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Review
. 2009 Feb;8(2):787-97.
doi: 10.1021/pr800538n.

Mass spectrometry based targeted protein quantification: methods and applications

Sheng Pan  1 , Ruedi Aebersold, Ru Chen, John Rush, David R Goodlett, Martin W McIntosh, Jing Zhang, Teresa A Brentnall
Affiliations
Review

Mass spectrometry based targeted protein quantification: methods and applications

Sheng Pan et al. J Proteome Res. 2009 Feb.

Abstract

The recent advance in technology for mass spectrometry-based targeted protein quantification has opened new avenues for a broad range of proteomic applications in clinical research. The major breakthroughs are highlighted by the capability of using a "universal" approach to perform quantitative assays for a wide spectrum of proteins with minimum restrictions and the ease of assembling multiplex detections in a single measurement. The quantitative approach relies on the use of synthetic stable isotope labeled peptides or proteins, which precisely mimic their endogenous counterparts and act as internal standards to quantify the corresponding candidate proteins. This report reviews recently developed platform technologies for emerging applications of clinical proteomics and biomarker development.

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Figures

Figure 1
Figure 1
General description of mass spectrometry based targeted quantitative strategy. The approach consists of three major components: generation of stable isotope labeled peptides/proteins as references for the corresponding targeted protein; an effective sample preparation protocol to reduce sample complexity and enrich the targeted surrogates; a data-driven highly specific mass spectrometry platform for candidate-based analysis. More details of each aspect will be discussed in the following sections.
Figure 2
Figure 2
A summary of some sample preparation strategies and their overall detection sensitivity for targeted protein analysis in plasma or serum.
Figure 3
Figure 3
The evaluation of the performance of a high throughput LC protocol for a LC MADLI TOF/TOF based platform. The precursor ions detected were categorized based on the number of consecutive spots that a precursor ion was eluted across. The high throughput LC protocol showed similar behavior with the conventional protocol in terms of the distribution of the precursor ions.
Figure 4
Figure 4
The detection of a subset of candidate N-linked glycopeptides in serum using an LC MALDI TOF/TOF based platform for targeted quantitative analysis. The targeted endogenous peptides were unambiguously identified within a complex background and can be quantified using the corresponding synthetic reference peptides. (Note: # indicates the amino acid that was stable isotope labeled (13C and 15N) in reference peptides; * indicates enzyme-catalyzed conversion of asparagine to aspartic acid at the site of carbohydrate attachment.)
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