Signature peptide approach

Signature-peptide approach to detecting proteins in complex mixtures. 

L. Riggs, C. Sioma, F. Regnier, Automated signature peptide approach for proteomics, J. Chromatogr. A, 924 (2001) 359. 

Quantitative proteomics requires global approaches to the proteome, as prefractionation of the proteome complicates quantification due to distribution of proteins over various fractions and difficulties in determining the recovery of proteins in complex analytical procedures. However, after labelling and tryptic digestion, the tryptic peptides relevant to the study are preferentially selectively isolated from the very complex digest of the proteome. In the ICAT procedure, this is performed by avidin AfC (Ch. 18.4.1). Alternative strategies are applied, in the liquid phase based on signature peptides, or in FT-ICR-MS. 

AQUA allows for direct comparison of proteomic data obtained on different instruments and in different laboratories. The need to measure the absolute abundance of proteins is achievable using a targeted quantitation approach. A synthetic, isotopically labeled peptide is used as the IS. This peptide is the isotopic counterpart of a signature peptide, which represents a 1 1 ratio... 

This labeled peptide, known as an AQUA peptide, acts as an internal standard. The sample is spiked with a known amount of the AQUA peptide and is analyzed by LC-selected reaction monitoring (SRM). The different masses of the endogenous signature peptide and the AQUA peptide are resolved by SRM tandem MS analysis, and the amount of the native peptide is calculated from the known amount of the AQUA peptide and the ratio of the area under the peaks. The AQUA approach can also be combined with MALDI-MS. 

Characterisation of isolated neutral peptides through their vibrational signature resulted from the synergy between two complementary approaches ... 

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