Quantification of XRCC and DNA-PK proteins in cancer cell lines and human tumors by LC-MS/MS.

Background: The x-ray repair cross-complementing (XRCC) proteins and a catalytic subunit of nuclear DNA-dependent serine/threonine protein kinase (DNA-PK) play important roles in cancer biology. Understanding the protein expression levels allows us to reconstruct in vivo functionality and to qualify protein biomarkers.

Methods & Results: XRCC and DNA-PK proteins in human cancer cells and tumor tissues have been identified and quantified by selected peptides using NanoLC and high-resolution mass spectrometry.

Label-free quantitation of protein modifications by pseudo selected reaction monitoring with internal reference peptides.

Liquid chromatography tandem mass spectrometry (LC-MS/MS) based methods provide powerful tools for the quantitative analysis of modified proteins. We have developed a label-free approach using internal reference peptides (IRP) from the target protein for signal normalization without the need for isotope labeling. Ion-trap mass spectrometry and pseudo-selected reaction monitoring (pSRM) were used to acquire full MS/MS and MS(3) spectra from target peptides.

Protein expression signatures for inhibition of epidermal growth factor receptor-mediated signaling.

Analysis of cellular signaling networks typically involves targeted measurements of phosphorylated protein intermediates. However, phosphoproteomic analyses usually require affinity enrichment of phosphopeptides and can be complicated by artifactual changes in phosphorylation caused by uncontrolled preanalytical variables, particularly in the analysis of tissue specimens. We asked whether changes in protein expression, which are more stable and easily analyzed, could reflect network stimulation and inhibition.