Multiple-Reaction Monitoring–Mass Spectrometric Assays Can Accurately Measure the Relative Protein Abundance in Complex Mixtures

The relative protein abundance

Accurate Measurement of the Relative Abundance of Different DNA Species in Complex DNA Mixtures

A molecular tool that can compare the abundances of different DNA sequences is necessary for comparing intergenic or interspecific gene expression. We devised and verified such a tool using a quantitative competitive polymerase chain reaction approach. For this approach, we adapted a competitor array, an artificially made plasmid DNA in which all the competitor templates for the target DNAs are...

Quantitative mass spectrometric multiple reaction monitoring assays for major plasma proteins.

Quantitative LC-MS/MS assays were designed for tryptic peptides representing 53 high and medium abundance proteins in human plasma using a multiplexed multiple reaction monitoring (MRM) approach. Of these, 47 produced acceptable quantitative data, demonstrating within-run coefficients of variation (CVs) (n = 10) of 2-22% (78% of assays had CV <10%). A number of peptides gave CVs in the range 2-...

How accurately can we measure the W cross section?

We study the QCD sources of systematic uncertainties in the experimental extraction of the W cross section at hadron colliders. The uncertainties appear in the evaluation of the detector acceptances used to convert the number of observed events into a total production cross section. We consider the effect of NLO corrections, as well as of the inclusion of parton showers, and evaluate the impact...

Combinatorial peptide libraries facilitate development of multiple reaction monitoring assays for low-abundance proteins.

Low-abundance proteins present in biological fluids are often considered an attractive source of new disease biomarkers. Since such proteins are poorly observed in proteome-scale discovery experiments due to an overwhelming mass of high-abundance proteins, the development of quantitative multiple reaction monitoring (MRM) assays for low-abundance proteins is a challenging task. Here, we present...