteomics experiments.” Bioinformatics, 2010, 26(7) p. 966-8.

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

Carr SA, Abbatiello SE, Ackermann BL, Borchers C, Domon B, Deutsch EW, Grant RP, Hoofnagle AN, Hüttenhain R, Koomen JM, Liebler DC, Liu T, MacLean B, Mani DR, Mansfield E, Neubert H, Paulovich AG, Reiter L, Vitek O, Aebersold R, Anderson L, Bethem R, Blonder J, Boja E, Botelho J, Boyne M, Bradshaw RA, Burlingame AL, Chan D, Keshishian H, Kuhn E, Kinsinger C, Lee JS, Lee SW, Moritz R, Oses-Prieto J, Rifai N, Ritchie J, Rodriguez H, Srinivas PR, Townsend RR, Van Eyk J, Whiteley G, Wiita A, Weintraub S “Targeted peptide measurements in biology and medicine: best practices for mass spectrometry-based assay development using a fit-for-purpose approach.” Mol Cell Proteomics, 2014, 13(3) p. 907-17.

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


Instruments Used

TSQ Quantiva

TSQ Quantum Ultra