Gallien S, Duriez E, Crone C, Kellmann M, Moehring T, Domon B.
Mol Cell Proteomics. 2012 Dec;11(12):1709-23.
There is an immediate need for improved methods to systematically and precisely
quantify large sets of peptides in complex biological samples. While to date protein
quantification in biological samples is routinely performed on triple quadrupole
instruments operated in selected reaction monitoring mode (SRM), two major
challenges remain. Firstly, the number of peptides to be included in one survey
experiment needs to be increased to routinely reach several hundreds, and secondly,
the degree of selectivity should be improved to reliably discriminate the targeted
analytes from background interferences. High resolution and accurate mass (HR/AM)
analysis on the recently developed Q‐Exactive mass spectrometer can potentially
address these issues. This instrument presents a unique configuration: it is constituted
of the orbitrap mass analyzer equipped with a quadrupole mass filter as front‐end for
precursor ion mass selection. This configuration enables new quantitative methods
based on HR/AM measurements, including targeted analysis in MS mode (single ion
monitoring, SIM) and in MS/MS mode (parallel reaction monitoring, PRM). While the
ability of the quadrupole to select a restricted m/z range allows overcoming the
dynamic range limitations associated with trapping devices, the MS/MS mode provides
an additional stage of selectivity. When applied to targeted protein quantification in
urine samples and benchmarked with the reference SRM technique, the quadrupole orbitrap instrument exhibits similar or better performances in terms of selectivity,
dynamic range, and sensitivity. These high performances are further enhanced by
leveraging the multiplexing capability of the instrument to design novel acquisition
methods and apply them to large targeted proteomic studies for the first time, as
demonstrated on 770 tryptic yeast peptides analyzed in one 60 minute experiment. The
increased quality of quadrupole‐orbitrap data has the potential to improve existing
protein quantification methods in complex samples and to cope with the pressing
demand of systems biology or biomarker evaluation studies.
http://www.mcponline.org/content/early/2012/09/07/mcp.O112.019802.full.pdfLuxembourg Clinical Proteomics Center (LCP), CRPâ€Santé, Strassen, Luxembourg